{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# R libraries and Bioconductor" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "## Packages and Libraries\n", "\n", "R is at heart a collection of 'packages'. There is a 'base' system that contains the truly basic commands, such as the assignment operator `->` or the command to create a vector. In addition to that, there are 'standard R' packages that are included when you install the R kernel (in the Jupyter notebook), or 'R' as a program to run either at the command line or with Rstudio. (I've shown some examples of these different ways to run R in class).\n", "\n", "### Libraries\n", "\n", "Many packages, even those included in [standard R] (https://www.r-project.org/), will need to be 'loaded' to be used. In other words, they exist on your computer (or in your container), but the R kernel doesn't know about them. This is because if it did, R would be using computer memory (RAM) to remember all their functions and variables. If all the available packages were loaded, you might not have any RAM left!\n", "\n", "A consequence of this is that you often have to tell R explicitly that you want to use a particular package. You do that using `library`. Let's read in the titanic data set to have something to play with.\n", "\n" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "titanic <- read.csv(\"titanic.csv\")" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A data.frame: 6 × 7
XNamePClassAgeSexSurvivedSexCode
<int><fct><fct><dbl><fct><int><int>
1Allen, Miss Elisabeth Walton 1st29.00female11
2Allison, Miss Helen Loraine 1st 2.00female01
3Allison, Mr Hudson Joshua Creighton 1st30.00male 00
4Allison, Mrs Hudson JC (Bessie Waldo Daniels)1st25.00female01
5Allison, Master Hudson Trevor 1st 0.92male 10
6Anderson, Mr Harry 1st47.00male 10
\n" ], "text/latex": [ "A data.frame: 6 × 7\n", "\\begin{tabular}{r|lllllll}\n", " X & Name & PClass & Age & Sex & Survived & SexCode\\\\\n", " & & & & & & \\\\\n", "\\hline\n", "\t 1 & Allen, Miss Elisabeth Walton & 1st & 29.00 & female & 1 & 1\\\\\n", "\t 2 & Allison, Miss Helen Loraine & 1st & 2.00 & female & 0 & 1\\\\\n", "\t 3 & Allison, Mr Hudson Joshua Creighton & 1st & 30.00 & male & 0 & 0\\\\\n", "\t 4 & Allison, Mrs Hudson JC (Bessie Waldo Daniels) & 1st & 25.00 & female & 0 & 1\\\\\n", "\t 5 & Allison, Master Hudson Trevor & 1st & 0.92 & male & 1 & 0\\\\\n", "\t 6 & Anderson, Mr Harry & 1st & 47.00 & male & 1 & 0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A data.frame: 6 × 7\n", "\n", "| X <int> | Name <fct> | PClass <fct> | Age <dbl> | Sex <fct> | Survived <int> | SexCode <int> |\n", "|---|---|---|---|---|---|---|\n", "| 1 | Allen, Miss Elisabeth Walton | 1st | 29.00 | female | 1 | 1 |\n", "| 2 | Allison, Miss Helen Loraine | 1st | 2.00 | female | 0 | 1 |\n", "| 3 | Allison, Mr Hudson Joshua Creighton | 1st | 30.00 | male | 0 | 0 |\n", "| 4 | Allison, Mrs Hudson JC (Bessie Waldo Daniels) | 1st | 25.00 | female | 0 | 1 |\n", "| 5 | Allison, Master Hudson Trevor | 1st | 0.92 | male | 1 | 0 |\n", "| 6 | Anderson, Mr Harry | 1st | 47.00 | male | 1 | 0 |\n", "\n" ], "text/plain": [ " X Name PClass Age Sex Survived\n", "1 1 Allen, Miss Elisabeth Walton 1st 29.00 female 1 \n", "2 2 Allison, Miss Helen Loraine 1st 2.00 female 0 \n", "3 3 Allison, Mr Hudson Joshua Creighton 1st 30.00 male 0 \n", "4 4 Allison, Mrs Hudson JC (Bessie Waldo Daniels) 1st 25.00 female 0 \n", "5 5 Allison, Master Hudson Trevor 1st 0.92 male 1 \n", "6 6 Anderson, Mr Harry 1st 47.00 male 1 \n", " SexCode\n", "1 1 \n", "2 1 \n", "3 0 \n", "4 1 \n", "5 0 \n", "6 0 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "head(titanic)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There is a cool R function that will allow us to look at some random rows from a data frame. It's called `sample_n`. Let's try it:" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "ename": "ERROR", "evalue": "Error in sample_n(titanic, 10): could not find function \"sample_n\"\n", "output_type": "error", "traceback": [ "Error in sample_n(titanic, 10): could not find function \"sample_n\"\nTraceback:\n" ] } ], "source": [ "sample_n(titanic, 10)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Oops. It turns out `sample_n` is in the dplyr package. It's installed in your container - but R doesn't know that! Let's tell R we want to use it:" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "Attaching package: ‘dplyr’\n", "\n", "The following objects are masked from ‘package:stats’:\n", "\n", " filter, lag\n", "\n", "The following objects are masked from ‘package:base’:\n", "\n", " intersect, setdiff, setequal, union\n", "\n" ] } ], "source": [ "library(dplyr)" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A data.frame: 10 × 7
XNamePClassAgeSexSurvivedSexCode
<int><fct><fct><dbl><fct><int><int>
304Geiger, Miss Emily 1stNAfemale11
675Birkeland, Mr Hans 3rd21male 00
555Sincock, Miss Maude 2nd20female11
52Case, Mr Howard Brown 1st49male 00
125Greenfield, Mrs Leo David (Blanche Strouse)1st45female11
427Harbeck, Mr William H 2nd44male 00
195Ostby, Miss Helen Raghnild 1st22female11
1183Salkjelsvik, Miss Anna 3rdNAfemale11
953Leeni, Mr Fahim 3rdNAmale 10
935Kink, Miss Maria 3rd22female01
\n" ], "text/latex": [ "A data.frame: 10 × 7\n", "\\begin{tabular}{r|lllllll}\n", " X & Name & PClass & Age & Sex & Survived & SexCode\\\\\n", " & & & & & & \\\\\n", "\\hline\n", "\t 304 & Geiger, Miss Emily & 1st & NA & female & 1 & 1\\\\\n", "\t 675 & Birkeland, Mr Hans & 3rd & 21 & male & 0 & 0\\\\\n", "\t 555 & Sincock, Miss Maude & 2nd & 20 & female & 1 & 1\\\\\n", "\t 52 & Case, Mr Howard Brown & 1st & 49 & male & 0 & 0\\\\\n", "\t 125 & Greenfield, Mrs Leo David (Blanche Strouse) & 1st & 45 & female & 1 & 1\\\\\n", "\t 427 & Harbeck, Mr William H & 2nd & 44 & male & 0 & 0\\\\\n", "\t 195 & Ostby, Miss Helen Raghnild & 1st & 22 & female & 1 & 1\\\\\n", "\t 1183 & Salkjelsvik, Miss Anna & 3rd & NA & female & 1 & 1\\\\\n", "\t 953 & Leeni, Mr Fahim & 3rd & NA & male & 1 & 0\\\\\n", "\t 935 & Kink, Miss Maria & 3rd & 22 & female & 0 & 1\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A data.frame: 10 × 7\n", "\n", "| X <int> | Name <fct> | PClass <fct> | Age <dbl> | Sex <fct> | Survived <int> | SexCode <int> |\n", "|---|---|---|---|---|---|---|\n", "| 304 | Geiger, Miss Emily | 1st | NA | female | 1 | 1 |\n", "| 675 | Birkeland, Mr Hans | 3rd | 21 | male | 0 | 0 |\n", "| 555 | Sincock, Miss Maude | 2nd | 20 | female | 1 | 1 |\n", "| 52 | Case, Mr Howard Brown | 1st | 49 | male | 0 | 0 |\n", "| 125 | Greenfield, Mrs Leo David (Blanche Strouse) | 1st | 45 | female | 1 | 1 |\n", "| 427 | Harbeck, Mr William H | 2nd | 44 | male | 0 | 0 |\n", "| 195 | Ostby, Miss Helen Raghnild | 1st | 22 | female | 1 | 1 |\n", "| 1183 | Salkjelsvik, Miss Anna | 3rd | NA | female | 1 | 1 |\n", "| 953 | Leeni, Mr Fahim | 3rd | NA | male | 1 | 0 |\n", "| 935 | Kink, Miss Maria | 3rd | 22 | female | 0 | 1 |\n", "\n" ], "text/plain": [ " X Name PClass Age Sex Survived\n", "1 304 Geiger, Miss Emily 1st NA female 1 \n", "2 675 Birkeland, Mr Hans 3rd 21 male 0 \n", "3 555 Sincock, Miss Maude 2nd 20 female 1 \n", "4 52 Case, Mr Howard Brown 1st 49 male 0 \n", "5 125 Greenfield, Mrs Leo David (Blanche Strouse) 1st 45 female 1 \n", "6 427 Harbeck, Mr William H 2nd 44 male 0 \n", "7 195 Ostby, Miss Helen Raghnild 1st 22 female 1 \n", "8 1183 Salkjelsvik, Miss Anna 3rd NA female 1 \n", "9 953 Leeni, Mr Fahim 3rd NA male 1 \n", "10 935 Kink, Miss Maria 3rd 22 female 0 \n", " SexCode\n", "1 1 \n", "2 0 \n", "3 1 \n", "4 0 \n", "5 1 \n", "6 0 \n", "7 1 \n", "8 1 \n", "9 0 \n", "10 1 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "sample_n(titanic, 10)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Installed and installing packages" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now, `dplyr` is actually not part of standard R. It's *installed* separately. There are a multitude of R packages out there. Anyone can write one (yes, even you!!!). They are shared with the public using the [CRAN archive.] (https://cran.r-project.org/) In order to be listed in CRAN, packages need to meet specific criteria for documentation purposes, testing, etc.\n", "\n", "You can check to see what packages are installed using `installed.packages()`" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 304 × 16 of type chr
PackageLibPathVersionPriorityDependsImportsLinkingToSuggestsEnhancesLicenseLicense_is_FOSSLicense_restricts_useOS_typeMD5sumNeedsCompilationBuilt
countrycodecountrycode /home/jovyan/R/x86_64-pc-linux-gnu-library/3.61.1.0 NAR (>= 2.10) NA NA testthat (>= 0.5) NA GPL-3 NANANANAno 3.6.0
acepackacepack /usr/local/lib/R/site-library 1.4.1 NANA NA NA testthat NA MIT + file LICENSENANANANAyes3.6.0
ade4ade4 /usr/local/lib/R/site-library 1.7-13 NAR (>= 2.10) graphics, grDevices, methods, stats, utils, MASS NA ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir,\n", "lattice, pixmap, sp, spdep, splancs, waveslim NA GPL (>= 2) NANANANAyes3.6.0
airwayairway /usr/local/lib/R/site-library 1.4.0 NAR (>= 2.10), SummarizedExperiment NA NA knitr, GEOquery NA LGPL NANANANAno 3.6.0
annotateannotate /usr/local/lib/R/site-library 1.62.0 NAR (>= 2.10), AnnotationDbi (>= 1.27.5), XML Biobase, DBI, xtable, graphics, utils, stats, methods,\n", "BiocGenerics (>= 0.13.8), RCurl NA hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\n", "rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\n", "org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, NA Artistic-2.0 NANANANAno 3.6.0
AnnotationDbiAnnotationDbi /usr/local/lib/R/site-library 1.46.0 NAR (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n", "0.29.2), Biobase (>= 1.17.0), IRanges DBI, RSQLite, S4Vectors (>= 0.9.25) NA hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,\n", "RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,\n", "org.Hs.eg.db, reactome.db, AnnotationForge, graph,\n", "EnsDb.Hsapiens.v75, BiocStyle, knitr NA Artistic-2.0 NANANANAno 3.6.0
AnnotationFilterAnnotationFilter/usr/local/lib/R/site-library 1.8.0 NAR (>= 3.4.0) utils, methods, GenomicRanges, lazyeval NA BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db NA Artistic-2.0 NANANANAno 3.6.0
apeape /usr/local/lib/R/site-library 5.3 NAR (>= 3.2.0) nlme, lattice, graphics, methods, stats, tools, utils,\n", "parallel, Rcpp (>= 0.12.0) Rcpp gee, expm, igraph NA GPL (>= 2) NANANANAyes3.6.0
askpassaskpass /usr/local/lib/R/site-library 1.1 NANA sys (>= 2.1) NA testthat NA MIT + file LICENSENANANANAyes3.6.0
assertthatassertthat /usr/local/lib/R/site-library 0.2.1 NANA tools NA testthat, covr NA GPL-3 NANANANAno 3.6.0
backportsbackports /usr/local/lib/R/site-library 1.1.4 NAR (>= 3.0.0) utils NA NA NA GPL-2 NANANANAyes3.6.0
base64encbase64enc /usr/local/lib/R/site-library 0.1-3 NAR (>= 2.9.0) NA NA NA png GPL-2 | GPL-3 NANANANAyes3.6.0
BHBH /usr/local/lib/R/site-library 1.69.0-1NANA NA NA NA NA BSL-1.0 NANANANAno 3.6.0
BiobaseBiobase /usr/local/lib/R/site-library 2.44.0 NAR (>= 2.10), BiocGenerics (>= 0.27.1), utils methods NA tools, tkWidgets, ALL, RUnit, golubEsets NA Artistic-2.0 NANANANAyes3.6.0
BiocGenericsBiocGenerics /usr/local/lib/R/site-library 0.30.0 NAR (>= 3.6.0), methods, utils, graphics, stats, parallel methods, utils, graphics, stats, parallel NA Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,\n", "AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,\n", "DESeq2, MSnbase, annotate, RUnit NA Artistic-2.0 NANANANAno 3.6.0
BiocManagerBiocManager /usr/local/lib/R/site-library 1.30.4 NAR (>= 3.5.0) utils NA BiocStyle, BiocVersion, remotes, testthat, knitr, withr NA Artistic-2.0 NANANANAno 3.6.0
BiocParallelBiocParallel /usr/local/lib/R/site-library 1.18.0 NAmethods stats, utils, futile.logger, parallel, snow BH BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\n", "Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\n", "TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\n", "Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,\n", "BiocStyle, knitr, batchtools, data.table NA GPL-2 | GPL-3 NANANANAyes3.6.0
BiocVersionBiocVersion /usr/local/lib/R/site-library 3.9.0 NAR (>= 3.6.0), R (< 3.7.0) NA NA NA NA Artistic-2.0 NANANANAno 3.6.0
biomaRtbiomaRt /usr/local/lib/R/site-library 2.40.0 NAmethods utils, XML, RCurl, AnnotationDbi, progress, stringr, httr NA annotate, BiocStyle, knitr, rmarkdown, testthat NA Artistic-2.0 NANANANAno 3.6.0
biomformatbiomformat /usr/local/lib/R/site-library 1.12.0 NAR (>= 3.2), methods plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 NA testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),\n", "rmarkdown (>= 0.7) NA GPL-2 NANANANAno 3.6.0
BiostringsBiostrings /usr/local/lib/R/site-library 2.52.0 NAR (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13),\n", "IRanges, XVector (>= 0.23.2) graphics, methods, stats, utils S4Vectors, IRanges, XVectorBSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n", "1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\n", "BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\n", "hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n", "(>= 1.41.3), affydata (>= 1.11.5), RUnit RmpiArtistic-2.0 NANANANAyes3.6.0
biovizBasebiovizBase /usr/local/lib/R/site-library 1.32.0 NAR (>= 2.10), methods grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,\n", "BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28),\n", "GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),\n", "SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=\n", "1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=\n", "1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),\n", "ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlangNA BSgenome.Hsapiens.UCSC.hg19,\n", "TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,\n", "EnsDb.Hsapiens.v75, RUnit NA Artistic-2.0 NANANANAyes3.6.0
bitbit /usr/local/lib/R/site-library 1.1-14 NAR (>= 2.9.2) NA NA NA NA GPL-2 NANANANAyes3.6.0
bit64bit64 /usr/local/lib/R/site-library 0.9-7 NAR (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats NA NA NA NA GPL-2 NANANANAyes3.6.0
bitopsbitops /usr/local/lib/R/site-library 1.0-6 NANA NA NA NA NA GPL (>= 2) NANANANAyes3.6.0
blobblob /usr/local/lib/R/site-library 1.1.1 NANA methods, prettyunits NA covr, pillar (>= 1.2.1), testthat NA GPL-3 NANANANAno 3.6.0
broombroom /usr/local/lib/R/site-library 0.5.2 NAR (>= 3.1) backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr,\n", "reshape2, stringr, tibble, tidyr NA AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms,\n", "btergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>=\n", "1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2,\n", "glmnet, gmm, Hmisc, irlba, joineRML, Kendall, knitr, ks,\n", "Lahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps,\n", "maptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network,\n", "nnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych,\n", "quantreg, rgeos, rmarkdown, robust, rsample, rstan, rstanarm,\n", "sp, speedglm, statnet.common, survey, survival, testthat,\n", "tseries, xergm, zooNA MIT + file LICENSENANANANAno 3.6.0
BSgenomeBSgenome /usr/local/lib/R/site-library 1.52.0 NAR (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=\n", "0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.15.2),\n", "GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer\n", "(>= 1.39.7)methods, utils, stats, BiocGenerics, S4Vectors, IRanges,\n", "XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,\n", "rtracklayer NA BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,\n", "BSgenome.Hsapiens.UCSC.hg38,\n", "BSgenome.Hsapiens.UCSC.hg38.masked,\n", "BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,\n", "BSgenome.Scerevisiae.UCSC.sacCer1,\n", "TxDb.Hsapiens.UCSC.hg38.knownGene,\n", "TxDb.Mmusculus.UCSC.mm10.knownGene,\n", "SNPlocs.Hsapiens.dbSNP144.GRCh38,\n", "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit NA Artistic-2.0 NANANANAno 3.6.0
callrcallr /usr/local/lib/R/site-library 3.2.0 NANA processx (>= 3.3.0), R6, utils NA cliapp, covr, crayon, pingr, ps, testthat, withr NA MIT + file LICENSENANANANAno 3.6.0
caretcaret /usr/local/lib/R/site-library 6.0-84 NAR (>= 3.2.0), lattice (>= 0.20), ggplot2 foreach, methods, plyr, ModelMetrics (>= 1.1.0), nlme,\n", "reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.4),\n", "withr (>= 2.0.0) NA BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>=\n", "1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv,\n", "mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, pROC,\n", "proxy, randomForest, RANN, spls, subselect, pamr, superpc,\n", "Cubist, testthat (>= 0.9.1), rpart, dplyr NA GPL (>= 2) NANANANAyes3.6.0
⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮
zoozoo /usr/local/lib/R/site-library1.8-6 NA R (>= 3.1.0), stats utils, graphics, grDevices, lattice (>= 0.20-27)NAcoda, chron, DAAG, fts, ggplot2, mondate, scales,\n", "strucchange, timeDate, timeSeries, tis, tseries, xtsNA GPL-2 | GPL-3 NANANANAyes3.6.0
basebase /usr/lib/R/library 3.6.0 base NA NA NAmethods NA Part of R 3.6.0 NANANANANA 3.6.0
bootboot /usr/lib/R/library 1.3-20 recommendedR (>= 3.0.0), graphics, stats NA NAMASS, survival NA Unlimited NANANANAno 3.5.1
classclass /usr/lib/R/library 7.3-15 recommendedR (>= 3.0.0), stats, utils MASS NANA NA GPL-2 | GPL-3 NANANANAyes3.6.0
clustercluster /usr/lib/R/library 2.0.8 recommendedR (>= 3.3.0) graphics, grDevices, stats, utils NAMASS, Matrix NA GPL (>= 2) NANANANAyes3.6.0
codetoolscodetools /usr/lib/R/library 0.2-16 recommendedR (>= 2.1) NA NANA NA GPL NANANANAno 3.5.3
compilercompiler /usr/lib/R/library 3.6.0 base NA NA NANA NA Part of R 3.6.0 NANANANANA 3.6.0
datasetsdatasets /usr/lib/R/library 3.6.0 base NA NA NANA NA Part of R 3.6.0 NANANANANA 3.6.0
foreignforeign /usr/lib/R/library 0.8-71 recommendedR (>= 3.0.0) methods, utils, stats NANA NA GPL (>= 2) NANANANAyes3.6.0
graphicsgraphics /usr/lib/R/library 3.6.0 base NA grDevices NANA NA Part of R 3.6.0 NANANANAyes3.6.0
grDevicesgrDevices /usr/lib/R/library 3.6.0 base NA NA NAKernSmooth NA Part of R 3.6.0 NANANANAyes3.6.0
gridgrid /usr/lib/R/library 3.6.0 base NA grDevices, utils NAlattice NA Part of R 3.6.0 NANANANAyes3.6.0
KernSmoothKernSmooth/usr/lib/R/library 2.23-15 recommendedR (>= 2.5.0), stats NA NAMASS NA Unlimited NANANANAyes3.6.0
latticelattice /usr/lib/R/library 0.20-38 recommendedR (>= 3.0.0) grid, grDevices, graphics, stats, utils NAKernSmooth, MASS, latticeExtra chron GPL (>= 2) NANANANAyes3.6.0
MASSMASS /usr/lib/R/library 7.3-51.3recommendedR (>= 3.1.0), grDevices, graphics, stats, utilsmethods NAlattice, nlme, nnet, survival NA GPL-2 | GPL-3 NANANANAyes3.6.0
MatrixMatrix /usr/lib/R/library 1.2-17 recommendedR (>= 3.2.0) methods, graphics, grid, stats, utils, lattice NAexpm, MASS MatrixModels, graph, SparseM, sfsmiscGPL (>= 2) | file LICENCENANANANAyes3.6.0
methodsmethods /usr/lib/R/library 3.6.0 base NA utils, stats NAcodetools NA Part of R 3.6.0 NANANANAyes3.6.0
mgcvmgcv /usr/lib/R/library 1.8-28 recommendedR (>= 2.14.0), nlme (>= 3.1-64) methods, stats, graphics, Matrix, splines, utilsNAparallel, survival, MASS NA GPL (>= 2) NANANANAyes3.6.0
nlmenlme /usr/lib/R/library 3.1-139 recommendedR (>= 3.4.0) graphics, stats, utils, lattice NAHmisc, MASS NA GPL (>= 2) | file LICENCENANANANAyes3.6.0
nnetnnet /usr/lib/R/library 7.3-12 recommendedR (>= 2.14.0), stats, utils NA NAMASS NA GPL-2 | GPL-3 NANANANAyes3.6.0
parallelparallel /usr/lib/R/library 3.6.0 base NA tools, compiler NAmethods snow, nws, Rmpi Part of R 3.6.0 NANANANAyes3.6.0
rpartrpart /usr/lib/R/library 4.1-15 recommendedR (>= 2.15.0), graphics, stats, grDevices NA NAsurvival NA GPL-2 | GPL-3 NANANANAyes3.6.0
spatialspatial /usr/lib/R/library 7.3-11 recommendedR (>= 3.0.0), graphics, stats, utils NA NAMASS NA GPL-2 | GPL-3 NANANANAyes3.6.0
splinessplines /usr/lib/R/library 3.6.0 base NA graphics, stats NAMatrix, methods NA Part of R 3.6.0 NANANANAyes3.6.0
statsstats /usr/lib/R/library 3.6.0 base NA utils, grDevices, graphics NAMASS, Matrix, SuppDists, methods, stats4 NA Part of R 3.6.0 NANANANAyes3.6.0
stats4stats4 /usr/lib/R/library 3.6.0 base NA graphics, methods, stats NANA NA Part of R 3.6.0 NANANANANA 3.6.0
survivalsurvival /usr/lib/R/library 2.44-1.1recommendedR (>= 2.13.0) graphics, Matrix, methods, splines, stats, utilsNANA NA LGPL (>= 2) NANANANAyes3.6.0
tcltktcltk /usr/lib/R/library 3.6.0 base NA utils NANA NA Part of R 3.6.0 NANANANAyes3.6.0
toolstools /usr/lib/R/library 3.6.0 base NA NA NAcodetools, methods, xml2, curl, commonmark NA Part of R 3.6.0 NANANANAyes3.6.0
utilsutils /usr/lib/R/library 3.6.0 base NA NA NAmethods, xml2, commonmark NA Part of R 3.6.0 NANANANAyes3.6.0
\n" ], "text/latex": [ "A matrix: 304 × 16 of type chr\n", "\\begin{tabular}{r|llllllllllllllll}\n", " & Package & LibPath & Version & Priority & Depends & Imports & LinkingTo & Suggests & Enhances & License & License\\_is\\_FOSS & License\\_restricts\\_use & OS\\_type & MD5sum & NeedsCompilation & Built\\\\\n", "\\hline\n", "\tcountrycode & countrycode & /home/jovyan/R/x86\\_64-pc-linux-gnu-library/3.6 & 1.1.0 & NA & R (>= 2.10) & NA & NA & testthat (>= 0.5) & NA & GPL-3 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tacepack & acepack & /usr/local/lib/R/site-library & 1.4.1 & NA & NA & NA & NA & testthat & NA & MIT + file LICENSE & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tade4 & ade4 & /usr/local/lib/R/site-library & 1.7-13 & NA & R (>= 2.10) & graphics, grDevices, methods, stats, utils, MASS & NA & ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir,\n", "lattice, pixmap, sp, spdep, splancs, waveslim & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tairway & airway & /usr/local/lib/R/site-library & 1.4.0 & NA & R (>= 2.10), SummarizedExperiment & NA & NA & knitr, GEOquery & NA & LGPL & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tannotate & annotate & /usr/local/lib/R/site-library & 1.62.0 & NA & R (>= 2.10), AnnotationDbi (>= 1.27.5), XML & Biobase, DBI, xtable, graphics, utils, stats, methods,\n", "BiocGenerics (>= 0.13.8), RCurl & NA & hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\n", "rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\n", "org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tAnnotationDbi & AnnotationDbi & /usr/local/lib/R/site-library & 1.46.0 & NA & R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n", "0.29.2), Biobase (>= 1.17.0), IRanges & DBI, RSQLite, S4Vectors (>= 0.9.25) & NA & hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,\n", "RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,\n", "org.Hs.eg.db, reactome.db, AnnotationForge, graph,\n", "EnsDb.Hsapiens.v75, BiocStyle, knitr & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tAnnotationFilter & AnnotationFilter & /usr/local/lib/R/site-library & 1.8.0 & NA & R (>= 3.4.0) & utils, methods, GenomicRanges, lazyeval & NA & BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tape & ape & /usr/local/lib/R/site-library & 5.3 & NA & R (>= 3.2.0) & nlme, lattice, graphics, methods, stats, tools, utils,\n", "parallel, Rcpp (>= 0.12.0) & Rcpp & gee, expm, igraph & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\taskpass & askpass & /usr/local/lib/R/site-library & 1.1 & NA & NA & sys (>= 2.1) & NA & testthat & NA & MIT + file LICENSE & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tassertthat & assertthat & /usr/local/lib/R/site-library & 0.2.1 & NA & NA & tools & NA & testthat, covr & NA & GPL-3 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tbackports & backports & /usr/local/lib/R/site-library & 1.1.4 & NA & R (>= 3.0.0) & utils & NA & NA & NA & GPL-2 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tbase64enc & base64enc & /usr/local/lib/R/site-library & 0.1-3 & NA & R (>= 2.9.0) & NA & NA & NA & png & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tBH & BH & /usr/local/lib/R/site-library & 1.69.0-1 & NA & NA & NA & NA & NA & NA & BSL-1.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tBiobase & Biobase & /usr/local/lib/R/site-library & 2.44.0 & NA & R (>= 2.10), BiocGenerics (>= 0.27.1), utils & methods & NA & tools, tkWidgets, ALL, RUnit, golubEsets & NA & Artistic-2.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tBiocGenerics & BiocGenerics & /usr/local/lib/R/site-library & 0.30.0 & NA & R (>= 3.6.0), methods, utils, graphics, stats, parallel & methods, utils, graphics, stats, parallel & NA & Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,\n", "AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,\n", "DESeq2, MSnbase, annotate, RUnit & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tBiocManager & BiocManager & /usr/local/lib/R/site-library & 1.30.4 & NA & R (>= 3.5.0) & utils & NA & BiocStyle, BiocVersion, remotes, testthat, knitr, withr & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tBiocParallel & BiocParallel & /usr/local/lib/R/site-library & 1.18.0 & NA & methods & stats, utils, futile.logger, parallel, snow & BH & BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\n", "Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\n", "TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\n", "Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,\n", "BiocStyle, knitr, batchtools, data.table & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tBiocVersion & BiocVersion & /usr/local/lib/R/site-library & 3.9.0 & NA & R (>= 3.6.0), R (< 3.7.0) & NA & NA & NA & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tbiomaRt & biomaRt & /usr/local/lib/R/site-library & 2.40.0 & NA & methods & utils, XML, RCurl, AnnotationDbi, progress, stringr, httr & NA & annotate, BiocStyle, knitr, rmarkdown, testthat & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tbiomformat & biomformat & /usr/local/lib/R/site-library & 1.12.0 & NA & R (>= 3.2), methods & plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 & NA & testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),\n", "rmarkdown (>= 0.7) & NA & GPL-2 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tBiostrings & Biostrings & /usr/local/lib/R/site-library & 2.52.0 & NA & R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13),\n", "IRanges, XVector (>= 0.23.2) & graphics, methods, stats, utils & S4Vectors, IRanges, XVector & BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n", "1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\n", "BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\n", "hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n", "(>= 1.41.3), affydata (>= 1.11.5), RUnit & Rmpi & Artistic-2.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tbiovizBase & biovizBase & /usr/local/lib/R/site-library & 1.32.0 & NA & R (>= 2.10), methods & grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,\n", "BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28),\n", "GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),\n", "SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=\n", "1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=\n", "1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),\n", "ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang & NA & BSgenome.Hsapiens.UCSC.hg19,\n", "TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,\n", "EnsDb.Hsapiens.v75, RUnit & NA & Artistic-2.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tbit & bit & /usr/local/lib/R/site-library & 1.1-14 & NA & R (>= 2.9.2) & NA & NA & NA & NA & GPL-2 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tbit64 & bit64 & /usr/local/lib/R/site-library & 0.9-7 & NA & R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats & NA & NA & NA & NA & GPL-2 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tbitops & bitops & /usr/local/lib/R/site-library & 1.0-6 & NA & NA & NA & NA & NA & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tblob & blob & /usr/local/lib/R/site-library & 1.1.1 & NA & NA & methods, prettyunits & NA & covr, pillar (>= 1.2.1), testthat & NA & GPL-3 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tbroom & broom & /usr/local/lib/R/site-library & 0.5.2 & NA & R (>= 3.1) & backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr,\n", "reshape2, stringr, tibble, tidyr & NA & AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms,\n", "btergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>=\n", "1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2,\n", "glmnet, gmm, Hmisc, irlba, joineRML, Kendall, knitr, ks,\n", "Lahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps,\n", "maptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network,\n", "nnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych,\n", "quantreg, rgeos, rmarkdown, robust, rsample, rstan, rstanarm,\n", "sp, speedglm, statnet.common, survey, survival, testthat,\n", "tseries, xergm, zoo & NA & MIT + file LICENSE & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tBSgenome & BSgenome & /usr/local/lib/R/site-library & 1.52.0 & NA & R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=\n", "0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.15.2),\n", "GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer\n", "(>= 1.39.7) & methods, utils, stats, BiocGenerics, S4Vectors, IRanges,\n", "XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,\n", "rtracklayer & NA & BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,\n", "BSgenome.Hsapiens.UCSC.hg38,\n", "BSgenome.Hsapiens.UCSC.hg38.masked,\n", "BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,\n", "BSgenome.Scerevisiae.UCSC.sacCer1,\n", "TxDb.Hsapiens.UCSC.hg38.knownGene,\n", "TxDb.Mmusculus.UCSC.mm10.knownGene,\n", "SNPlocs.Hsapiens.dbSNP144.GRCh38,\n", "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit & NA & Artistic-2.0 & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tcallr & callr & /usr/local/lib/R/site-library & 3.2.0 & NA & NA & processx (>= 3.3.0), R6, utils & NA & cliapp, covr, crayon, pingr, ps, testthat, withr & NA & MIT + file LICENSE & NA & NA & NA & NA & no & 3.6.0\\\\\n", "\tcaret & caret & /usr/local/lib/R/site-library & 6.0-84 & NA & R (>= 3.2.0), lattice (>= 0.20), ggplot2 & foreach, methods, plyr, ModelMetrics (>= 1.1.0), nlme,\n", "reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.4),\n", "withr (>= 2.0.0) & NA & BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>=\n", "1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv,\n", "mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, pROC,\n", "proxy, randomForest, RANN, spls, subselect, pamr, superpc,\n", "Cubist, testthat (>= 0.9.1), rpart, dplyr & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\t⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮\\\\\n", "\tzoo & zoo & /usr/local/lib/R/site-library & 1.8-6 & NA & R (>= 3.1.0), stats & utils, graphics, grDevices, lattice (>= 0.20-27) & NA & coda, chron, DAAG, fts, ggplot2, mondate, scales,\n", "strucchange, timeDate, timeSeries, tis, tseries, xts & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tbase & base & /usr/lib/R/library & 3.6.0 & base & NA & NA & NA & methods & NA & Part of R 3.6.0 & NA & NA & NA & NA & NA & 3.6.0\\\\\n", "\tboot & boot & /usr/lib/R/library & 1.3-20 & recommended & R (>= 3.0.0), graphics, stats & NA & NA & MASS, survival & NA & Unlimited & NA & NA & NA & NA & no & 3.5.1\\\\\n", "\tclass & class & /usr/lib/R/library & 7.3-15 & recommended & R (>= 3.0.0), stats, utils & MASS & NA & NA & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tcluster & cluster & /usr/lib/R/library & 2.0.8 & recommended & R (>= 3.3.0) & graphics, grDevices, stats, utils & NA & MASS, Matrix & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tcodetools & codetools & /usr/lib/R/library & 0.2-16 & recommended & R (>= 2.1) & NA & NA & NA & NA & GPL & NA & NA & NA & NA & no & 3.5.3\\\\\n", "\tcompiler & compiler & /usr/lib/R/library & 3.6.0 & base & NA & NA & NA & NA & NA & Part of R 3.6.0 & NA & NA & NA & NA & NA & 3.6.0\\\\\n", "\tdatasets & datasets & /usr/lib/R/library & 3.6.0 & base & NA & NA & NA & NA & NA & Part of R 3.6.0 & NA & NA & NA & NA & NA & 3.6.0\\\\\n", "\tforeign & foreign & /usr/lib/R/library & 0.8-71 & recommended & R (>= 3.0.0) & methods, utils, stats & NA & NA & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tgraphics & graphics & /usr/lib/R/library & 3.6.0 & base & NA & grDevices & NA & NA & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tgrDevices & grDevices & /usr/lib/R/library & 3.6.0 & base & NA & NA & NA & KernSmooth & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tgrid & grid & /usr/lib/R/library & 3.6.0 & base & NA & grDevices, utils & NA & lattice & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tKernSmooth & KernSmooth & /usr/lib/R/library & 2.23-15 & recommended & R (>= 2.5.0), stats & NA & NA & MASS & NA & Unlimited & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tlattice & lattice & /usr/lib/R/library & 0.20-38 & recommended & R (>= 3.0.0) & grid, grDevices, graphics, stats, utils & NA & KernSmooth, MASS, latticeExtra & chron & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tMASS & MASS & /usr/lib/R/library & 7.3-51.3 & recommended & R (>= 3.1.0), grDevices, graphics, stats, utils & methods & NA & lattice, nlme, nnet, survival & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tMatrix & Matrix & /usr/lib/R/library & 1.2-17 & recommended & R (>= 3.2.0) & methods, graphics, grid, stats, utils, lattice & NA & expm, MASS & MatrixModels, graph, SparseM, sfsmisc & GPL (>= 2) \\textbar{} file LICENCE & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tmethods & methods & /usr/lib/R/library & 3.6.0 & base & NA & utils, stats & NA & codetools & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tmgcv & mgcv & /usr/lib/R/library & 1.8-28 & recommended & R (>= 2.14.0), nlme (>= 3.1-64) & methods, stats, graphics, Matrix, splines, utils & NA & parallel, survival, MASS & NA & GPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tnlme & nlme & /usr/lib/R/library & 3.1-139 & recommended & R (>= 3.4.0) & graphics, stats, utils, lattice & NA & Hmisc, MASS & NA & GPL (>= 2) \\textbar{} file LICENCE & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tnnet & nnet & /usr/lib/R/library & 7.3-12 & recommended & R (>= 2.14.0), stats, utils & NA & NA & MASS & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tparallel & parallel & /usr/lib/R/library & 3.6.0 & base & NA & tools, compiler & NA & methods & snow, nws, Rmpi & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\trpart & rpart & /usr/lib/R/library & 4.1-15 & recommended & R (>= 2.15.0), graphics, stats, grDevices & NA & NA & survival & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tspatial & spatial & /usr/lib/R/library & 7.3-11 & recommended & R (>= 3.0.0), graphics, stats, utils & NA & NA & MASS & NA & GPL-2 \\textbar{} GPL-3 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tsplines & splines & /usr/lib/R/library & 3.6.0 & base & NA & graphics, stats & NA & Matrix, methods & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tstats & stats & /usr/lib/R/library & 3.6.0 & base & NA & utils, grDevices, graphics & NA & MASS, Matrix, SuppDists, methods, stats4 & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tstats4 & stats4 & /usr/lib/R/library & 3.6.0 & base & NA & graphics, methods, stats & NA & NA & NA & Part of R 3.6.0 & NA & NA & NA & NA & NA & 3.6.0\\\\\n", "\tsurvival & survival & /usr/lib/R/library & 2.44-1.1 & recommended & R (>= 2.13.0) & graphics, Matrix, methods, splines, stats, utils & NA & NA & NA & LGPL (>= 2) & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\ttcltk & tcltk & /usr/lib/R/library & 3.6.0 & base & NA & utils & NA & NA & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\ttools & tools & /usr/lib/R/library & 3.6.0 & base & NA & NA & NA & codetools, methods, xml2, curl, commonmark & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\tutils & utils & /usr/lib/R/library & 3.6.0 & base & NA & NA & NA & methods, xml2, commonmark & NA & Part of R 3.6.0 & NA & NA & NA & NA & yes & 3.6.0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 304 × 16 of type chr\n", "\n", "| | Package | LibPath | Version | Priority | Depends | Imports | LinkingTo | Suggests | Enhances | License | License_is_FOSS | License_restricts_use | OS_type | MD5sum | NeedsCompilation | Built |\n", "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", "| countrycode | countrycode | /home/jovyan/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | R (>= 2.10) | NA | NA | testthat (>= 0.5) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |\n", "| acepack | acepack | /usr/local/lib/R/site-library | 1.4.1 | NA | NA | NA | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |\n", "| ade4 | ade4 | /usr/local/lib/R/site-library | 1.7-13 | NA | R (>= 2.10) | graphics, grDevices, methods, stats, utils, MASS | NA | ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir,\n", "lattice, pixmap, sp, spdep, splancs, waveslim | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| airway | airway | /usr/local/lib/R/site-library | 1.4.0 | NA | R (>= 2.10), SummarizedExperiment | NA | NA | knitr, GEOquery | NA | LGPL | NA | NA | NA | NA | no | 3.6.0 |\n", "| annotate | annotate | /usr/local/lib/R/site-library | 1.62.0 | NA | R (>= 2.10), AnnotationDbi (>= 1.27.5), XML | Biobase, DBI, xtable, graphics, utils, stats, methods,\n", "BiocGenerics (>= 0.13.8), RCurl | NA | hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\n", "rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\n", "org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| AnnotationDbi | AnnotationDbi | /usr/local/lib/R/site-library | 1.46.0 | NA | R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n", "0.29.2), Biobase (>= 1.17.0), IRanges | DBI, RSQLite, S4Vectors (>= 0.9.25) | NA | hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,\n", "RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,\n", "org.Hs.eg.db, reactome.db, AnnotationForge, graph,\n", "EnsDb.Hsapiens.v75, BiocStyle, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| AnnotationFilter | AnnotationFilter | /usr/local/lib/R/site-library | 1.8.0 | NA | R (>= 3.4.0) | utils, methods, GenomicRanges, lazyeval | NA | BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| ape | ape | /usr/local/lib/R/site-library | 5.3 | NA | R (>= 3.2.0) | nlme, lattice, graphics, methods, stats, tools, utils,\n", "parallel, Rcpp (>= 0.12.0) | Rcpp | gee, expm, igraph | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| askpass | askpass | /usr/local/lib/R/site-library | 1.1 | NA | NA | sys (>= 2.1) | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |\n", "| assertthat | assertthat | /usr/local/lib/R/site-library | 0.2.1 | NA | NA | tools | NA | testthat, covr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |\n", "| backports | backports | /usr/local/lib/R/site-library | 1.1.4 | NA | R (>= 3.0.0) | utils | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| base64enc | base64enc | /usr/local/lib/R/site-library | 0.1-3 | NA | R (>= 2.9.0) | NA | NA | NA | png | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| BH | BH | /usr/local/lib/R/site-library | 1.69.0-1 | NA | NA | NA | NA | NA | NA | BSL-1.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| Biobase | Biobase | /usr/local/lib/R/site-library | 2.44.0 | NA | R (>= 2.10), BiocGenerics (>= 0.27.1), utils | methods | NA | tools, tkWidgets, ALL, RUnit, golubEsets | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| BiocGenerics | BiocGenerics | /usr/local/lib/R/site-library | 0.30.0 | NA | R (>= 3.6.0), methods, utils, graphics, stats, parallel | methods, utils, graphics, stats, parallel | NA | Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,\n", "AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,\n", "DESeq2, MSnbase, annotate, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| BiocManager | BiocManager | /usr/local/lib/R/site-library | 1.30.4 | NA | R (>= 3.5.0) | utils | NA | BiocStyle, BiocVersion, remotes, testthat, knitr, withr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| BiocParallel | BiocParallel | /usr/local/lib/R/site-library | 1.18.0 | NA | methods | stats, utils, futile.logger, parallel, snow | BH | BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\n", "Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\n", "TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\n", "Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,\n", "BiocStyle, knitr, batchtools, data.table | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| BiocVersion | BiocVersion | /usr/local/lib/R/site-library | 3.9.0 | NA | R (>= 3.6.0), R (< 3.7.0) | NA | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| biomaRt | biomaRt | /usr/local/lib/R/site-library | 2.40.0 | NA | methods | utils, XML, RCurl, AnnotationDbi, progress, stringr, httr | NA | annotate, BiocStyle, knitr, rmarkdown, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| biomformat | biomformat | /usr/local/lib/R/site-library | 1.12.0 | NA | R (>= 3.2), methods | plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 | NA | testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),\n", "rmarkdown (>= 0.7) | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |\n", "| Biostrings | Biostrings | /usr/local/lib/R/site-library | 2.52.0 | NA | R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13),\n", "IRanges, XVector (>= 0.23.2) | graphics, methods, stats, utils | S4Vectors, IRanges, XVector | BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n", "1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\n", "BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\n", "hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n", "(>= 1.41.3), affydata (>= 1.11.5), RUnit | Rmpi | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| biovizBase | biovizBase | /usr/local/lib/R/site-library | 1.32.0 | NA | R (>= 2.10), methods | grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,\n", "BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28),\n", "GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),\n", "SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=\n", "1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=\n", "1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),\n", "ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang | NA | BSgenome.Hsapiens.UCSC.hg19,\n", "TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,\n", "EnsDb.Hsapiens.v75, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| bit | bit | /usr/local/lib/R/site-library | 1.1-14 | NA | R (>= 2.9.2) | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| bit64 | bit64 | /usr/local/lib/R/site-library | 0.9-7 | NA | R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| bitops | bitops | /usr/local/lib/R/site-library | 1.0-6 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| blob | blob | /usr/local/lib/R/site-library | 1.1.1 | NA | NA | methods, prettyunits | NA | covr, pillar (>= 1.2.1), testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |\n", "| broom | broom | /usr/local/lib/R/site-library | 0.5.2 | NA | R (>= 3.1) | backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr,\n", "reshape2, stringr, tibble, tidyr | NA | AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms,\n", "btergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>=\n", "1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2,\n", "glmnet, gmm, Hmisc, irlba, joineRML, Kendall, knitr, ks,\n", "Lahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps,\n", "maptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network,\n", "nnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych,\n", "quantreg, rgeos, rmarkdown, robust, rsample, rstan, rstanarm,\n", "sp, speedglm, statnet.common, survey, survival, testthat,\n", "tseries, xergm, zoo | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |\n", "| BSgenome | BSgenome | /usr/local/lib/R/site-library | 1.52.0 | NA | R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=\n", "0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.15.2),\n", "GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer\n", "(>= 1.39.7) | methods, utils, stats, BiocGenerics, S4Vectors, IRanges,\n", "XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,\n", "rtracklayer | NA | BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,\n", "BSgenome.Hsapiens.UCSC.hg38,\n", "BSgenome.Hsapiens.UCSC.hg38.masked,\n", "BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,\n", "BSgenome.Scerevisiae.UCSC.sacCer1,\n", "TxDb.Hsapiens.UCSC.hg38.knownGene,\n", "TxDb.Mmusculus.UCSC.mm10.knownGene,\n", "SNPlocs.Hsapiens.dbSNP144.GRCh38,\n", "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |\n", "| callr | callr | /usr/local/lib/R/site-library | 3.2.0 | NA | NA | processx (>= 3.3.0), R6, utils | NA | cliapp, covr, crayon, pingr, ps, testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |\n", "| caret | caret | /usr/local/lib/R/site-library | 6.0-84 | NA | R (>= 3.2.0), lattice (>= 0.20), ggplot2 | foreach, methods, plyr, ModelMetrics (>= 1.1.0), nlme,\n", "reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.4),\n", "withr (>= 2.0.0) | NA | BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>=\n", "1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv,\n", "mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, pROC,\n", "proxy, randomForest, RANN, spls, subselect, pamr, superpc,\n", "Cubist, testthat (>= 0.9.1), rpart, dplyr | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |\n", "| zoo | zoo | /usr/local/lib/R/site-library | 1.8-6 | NA | R (>= 3.1.0), stats | utils, graphics, grDevices, lattice (>= 0.20-27) | NA | coda, chron, DAAG, fts, ggplot2, mondate, scales,\n", "strucchange, timeDate, timeSeries, tis, tseries, xts | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| base | base | /usr/lib/R/library | 3.6.0 | base | NA | NA | NA | methods | NA | Part of R 3.6.0 | NA | NA | NA | NA | NA | 3.6.0 |\n", "| boot | boot | /usr/lib/R/library | 1.3-20 | recommended | R (>= 3.0.0), graphics, stats | NA | NA | MASS, survival | NA | Unlimited | NA | NA | NA | NA | no | 3.5.1 |\n", "| class | class | /usr/lib/R/library | 7.3-15 | recommended | R (>= 3.0.0), stats, utils | MASS | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| cluster | cluster | /usr/lib/R/library | 2.0.8 | recommended | R (>= 3.3.0) | graphics, grDevices, stats, utils | NA | MASS, Matrix | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| codetools | codetools | /usr/lib/R/library | 0.2-16 | recommended | R (>= 2.1) | NA | NA | NA | NA | GPL | NA | NA | NA | NA | no | 3.5.3 |\n", "| compiler | compiler | /usr/lib/R/library | 3.6.0 | base | NA | NA | NA | NA | NA | Part of R 3.6.0 | NA | NA | NA | NA | NA | 3.6.0 |\n", "| datasets | datasets | /usr/lib/R/library | 3.6.0 | base | NA | NA | NA | NA | NA | Part of R 3.6.0 | NA | NA | NA | NA | NA | 3.6.0 |\n", "| foreign | foreign | /usr/lib/R/library | 0.8-71 | recommended | R (>= 3.0.0) | methods, utils, stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| graphics | graphics | /usr/lib/R/library | 3.6.0 | base | NA | grDevices | NA | NA | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| grDevices | grDevices | /usr/lib/R/library | 3.6.0 | base | NA | NA | NA | KernSmooth | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| grid | grid | /usr/lib/R/library | 3.6.0 | base | NA | grDevices, utils | NA | lattice | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| KernSmooth | KernSmooth | /usr/lib/R/library | 2.23-15 | recommended | R (>= 2.5.0), stats | NA | NA | MASS | NA | Unlimited | NA | NA | NA | NA | yes | 3.6.0 |\n", "| lattice | lattice | /usr/lib/R/library | 0.20-38 | recommended | R (>= 3.0.0) | grid, grDevices, graphics, stats, utils | NA | KernSmooth, MASS, latticeExtra | chron | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| MASS | MASS | /usr/lib/R/library | 7.3-51.3 | recommended | R (>= 3.1.0), grDevices, graphics, stats, utils | methods | NA | lattice, nlme, nnet, survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| Matrix | Matrix | /usr/lib/R/library | 1.2-17 | recommended | R (>= 3.2.0) | methods, graphics, grid, stats, utils, lattice | NA | expm, MASS | MatrixModels, graph, SparseM, sfsmisc | GPL (>= 2) | file LICENCE | NA | NA | NA | NA | yes | 3.6.0 |\n", "| methods | methods | /usr/lib/R/library | 3.6.0 | base | NA | utils, stats | NA | codetools | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| mgcv | mgcv | /usr/lib/R/library | 1.8-28 | recommended | R (>= 2.14.0), nlme (>= 3.1-64) | methods, stats, graphics, Matrix, splines, utils | NA | parallel, survival, MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| nlme | nlme | /usr/lib/R/library | 3.1-139 | recommended | R (>= 3.4.0) | graphics, stats, utils, lattice | NA | Hmisc, MASS | NA | GPL (>= 2) | file LICENCE | NA | NA | NA | NA | yes | 3.6.0 |\n", "| nnet | nnet | /usr/lib/R/library | 7.3-12 | recommended | R (>= 2.14.0), stats, utils | NA | NA | MASS | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| parallel | parallel | /usr/lib/R/library | 3.6.0 | base | NA | tools, compiler | NA | methods | snow, nws, Rmpi | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| rpart | rpart | /usr/lib/R/library | 4.1-15 | recommended | R (>= 2.15.0), graphics, stats, grDevices | NA | NA | survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| spatial | spatial | /usr/lib/R/library | 7.3-11 | recommended | R (>= 3.0.0), graphics, stats, utils | NA | NA | MASS | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| splines | splines | /usr/lib/R/library | 3.6.0 | base | NA | graphics, stats | NA | Matrix, methods | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| stats | stats | /usr/lib/R/library | 3.6.0 | base | NA | utils, grDevices, graphics | NA | MASS, Matrix, SuppDists, methods, stats4 | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| stats4 | stats4 | /usr/lib/R/library | 3.6.0 | base | NA | graphics, methods, stats | NA | NA | NA | Part of R 3.6.0 | NA | NA | NA | NA | NA | 3.6.0 |\n", "| survival | survival | /usr/lib/R/library | 2.44-1.1 | recommended | R (>= 2.13.0) | graphics, Matrix, methods, splines, stats, utils | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |\n", "| tcltk | tcltk | /usr/lib/R/library | 3.6.0 | base | NA | utils | NA | NA | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| tools | tools | /usr/lib/R/library | 3.6.0 | base | NA | NA | NA | codetools, methods, xml2, curl, commonmark | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "| utils | utils | /usr/lib/R/library | 3.6.0 | base | NA | NA | NA | methods, xml2, commonmark | NA | Part of R 3.6.0 | NA | NA | NA | NA | yes | 3.6.0 |\n", "\n" ], "text/plain": [ " Package \n", "countrycode countrycode \n", "acepack acepack \n", "ade4 ade4 \n", "airway airway \n", "annotate annotate \n", "AnnotationDbi AnnotationDbi \n", "AnnotationFilter AnnotationFilter\n", "ape ape \n", "askpass askpass \n", "assertthat assertthat \n", "backports backports \n", "base64enc base64enc \n", "BH BH \n", "Biobase Biobase \n", "BiocGenerics BiocGenerics \n", "BiocManager BiocManager \n", "BiocParallel BiocParallel \n", "BiocVersion BiocVersion \n", "biomaRt biomaRt \n", "biomformat biomformat \n", "Biostrings Biostrings \n", "biovizBase biovizBase \n", "bit bit \n", "bit64 bit64 \n", "bitops bitops \n", "blob blob \n", "broom broom \n", "BSgenome BSgenome \n", "callr callr \n", "caret caret \n", "⋮ ⋮ \n", "zoo zoo \n", "base base \n", "boot boot \n", "class class \n", "cluster cluster \n", "codetools codetools \n", "compiler compiler \n", "datasets datasets \n", "foreign foreign \n", "graphics graphics \n", "grDevices grDevices \n", "grid grid \n", "KernSmooth KernSmooth \n", "lattice lattice \n", "MASS MASS \n", "Matrix Matrix \n", "methods methods \n", "mgcv mgcv \n", "nlme nlme \n", "nnet nnet \n", "parallel parallel \n", "rpart rpart \n", "spatial spatial \n", "splines splines \n", "stats stats \n", "stats4 stats4 \n", "survival survival \n", "tcltk tcltk \n", "tools tools \n", "utils utils \n", " LibPath Version \n", "countrycode /home/jovyan/R/x86_64-pc-linux-gnu-library/3.6 1.1.0 \n", "acepack /usr/local/lib/R/site-library 1.4.1 \n", "ade4 /usr/local/lib/R/site-library 1.7-13 \n", "airway /usr/local/lib/R/site-library 1.4.0 \n", "annotate /usr/local/lib/R/site-library 1.62.0 \n", "AnnotationDbi /usr/local/lib/R/site-library 1.46.0 \n", "AnnotationFilter /usr/local/lib/R/site-library 1.8.0 \n", "ape /usr/local/lib/R/site-library 5.3 \n", "askpass /usr/local/lib/R/site-library 1.1 \n", "assertthat /usr/local/lib/R/site-library 0.2.1 \n", "backports /usr/local/lib/R/site-library 1.1.4 \n", "base64enc /usr/local/lib/R/site-library 0.1-3 \n", "BH /usr/local/lib/R/site-library 1.69.0-1\n", "Biobase /usr/local/lib/R/site-library 2.44.0 \n", "BiocGenerics /usr/local/lib/R/site-library 0.30.0 \n", "BiocManager /usr/local/lib/R/site-library 1.30.4 \n", "BiocParallel /usr/local/lib/R/site-library 1.18.0 \n", "BiocVersion /usr/local/lib/R/site-library 3.9.0 \n", "biomaRt /usr/local/lib/R/site-library 2.40.0 \n", "biomformat /usr/local/lib/R/site-library 1.12.0 \n", "Biostrings /usr/local/lib/R/site-library 2.52.0 \n", "biovizBase /usr/local/lib/R/site-library 1.32.0 \n", "bit /usr/local/lib/R/site-library 1.1-14 \n", "bit64 /usr/local/lib/R/site-library 0.9-7 \n", "bitops /usr/local/lib/R/site-library 1.0-6 \n", "blob /usr/local/lib/R/site-library 1.1.1 \n", "broom /usr/local/lib/R/site-library 0.5.2 \n", "BSgenome /usr/local/lib/R/site-library 1.52.0 \n", "callr /usr/local/lib/R/site-library 3.2.0 \n", "caret /usr/local/lib/R/site-library 6.0-84 \n", "⋮ ⋮ ⋮ \n", "zoo /usr/local/lib/R/site-library 1.8-6 \n", "base /usr/lib/R/library 3.6.0 \n", "boot /usr/lib/R/library 1.3-20 \n", "class /usr/lib/R/library 7.3-15 \n", "cluster /usr/lib/R/library 2.0.8 \n", "codetools /usr/lib/R/library 0.2-16 \n", "compiler /usr/lib/R/library 3.6.0 \n", "datasets /usr/lib/R/library 3.6.0 \n", "foreign /usr/lib/R/library 0.8-71 \n", "graphics /usr/lib/R/library 3.6.0 \n", "grDevices /usr/lib/R/library 3.6.0 \n", "grid /usr/lib/R/library 3.6.0 \n", "KernSmooth /usr/lib/R/library 2.23-15 \n", "lattice /usr/lib/R/library 0.20-38 \n", "MASS /usr/lib/R/library 7.3-51.3\n", "Matrix /usr/lib/R/library 1.2-17 \n", "methods /usr/lib/R/library 3.6.0 \n", "mgcv /usr/lib/R/library 1.8-28 \n", "nlme /usr/lib/R/library 3.1-139 \n", "nnet /usr/lib/R/library 7.3-12 \n", "parallel /usr/lib/R/library 3.6.0 \n", "rpart /usr/lib/R/library 4.1-15 \n", "spatial /usr/lib/R/library 7.3-11 \n", "splines /usr/lib/R/library 3.6.0 \n", "stats /usr/lib/R/library 3.6.0 \n", "stats4 /usr/lib/R/library 3.6.0 \n", "survival /usr/lib/R/library 2.44-1.1\n", "tcltk /usr/lib/R/library 3.6.0 \n", "tools /usr/lib/R/library 3.6.0 \n", "utils /usr/lib/R/library 3.6.0 \n", " Priority \n", "countrycode NA \n", "acepack NA \n", "ade4 NA \n", "airway NA \n", "annotate NA \n", "AnnotationDbi NA \n", "AnnotationFilter NA \n", "ape NA \n", "askpass NA \n", "assertthat NA \n", "backports NA \n", "base64enc NA \n", "BH NA \n", "Biobase NA \n", "BiocGenerics NA \n", "BiocManager NA \n", "BiocParallel NA \n", "BiocVersion NA \n", "biomaRt NA \n", "biomformat NA \n", "Biostrings NA \n", "biovizBase NA \n", "bit NA \n", "bit64 NA \n", "bitops NA \n", "blob NA \n", "broom NA \n", "BSgenome NA \n", "callr NA \n", "caret NA \n", "⋮ ⋮ \n", "zoo NA \n", "base base \n", "boot recommended\n", "class recommended\n", "cluster recommended\n", "codetools recommended\n", "compiler base \n", "datasets base \n", "foreign recommended\n", "graphics base \n", "grDevices base \n", "grid base \n", "KernSmooth recommended\n", "lattice recommended\n", "MASS recommended\n", "Matrix recommended\n", "methods base \n", "mgcv recommended\n", "nlme recommended\n", "nnet recommended\n", "parallel base \n", "rpart recommended\n", "spatial recommended\n", "splines base \n", "stats base \n", "stats4 base \n", "survival recommended\n", "tcltk base \n", "tools base \n", "utils base \n", " Depends \n", "countrycode R (>= 2.10) \n", "acepack NA \n", "ade4 R (>= 2.10) \n", "airway R (>= 2.10), SummarizedExperiment \n", "annotate R (>= 2.10), AnnotationDbi (>= 1.27.5), XML \n", "AnnotationDbi R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\\n0.29.2), Biobase (>= 1.17.0), IRanges \n", "AnnotationFilter R (>= 3.4.0) \n", "ape R (>= 3.2.0) \n", "askpass NA \n", "assertthat NA \n", "backports R (>= 3.0.0) \n", "base64enc R (>= 2.9.0) \n", "BH NA \n", "Biobase R (>= 2.10), BiocGenerics (>= 0.27.1), utils \n", "BiocGenerics R (>= 3.6.0), methods, utils, graphics, stats, parallel \n", "BiocManager R (>= 3.5.0) \n", "BiocParallel methods \n", "BiocVersion R (>= 3.6.0), R (< 3.7.0) \n", "biomaRt methods \n", "biomformat R (>= 3.2), methods \n", "Biostrings R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13),\\nIRanges, XVector (>= 0.23.2) \n", "biovizBase R (>= 2.10), methods \n", "bit R (>= 2.9.2) \n", "bit64 R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats \n", "bitops NA \n", "blob NA \n", "broom R (>= 3.1) \n", "BSgenome R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=\\n0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.15.2),\\nGenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer\\n(>= 1.39.7)\n", "callr NA \n", "caret R (>= 3.2.0), lattice (>= 0.20), ggplot2 \n", "⋮ ⋮ \n", "zoo R (>= 3.1.0), stats \n", "base NA \n", "boot R (>= 3.0.0), graphics, stats \n", "class R (>= 3.0.0), stats, utils \n", "cluster R (>= 3.3.0) \n", "codetools R (>= 2.1) \n", "compiler NA \n", "datasets NA \n", "foreign R (>= 3.0.0) \n", "graphics NA \n", "grDevices NA \n", "grid NA \n", "KernSmooth R (>= 2.5.0), stats \n", "lattice R (>= 3.0.0) \n", "MASS R (>= 3.1.0), grDevices, graphics, stats, utils \n", "Matrix R (>= 3.2.0) \n", "methods NA \n", "mgcv R (>= 2.14.0), nlme (>= 3.1-64) \n", "nlme R (>= 3.4.0) \n", "nnet R (>= 2.14.0), stats, utils \n", "parallel NA \n", "rpart R (>= 2.15.0), graphics, stats, grDevices \n", "spatial R (>= 3.0.0), graphics, stats, utils \n", "splines NA \n", "stats NA \n", "stats4 NA \n", "survival R (>= 2.13.0) \n", "tcltk NA \n", "tools NA \n", "utils NA \n", " Imports \n", "countrycode NA \n", "acepack NA \n", "ade4 graphics, grDevices, methods, stats, utils, MASS \n", "airway NA \n", "annotate Biobase, DBI, xtable, graphics, utils, stats, methods,\\nBiocGenerics (>= 0.13.8), RCurl \n", "AnnotationDbi DBI, RSQLite, S4Vectors (>= 0.9.25) \n", "AnnotationFilter utils, methods, GenomicRanges, lazyeval \n", "ape nlme, lattice, graphics, methods, stats, tools, utils,\\nparallel, Rcpp (>= 0.12.0) \n", "askpass sys (>= 2.1) \n", "assertthat tools \n", "backports utils \n", "base64enc NA \n", "BH NA \n", "Biobase methods \n", "BiocGenerics methods, utils, graphics, stats, parallel \n", "BiocManager utils \n", "BiocParallel stats, utils, futile.logger, parallel, snow \n", "BiocVersion NA \n", "biomaRt utils, XML, RCurl, AnnotationDbi, progress, stringr, httr \n", "biomformat plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 \n", "Biostrings graphics, methods, stats, utils \n", "biovizBase grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,\\nBiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28),\\nGenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),\\nSummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=\\n1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=\\n1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),\\nensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang\n", "bit NA \n", "bit64 NA \n", "bitops NA \n", "blob methods, prettyunits \n", "broom backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr,\\nreshape2, stringr, tibble, tidyr \n", "BSgenome methods, utils, stats, BiocGenerics, S4Vectors, IRanges,\\nXVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,\\nrtracklayer \n", "callr processx (>= 3.3.0), R6, utils \n", "caret foreach, methods, plyr, ModelMetrics (>= 1.1.0), nlme,\\nreshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.4),\\nwithr (>= 2.0.0) \n", "⋮ ⋮ \n", "zoo utils, graphics, grDevices, lattice (>= 0.20-27) \n", "base NA \n", "boot NA \n", "class MASS \n", "cluster graphics, grDevices, stats, utils \n", "codetools NA \n", "compiler NA \n", "datasets NA \n", "foreign methods, utils, stats \n", "graphics grDevices \n", "grDevices NA \n", "grid grDevices, utils \n", "KernSmooth NA \n", "lattice grid, grDevices, graphics, stats, utils \n", "MASS methods \n", "Matrix methods, graphics, grid, stats, utils, lattice \n", "methods utils, stats \n", "mgcv methods, stats, graphics, Matrix, splines, utils \n", "nlme graphics, stats, utils, lattice \n", "nnet NA \n", "parallel tools, compiler \n", "rpart NA \n", "spatial NA \n", "splines graphics, stats \n", "stats utils, grDevices, graphics \n", "stats4 graphics, methods, stats \n", "survival graphics, Matrix, methods, splines, stats, utils \n", "tcltk utils \n", "tools NA \n", "utils NA \n", " LinkingTo \n", "countrycode NA \n", "acepack NA \n", "ade4 NA \n", "airway NA \n", "annotate NA \n", "AnnotationDbi NA \n", "AnnotationFilter NA \n", "ape Rcpp \n", "askpass NA \n", "assertthat NA \n", "backports NA \n", "base64enc NA \n", "BH NA \n", "Biobase NA \n", "BiocGenerics NA \n", "BiocManager NA \n", "BiocParallel BH \n", "BiocVersion NA \n", "biomaRt NA \n", "biomformat NA \n", "Biostrings S4Vectors, IRanges, XVector\n", "biovizBase NA \n", "bit NA \n", "bit64 NA \n", "bitops NA \n", "blob NA \n", "broom NA \n", "BSgenome NA \n", "callr NA \n", "caret NA \n", "⋮ ⋮ \n", "zoo NA \n", "base NA \n", "boot NA \n", "class NA \n", "cluster NA \n", "codetools NA \n", "compiler NA \n", "datasets NA \n", "foreign NA \n", "graphics NA \n", "grDevices NA \n", "grid NA \n", "KernSmooth NA \n", "lattice NA \n", "MASS NA \n", "Matrix NA \n", "methods NA \n", "mgcv NA \n", "nlme NA \n", "nnet NA \n", "parallel NA \n", "rpart NA \n", "spatial NA \n", "splines NA \n", "stats NA \n", "stats4 NA \n", "survival NA \n", "tcltk NA \n", "tools NA \n", "utils NA \n", " Suggests \n", "countrycode testthat (>= 0.5) \n", "acepack testthat \n", "ade4 ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir,\\nlattice, pixmap, sp, spdep, splancs, waveslim \n", "airway knitr, GEOquery \n", "annotate hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\\nrae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\\norg.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, \n", "AnnotationDbi hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,\\nRUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,\\norg.Hs.eg.db, reactome.db, AnnotationForge, graph,\\nEnsDb.Hsapiens.v75, BiocStyle, knitr \n", "AnnotationFilter BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db \n", "ape gee, expm, igraph \n", "askpass testthat \n", "assertthat testthat, covr \n", "backports NA \n", "base64enc NA \n", "BH NA \n", "Biobase tools, tkWidgets, ALL, RUnit, golubEsets \n", "BiocGenerics Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,\\nAnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,\\nDESeq2, MSnbase, annotate, RUnit \n", "BiocManager BiocStyle, BiocVersion, remotes, testthat, knitr, withr \n", "BiocParallel BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\\nRmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\\nTxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\\nRsamtools, GenomicAlignments, ShortRead, codetools, RUnit,\\nBiocStyle, knitr, batchtools, data.table \n", "BiocVersion NA \n", "biomaRt annotate, BiocStyle, knitr, rmarkdown, testthat \n", "biomformat testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),\\nrmarkdown (>= 0.7) \n", "Biostrings BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\\nBSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\\nhgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\\n(>= 1.41.3), affydata (>= 1.11.5), RUnit \n", "biovizBase BSgenome.Hsapiens.UCSC.hg19,\\nTxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,\\nEnsDb.Hsapiens.v75, RUnit \n", "bit NA \n", "bit64 NA \n", "bitops NA \n", "blob covr, pillar (>= 1.2.1), testthat \n", "broom AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms,\\nbtergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>=\\n1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2,\\nglmnet, gmm, Hmisc, irlba, joineRML, Kendall, knitr, ks,\\nLahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps,\\nmaptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network,\\nnnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych,\\nquantreg, rgeos, rmarkdown, robust, rsample, rstan, rstanarm,\\nsp, speedglm, statnet.common, survey, survival, testthat,\\ntseries, xergm, zoo\n", "BSgenome BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,\\nBSgenome.Hsapiens.UCSC.hg38,\\nBSgenome.Hsapiens.UCSC.hg38.masked,\\nBSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,\\nBSgenome.Scerevisiae.UCSC.sacCer1,\\nTxDb.Hsapiens.UCSC.hg38.knownGene,\\nTxDb.Mmusculus.UCSC.mm10.knownGene,\\nSNPlocs.Hsapiens.dbSNP144.GRCh38,\\nXtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit \n", "callr cliapp, covr, crayon, pingr, ps, testthat, withr \n", "caret BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>=\\n1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv,\\nmlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, pROC,\\nproxy, randomForest, RANN, spls, subselect, pamr, superpc,\\nCubist, testthat (>= 0.9.1), rpart, dplyr \n", "⋮ ⋮ \n", "zoo coda, chron, DAAG, fts, ggplot2, mondate, scales,\\nstrucchange, timeDate, timeSeries, tis, tseries, xts \n", "base methods \n", "boot MASS, survival \n", "class NA \n", "cluster MASS, Matrix \n", "codetools NA \n", "compiler NA \n", "datasets NA \n", "foreign NA \n", "graphics NA \n", "grDevices KernSmooth \n", "grid lattice \n", "KernSmooth MASS \n", "lattice KernSmooth, MASS, latticeExtra \n", "MASS lattice, nlme, nnet, survival \n", "Matrix expm, MASS \n", "methods codetools \n", "mgcv parallel, survival, MASS \n", "nlme Hmisc, MASS \n", "nnet MASS \n", "parallel methods \n", "rpart survival \n", "spatial MASS \n", "splines Matrix, methods \n", "stats MASS, Matrix, SuppDists, methods, stats4 \n", "stats4 NA \n", "survival NA \n", "tcltk NA \n", "tools codetools, methods, xml2, curl, commonmark \n", "utils methods, xml2, commonmark \n", " Enhances \n", "countrycode NA \n", "acepack NA \n", "ade4 NA \n", "airway NA \n", "annotate NA \n", "AnnotationDbi NA \n", "AnnotationFilter NA \n", "ape NA \n", "askpass NA \n", "assertthat NA \n", "backports NA \n", "base64enc png \n", "BH NA \n", "Biobase NA \n", "BiocGenerics NA \n", "BiocManager NA \n", "BiocParallel NA \n", "BiocVersion NA \n", "biomaRt NA \n", "biomformat NA \n", "Biostrings Rmpi \n", "biovizBase NA \n", "bit NA \n", "bit64 NA \n", "bitops NA \n", "blob NA \n", "broom NA \n", "BSgenome NA \n", "callr NA \n", "caret NA \n", "⋮ ⋮ \n", "zoo NA \n", "base NA \n", "boot NA \n", "class NA \n", "cluster NA \n", "codetools NA \n", "compiler NA \n", "datasets NA \n", "foreign NA \n", "graphics NA \n", "grDevices NA \n", "grid NA \n", "KernSmooth NA \n", "lattice chron \n", "MASS NA \n", "Matrix MatrixModels, graph, SparseM, sfsmisc\n", "methods NA \n", "mgcv NA \n", "nlme NA \n", "nnet NA \n", "parallel snow, nws, Rmpi \n", "rpart NA \n", "spatial NA \n", "splines NA \n", "stats NA \n", "stats4 NA \n", "survival NA \n", "tcltk NA \n", "tools NA \n", "utils NA \n", " License License_is_FOSS\n", "countrycode GPL-3 NA \n", "acepack MIT + file LICENSE NA \n", "ade4 GPL (>= 2) NA \n", "airway LGPL NA \n", "annotate Artistic-2.0 NA \n", "AnnotationDbi Artistic-2.0 NA \n", "AnnotationFilter Artistic-2.0 NA \n", "ape GPL (>= 2) NA \n", "askpass MIT + file LICENSE NA \n", "assertthat GPL-3 NA \n", "backports GPL-2 NA \n", "base64enc GPL-2 | GPL-3 NA \n", "BH BSL-1.0 NA \n", "Biobase Artistic-2.0 NA \n", "BiocGenerics Artistic-2.0 NA \n", "BiocManager Artistic-2.0 NA \n", "BiocParallel GPL-2 | GPL-3 NA \n", "BiocVersion Artistic-2.0 NA \n", "biomaRt Artistic-2.0 NA \n", "biomformat GPL-2 NA \n", "Biostrings Artistic-2.0 NA \n", "biovizBase Artistic-2.0 NA \n", "bit GPL-2 NA \n", "bit64 GPL-2 NA \n", "bitops GPL (>= 2) NA \n", "blob GPL-3 NA \n", "broom MIT + file LICENSE NA \n", "BSgenome Artistic-2.0 NA \n", "callr MIT + file LICENSE NA \n", "caret GPL (>= 2) NA \n", "⋮ ⋮ ⋮ \n", "zoo GPL-2 | GPL-3 NA \n", "base Part of R 3.6.0 NA \n", "boot Unlimited NA \n", "class GPL-2 | GPL-3 NA \n", "cluster GPL (>= 2) NA \n", "codetools GPL NA \n", "compiler Part of R 3.6.0 NA \n", "datasets Part of R 3.6.0 NA \n", "foreign GPL (>= 2) NA \n", "graphics Part of R 3.6.0 NA \n", "grDevices Part of R 3.6.0 NA \n", "grid Part of R 3.6.0 NA \n", "KernSmooth Unlimited NA \n", "lattice GPL (>= 2) NA \n", "MASS GPL-2 | GPL-3 NA \n", "Matrix GPL (>= 2) | file LICENCE NA \n", "methods Part of R 3.6.0 NA \n", "mgcv GPL (>= 2) NA \n", "nlme GPL (>= 2) | file LICENCE NA \n", "nnet GPL-2 | GPL-3 NA \n", "parallel Part of R 3.6.0 NA \n", "rpart GPL-2 | GPL-3 NA \n", "spatial GPL-2 | GPL-3 NA \n", "splines Part of R 3.6.0 NA \n", "stats Part of R 3.6.0 NA \n", "stats4 Part of R 3.6.0 NA \n", "survival LGPL (>= 2) NA \n", "tcltk Part of R 3.6.0 NA \n", "tools Part of R 3.6.0 NA \n", "utils Part of R 3.6.0 NA \n", " License_restricts_use OS_type MD5sum NeedsCompilation Built\n", "countrycode NA NA NA no 3.6.0\n", "acepack NA NA NA yes 3.6.0\n", "ade4 NA NA NA yes 3.6.0\n", "airway NA NA NA no 3.6.0\n", "annotate NA NA NA no 3.6.0\n", "AnnotationDbi NA NA NA no 3.6.0\n", "AnnotationFilter NA NA NA no 3.6.0\n", "ape NA NA NA yes 3.6.0\n", "askpass NA NA NA yes 3.6.0\n", "assertthat NA NA NA no 3.6.0\n", "backports NA NA NA yes 3.6.0\n", "base64enc NA NA NA yes 3.6.0\n", "BH NA NA NA no 3.6.0\n", "Biobase NA NA NA yes 3.6.0\n", "BiocGenerics NA NA NA no 3.6.0\n", "BiocManager NA NA NA no 3.6.0\n", "BiocParallel NA NA NA yes 3.6.0\n", "BiocVersion NA NA NA no 3.6.0\n", "biomaRt NA NA NA no 3.6.0\n", "biomformat NA NA NA no 3.6.0\n", "Biostrings NA NA NA yes 3.6.0\n", "biovizBase NA NA NA yes 3.6.0\n", "bit NA NA NA yes 3.6.0\n", "bit64 NA NA NA yes 3.6.0\n", "bitops NA NA NA yes 3.6.0\n", "blob NA NA NA no 3.6.0\n", "broom NA NA NA no 3.6.0\n", "BSgenome NA NA NA no 3.6.0\n", "callr NA NA NA no 3.6.0\n", "caret NA NA NA yes 3.6.0\n", "⋮ ⋮ ⋮ ⋮ ⋮ ⋮ \n", "zoo NA NA NA yes 3.6.0\n", "base NA NA NA NA 3.6.0\n", "boot NA NA NA no 3.5.1\n", "class NA NA NA yes 3.6.0\n", "cluster NA NA NA yes 3.6.0\n", "codetools NA NA NA no 3.5.3\n", "compiler NA NA NA NA 3.6.0\n", "datasets NA NA NA NA 3.6.0\n", "foreign NA NA NA yes 3.6.0\n", "graphics NA NA NA yes 3.6.0\n", "grDevices NA NA NA yes 3.6.0\n", "grid NA NA NA yes 3.6.0\n", "KernSmooth NA NA NA yes 3.6.0\n", "lattice NA NA NA yes 3.6.0\n", "MASS NA NA NA yes 3.6.0\n", "Matrix NA NA NA yes 3.6.0\n", "methods NA NA NA yes 3.6.0\n", "mgcv NA NA NA yes 3.6.0\n", "nlme NA NA NA yes 3.6.0\n", "nnet NA NA NA yes 3.6.0\n", "parallel NA NA NA yes 3.6.0\n", "rpart NA NA NA yes 3.6.0\n", "spatial NA NA NA yes 3.6.0\n", "splines NA NA NA yes 3.6.0\n", "stats NA NA NA yes 3.6.0\n", "stats4 NA NA NA NA 3.6.0\n", "survival NA NA NA yes 3.6.0\n", "tcltk NA NA NA yes 3.6.0\n", "tools NA NA NA yes 3.6.0\n", "utils NA NA NA yes 3.6.0" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "installed.packages()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "You can install new packages using the command `install.packages()`\n" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "install.packages(\"auk\", lib = \"~/work\")" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "auk 0.3.3 is designed for EBD files downloaded after 2018-08-15. \n", "No EBD data directory set, see ?auk_set_ebd_path to set EBD_PATH \n", "eBird taxonomy version: 2018\n" ] } ], "source": [ ".libPaths(\"~/work\")\n", "library(auk)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Removing package from ‘/home/jovyan/work’\n", "(as ‘lib’ is unspecified)\n" ] } ], "source": [ "remove.packages(\"auk\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## BioConductor" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "CRAN is home to many, many R packages. But there is a whole other world out there when it comes to bioinformatics in R. It's called [BioConductor](https://bioconductor.org/). BioConductor is a comprehensive toolkit for all things having to do with high-throughput sequencing data processing and analysis. In this course, we will use the BioConductor package `DESeq2` to perform differential expression analysis. It's the end of the pipeline, after QC, clipping and trimming, aligning and counting. \n", "\n", "### Installing BioConductor packages\n", "\n", "BioConductor has it's own installation procedure (and it's own criteria for documentation, testing, etc.) - separate from CRAN. Let's have a look at the page for [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "#source(\"https://bioconductor.org/biocLite.R\")\n", "#biocLite(\"DESeq2\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### DESeq2 and S4 Objects" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We'll walk through an example using a sample data set called 'airway'. Airway is an object of type 'SummarizedExperiment'. This kind of object is the basis for many objects used in Bioconductor packages." ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Loading required package: SummarizedExperiment\n", "Loading required package: GenomicRanges\n", "Loading required package: stats4\n", "Loading required package: BiocGenerics\n", "Loading required package: parallel\n", "\n", "Attaching package: ‘BiocGenerics’\n", "\n", "The following objects are masked from ‘package:parallel’:\n", "\n", " clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n", " clusterExport, clusterMap, parApply, parCapply, parLapply,\n", " parLapplyLB, parRapply, parSapply, parSapplyLB\n", "\n", "The following objects are masked from ‘package:dplyr’:\n", "\n", " combine, intersect, setdiff, union\n", "\n", "The following objects are masked from ‘package:stats’:\n", "\n", " IQR, mad, sd, var, xtabs\n", "\n", "The following objects are masked from ‘package:base’:\n", "\n", " anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n", " dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n", " grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n", " order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n", " rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n", " union, unique, unsplit, which, which.max, which.min\n", "\n", "Loading required package: S4Vectors\n", "\n", "Attaching package: ‘S4Vectors’\n", "\n", "The following objects are masked from ‘package:dplyr’:\n", "\n", " first, rename\n", "\n", "The following object is masked from ‘package:base’:\n", "\n", " expand.grid\n", "\n", "Loading required package: IRanges\n", "\n", "Attaching package: ‘IRanges’\n", "\n", "The following objects are masked from ‘package:dplyr’:\n", "\n", " collapse, desc, slice\n", "\n", "Loading required package: GenomeInfoDb\n", "Loading required package: Biobase\n", "Welcome to Bioconductor\n", "\n", " Vignettes contain introductory material; view with\n", " 'browseVignettes()'. To cite Bioconductor, see\n", " 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n", "\n", "Loading required package: DelayedArray\n", "Loading required package: matrixStats\n", "\n", "Attaching package: ‘matrixStats’\n", "\n", "The following objects are masked from ‘package:Biobase’:\n", "\n", " anyMissing, rowMedians\n", "\n", "The following object is masked from ‘package:dplyr’:\n", "\n", " count\n", "\n", "Loading required package: BiocParallel\n", "\n", "Attaching package: ‘DelayedArray’\n", "\n", "The following objects are masked from ‘package:matrixStats’:\n", "\n", " colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\n", "\n", "The following objects are masked from ‘package:base’:\n", "\n", " aperm, apply, rowsum\n", "\n" ] } ], "source": [ "library(\"airway\")\n", "data(\"airway\")\n", "se <- airway" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Formal class 'RangedSummarizedExperiment' [package \"SummarizedExperiment\"] with 6 slots\n", " ..@ rowRanges :Formal class 'GRangesList' [package \"GenomicRanges\"] with 5 slots\n", " .. .. ..@ unlistData :Formal class 'GRanges' [package \"GenomicRanges\"] with 7 slots\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Warning message:\n", "“Not a validObject(): no slot of name \"elementType\" for this object of class \"GRanges\"”" ] }, { "name": "stdout", "output_type": "stream", "text": [ " .. .. .. .. ..@ seqnames :Formal class 'Rle' [package \"S4Vectors\"] with 4 slots\n", " .. .. .. .. .. .. ..@ values : Factor w/ 722 levels \"1\",\"2\",\"3\",\"4\",..: 23 20 1 6 1 23 6 3 7 12 ...\n", " .. .. .. .. .. .. ..@ lengths : int [1:47916] 27 29 173 80 75 27 4 41 196 71 ...\n", " .. .. .. .. .. .. ..@ elementMetadata: NULL\n", " .. .. .. .. .. .. ..@ metadata : list()\n", " .. .. .. .. ..@ strand :Formal class 'Rle' [package \"S4Vectors\"] with 4 slots\n", " .. .. .. .. .. .. ..@ values : Factor w/ 3 levels \"+\",\"-\",\"*\": 2 1 2 1 2 1 2 1 2 1 ...\n", " .. .. .. .. .. .. ..@ lengths : int [1:31658] 17 10 59 72 26 45 68 12 42 33 ...\n", " .. .. .. .. .. .. ..@ elementMetadata: NULL\n", " .. .. .. .. .. .. ..@ metadata : list()\n", " .. .. .. .. ..@ ranges :Formal class 'IRanges' [package \"IRanges\"] with 6 slots\n", " .. .. .. .. .. .. ..@ start : int [1:745593] 99883667 99885756 99887482 99887538 99888402 99888402 99888439 99888928 99888928 99890175 ...\n", " .. .. .. .. .. .. ..@ width : int [1:745593] 1317 108 84 28 135 135 98 99 99 75 ...\n", " .. .. .. .. .. .. ..@ NAMES : NULL\n", " .. .. .. .. .. .. ..@ elementType : chr \"integer\"\n", " .. .. .. .. .. .. ..@ elementMetadata: NULL\n", " .. .. .. .. .. .. ..@ metadata : list()\n", " .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package \"IRanges\"] with 6 slots\n", " .. .. .. .. .. .. ..@ rownames : NULL\n", " .. .. .. .. .. .. ..@ nrows : int 745593\n", " .. .. .. .. .. .. ..@ listData :List of 2\n", " .. .. .. .. .. .. .. ..$ exon_id : int [1:745593] 667145 667146 667147 667148 667149 667150 667151 667153 667152 667154 ...\n", " .. .. .. .. .. .. .. ..$ exon_name: chr [1:745593] \"ENSE00001459322\" \"ENSE00000868868\" \"ENSE00000401072\" \"ENSE00001849132\" ...\n", " .. .. .. .. .. .. ..@ elementType : chr \"ANY\"\n", " .. .. .. .. .. .. ..@ elementMetadata: NULL\n", " .. .. .. .. .. .. ..@ metadata : list()\n", " .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package \"GenomeInfoDb\"] with 4 slots\n", " .. .. .. .. .. .. ..@ seqnames : chr [1:722] \"1\" \"2\" \"3\" \"4\" ...\n", " .. .. .. .. .. .. ..@ seqlengths : int [1:722] 249250621 243199373 198022430 191154276 180915260 171115067 159138663 146364022 141213431 135534747 ...\n", " .. .. .. .. .. .. ..@ is_circular: logi [1:722] FALSE FALSE FALSE FALSE FALSE FALSE ...\n", " .. .. .. .. .. .. ..@ genome : chr [1:722] NA NA NA NA ...\n", " .. .. .. .. ..@ metadata : list()\n", " .. .. .. .. ..@ NA : NULL\n", " .. .. ..@ elementMetadata:Formal class 'DataFrame' [package \"IRanges\"] with 6 slots\n", " .. .. .. .. ..@ rownames : NULL\n", " .. .. .. .. ..@ nrows : int 64102\n", " .. .. .. .. ..@ listData : Named list()\n", " .. .. .. .. ..@ elementType : chr \"ANY\"\n", " .. .. .. .. ..@ elementMetadata: NULL\n", " .. .. .. .. ..@ metadata : list()\n", " .. .. ..@ elementType : chr \"GRanges\"\n", " .. .. ..@ metadata :List of 1\n", " .. .. .. ..$ genomeInfo:List of 20\n", " .. .. .. .. ..$ Db type : chr \"TranscriptDb\"\n", " .. .. .. .. ..$ Supporting package : chr \"GenomicFeatures\"\n", " .. .. .. .. ..$ Data source : chr \"BioMart\"\n", " .. .. .. .. ..$ Organism : chr \"Homo sapiens\"\n", " .. .. .. .. ..$ Resource URL : chr \"www.biomart.org:80\"\n", " .. .. .. .. ..$ BioMart database : chr \"ensembl\"\n", " .. .. .. .. ..$ BioMart database version : chr \"ENSEMBL GENES 75 (SANGER UK)\"\n", " .. .. .. .. ..$ BioMart dataset : chr \"hsapiens_gene_ensembl\"\n", " .. .. .. .. ..$ BioMart dataset description : chr \"Homo sapiens genes (GRCh37.p13)\"\n", " .. .. .. .. ..$ BioMart dataset version : chr \"GRCh37.p13\"\n", " .. .. .. .. ..$ Full dataset : chr \"yes\"\n", " .. .. .. .. ..$ miRBase build ID : chr NA\n", " .. .. .. .. ..$ transcript_nrow : chr \"215647\"\n", " .. .. .. .. ..$ exon_nrow : chr \"745593\"\n", " .. .. .. .. ..$ cds_nrow : chr \"537555\"\n", " .. .. .. .. ..$ Db created by : chr \"GenomicFeatures package from Bioconductor\"\n", " .. .. .. .. ..$ Creation time : chr \"2014-07-10 14:55:55 -0400 (Thu, 10 Jul 2014)\"\n", " .. .. .. .. ..$ GenomicFeatures version at creation time: chr \"1.17.9\"\n", " .. .. .. .. ..$ RSQLite version at creation time : chr \"0.11.4\"\n", " .. .. .. .. ..$ DBSCHEMAVERSION : chr \"1.0\"\n", " .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package \"IRanges\"] with 5 slots\n", " .. .. .. .. ..@ end : int [1:64102] 17 27 56 86 158 184 229 243 297 309 ...\n", " .. .. .. .. ..@ NAMES : chr [1:64102] \"ENSG00000000003\" \"ENSG00000000005\" \"ENSG00000000419\" \"ENSG00000000457\" ...\n", " .. .. .. .. ..@ elementType : chr \"integer\"\n", " .. .. .. .. ..@ elementMetadata: NULL\n", " .. .. .. .. ..@ metadata : list()\n", " ..@ colData :Formal class 'DataFrame' [package \"IRanges\"] with 6 slots\n", " .. .. ..@ rownames : chr [1:8] \"SRR1039508\" \"SRR1039509\" \"SRR1039512\" \"SRR1039513\" ...\n", " .. .. ..@ nrows : int 8\n", " .. .. ..@ listData :List of 9\n", " .. .. .. ..$ SampleName: Factor w/ 8 levels \"GSM1275862\",\"GSM1275863\",..: 1 2 3 4 5 6 7 8\n", " .. .. .. ..$ cell : Factor w/ 4 levels \"N052611\",\"N061011\",..: 4 4 1 1 3 3 2 2\n", " .. .. .. ..$ dex : Factor w/ 2 levels \"trt\",\"untrt\": 2 1 2 1 2 1 2 1\n", " .. .. .. ..$ albut : Factor w/ 1 level \"untrt\": 1 1 1 1 1 1 1 1\n", " .. .. .. ..$ Run : Factor w/ 8 levels \"SRR1039508\",\"SRR1039509\",..: 1 2 3 4 5 6 7 8\n", " .. .. .. ..$ avgLength : int [1:8] 126 126 126 87 120 126 101 98\n", " .. .. .. ..$ Experiment: Factor w/ 8 levels \"SRX384345\",\"SRX384346\",..: 1 2 3 4 5 6 7 8\n", " .. .. .. ..$ Sample : Factor w/ 8 levels \"SRS508567\",\"SRS508568\",..: 2 1 3 4 5 6 7 8\n", " .. .. .. ..$ BioSample : Factor w/ 8 levels \"SAMN02422669\",..: 1 4 6 2 7 3 8 5\n", " .. .. ..@ elementType : chr \"ANY\"\n", " .. .. ..@ elementMetadata: NULL\n", " .. .. ..@ metadata : list()\n", " ..@ assays :Reference class 'ShallowSimpleListAssays' [package \"GenomicRanges\"] with 1 field\n", " .. ..$ data: NULL\n", " .. ..and 12 methods.\n", " ..@ NAMES : NULL\n", " ..@ elementMetadata:Formal class 'DataFrame' [package \"S4Vectors\"] with 6 slots\n", " .. .. ..@ rownames : NULL\n", " .. .. ..@ nrows : int 64102\n", " .. .. ..@ listData : Named list()\n", " .. .. ..@ elementType : chr \"ANY\"\n", " .. .. ..@ elementMetadata: NULL\n", " .. .. ..@ metadata : list()\n", " ..@ metadata :List of 1\n", " .. ..$ :Formal class 'MIAME' [package \"Biobase\"] with 13 slots\n", " .. .. .. ..@ name : chr \"Himes BE\"\n", " .. .. .. ..@ lab : chr NA\n", " .. .. .. ..@ contact : chr \"\"\n", " .. .. .. ..@ title : chr \"RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine\"| __truncated__\n", " .. .. .. ..@ abstract : chr \"Asthma is a chronic inflammatory respiratory disease that affects over 300 million people worldwide. Glucocorti\"| __truncated__\n", " .. .. .. ..@ url : chr \"http://www.ncbi.nlm.nih.gov/pubmed/24926665\"\n", " .. .. .. ..@ pubMedIds : chr \"24926665\"\n", " .. .. .. ..@ samples : list()\n", " .. .. .. ..@ hybridizations : list()\n", " .. .. .. ..@ normControls : list()\n", " .. .. .. ..@ preprocessing : list()\n", " .. .. .. ..@ other : list()\n", " .. .. .. ..@ .__classVersion__:Formal class 'Versions' [package \"Biobase\"] with 1 slot\n", " .. .. .. .. .. ..@ .Data:List of 2\n", " .. .. .. .. .. .. ..$ : int [1:3] 1 0 0\n", " .. .. .. .. .. .. ..$ : int [1:3] 1 1 0\n" ] } ], "source": [ "str(se)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "[This tutorial](https://bioconductor.org/packages/devel/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html) gives a great introduction to the SummarizedExperiment object. We'll take a peek, and then move on to DESeq2 " ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "List of length 1\n", "names(1): counts" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "assays(se)" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 64102 × 8 of type int
SRR1039508SRR1039509SRR1039512SRR1039513SRR1039516SRR1039517SRR1039520SRR1039521
ENSG00000000003 679 448 873 408 1138 1047 770 572
ENSG00000000005 0 0 0 0 0 0 0 0
ENSG00000000419 467 515 621 365 587 799 417 508
ENSG00000000457 260 211 263 164 245 331 233 229
ENSG00000000460 60 55 40 35 78 63 76 60
ENSG00000000938 0 0 2 0 1 0 0 0
ENSG000000009713251367961774252 67211102751767995
ENSG00000001036143310621733 881 1424 143913591109
ENSG00000001084 519 380 595 493 820 714 696 704
ENSG00000001167 394 236 464 175 658 584 360 269
ENSG00000001460 172 168 264 118 241 210 155 177
ENSG000000014612112186751372657 2735 275124672905
ENSG00000001497 524 488 638 357 676 806 493 475
ENSG00000001561 71 51 211 156 23 38 134 172
ENSG00000001617 555 394 905 415 727 697 618 599
ENSG00000001626 10 2 9 2 10 6 5 5
ENSG000000016291660125122591079 2462 251418881660
ENSG00000001630 59 54 66 23 84 87 31 59
ENSG00000001631 729 692 943 475 1034 1163 731 744
ENSG00000002016 201 161 256 99 268 257 160 137
ENSG00000002079 3 0 3 1 4 0 0 1
ENSG00000002330 206 174 184 111 194 260 156 177
ENSG00000002549145912941317 998 1451 1824 8531031
ENSG000000025867507720395016214109731286368347225
ENSG00000002587 2 0 1 0 0 2 0 0
ENSG00000002726 0 0 1 0 0 0 0 0
ENSG00000002745 4 6 22 10 2 1 5 3
ENSG00000002746 151 139 117 65 90 102 86 119
ENSG00000002822 411 303 446 195 445 523 295 300
ENSG000000028346314636478315809 66771197057667825
⋮⋮⋮⋮⋮⋮⋮⋮⋮
LRG_7000000000
LRG_7100000000
LRG_71500000000
LRG_71700000000
LRG_7200000000
LRG_7300000000
LRG_7400000000
LRG_7500000000
LRG_7600000000
LRG_7700000000
LRG_7800000000
LRG_7900000000
LRG_800000000
LRG_8000000000
LRG_8100000000
LRG_8300000000
LRG_8400000000
LRG_8500000000
LRG_8600000000
LRG_8800000000
LRG_8900000000
LRG_9000000000
LRG_9100000000
LRG_9200000000
LRG_9300000000
LRG_9400000000
LRG_9600000000
LRG_9700000000
LRG_9800000000
LRG_9900000000
\n" ], "text/latex": [ "A matrix: 64102 × 8 of type int\n", "\\begin{tabular}{r|llllllll}\n", " & SRR1039508 & SRR1039509 & SRR1039512 & SRR1039513 & SRR1039516 & SRR1039517 & SRR1039520 & SRR1039521\\\\\n", "\\hline\n", "\tENSG00000000003 & 679 & 448 & 873 & 408 & 1138 & 1047 & 770 & 572\\\\\n", "\tENSG00000000005 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000000419 & 467 & 515 & 621 & 365 & 587 & 799 & 417 & 508\\\\\n", "\tENSG00000000457 & 260 & 211 & 263 & 164 & 245 & 331 & 233 & 229\\\\\n", "\tENSG00000000460 & 60 & 55 & 40 & 35 & 78 & 63 & 76 & 60\\\\\n", "\tENSG00000000938 & 0 & 0 & 2 & 0 & 1 & 0 & 0 & 0\\\\\n", "\tENSG00000000971 & 3251 & 3679 & 6177 & 4252 & 6721 & 11027 & 5176 & 7995\\\\\n", "\tENSG00000001036 & 1433 & 1062 & 1733 & 881 & 1424 & 1439 & 1359 & 1109\\\\\n", "\tENSG00000001084 & 519 & 380 & 595 & 493 & 820 & 714 & 696 & 704\\\\\n", "\tENSG00000001167 & 394 & 236 & 464 & 175 & 658 & 584 & 360 & 269\\\\\n", "\tENSG00000001460 & 172 & 168 & 264 & 118 & 241 & 210 & 155 & 177\\\\\n", "\tENSG00000001461 & 2112 & 1867 & 5137 & 2657 & 2735 & 2751 & 2467 & 2905\\\\\n", "\tENSG00000001497 & 524 & 488 & 638 & 357 & 676 & 806 & 493 & 475\\\\\n", "\tENSG00000001561 & 71 & 51 & 211 & 156 & 23 & 38 & 134 & 172\\\\\n", "\tENSG00000001617 & 555 & 394 & 905 & 415 & 727 & 697 & 618 & 599\\\\\n", "\tENSG00000001626 & 10 & 2 & 9 & 2 & 10 & 6 & 5 & 5\\\\\n", "\tENSG00000001629 & 1660 & 1251 & 2259 & 1079 & 2462 & 2514 & 1888 & 1660\\\\\n", "\tENSG00000001630 & 59 & 54 & 66 & 23 & 84 & 87 & 31 & 59\\\\\n", "\tENSG00000001631 & 729 & 692 & 943 & 475 & 1034 & 1163 & 731 & 744\\\\\n", "\tENSG00000002016 & 201 & 161 & 256 & 99 & 268 & 257 & 160 & 137\\\\\n", "\tENSG00000002079 & 3 & 0 & 3 & 1 & 4 & 0 & 0 & 1\\\\\n", "\tENSG00000002330 & 206 & 174 & 184 & 111 & 194 & 260 & 156 & 177\\\\\n", "\tENSG00000002549 & 1459 & 1294 & 1317 & 998 & 1451 & 1824 & 853 & 1031\\\\\n", "\tENSG00000002586 & 7507 & 7203 & 9501 & 6214 & 10973 & 12863 & 6834 & 7225\\\\\n", "\tENSG00000002587 & 2 & 0 & 1 & 0 & 0 & 2 & 0 & 0\\\\\n", "\tENSG00000002726 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000002745 & 4 & 6 & 22 & 10 & 2 & 1 & 5 & 3\\\\\n", "\tENSG00000002746 & 151 & 139 & 117 & 65 & 90 & 102 & 86 & 119\\\\\n", "\tENSG00000002822 & 411 & 303 & 446 & 195 & 445 & 523 & 295 & 300\\\\\n", "\tENSG00000002834 & 6314 & 6364 & 7831 & 5809 & 6677 & 11970 & 5766 & 7825\\\\\n", "\t⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮\\\\\n", "\tLRG\\_70 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_71 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_715 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_717 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_72 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_73 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_74 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_75 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_76 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_77 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_78 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_79 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_8 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_80 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_81 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_83 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_84 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_85 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_86 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_88 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_89 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_90 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_91 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_92 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_93 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_94 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_96 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_97 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_98 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tLRG\\_99 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 64102 × 8 of type int\n", "\n", "| | SRR1039508 | SRR1039509 | SRR1039512 | SRR1039513 | SRR1039516 | SRR1039517 | SRR1039520 | SRR1039521 |\n", "|---|---|---|---|---|---|---|---|---|\n", "| ENSG00000000003 | 679 | 448 | 873 | 408 | 1138 | 1047 | 770 | 572 |\n", "| ENSG00000000005 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000000419 | 467 | 515 | 621 | 365 | 587 | 799 | 417 | 508 |\n", "| ENSG00000000457 | 260 | 211 | 263 | 164 | 245 | 331 | 233 | 229 |\n", "| ENSG00000000460 | 60 | 55 | 40 | 35 | 78 | 63 | 76 | 60 |\n", "| ENSG00000000938 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 0 |\n", "| ENSG00000000971 | 3251 | 3679 | 6177 | 4252 | 6721 | 11027 | 5176 | 7995 |\n", "| ENSG00000001036 | 1433 | 1062 | 1733 | 881 | 1424 | 1439 | 1359 | 1109 |\n", "| ENSG00000001084 | 519 | 380 | 595 | 493 | 820 | 714 | 696 | 704 |\n", "| ENSG00000001167 | 394 | 236 | 464 | 175 | 658 | 584 | 360 | 269 |\n", "| ENSG00000001460 | 172 | 168 | 264 | 118 | 241 | 210 | 155 | 177 |\n", "| ENSG00000001461 | 2112 | 1867 | 5137 | 2657 | 2735 | 2751 | 2467 | 2905 |\n", "| ENSG00000001497 | 524 | 488 | 638 | 357 | 676 | 806 | 493 | 475 |\n", "| ENSG00000001561 | 71 | 51 | 211 | 156 | 23 | 38 | 134 | 172 |\n", "| ENSG00000001617 | 555 | 394 | 905 | 415 | 727 | 697 | 618 | 599 |\n", "| ENSG00000001626 | 10 | 2 | 9 | 2 | 10 | 6 | 5 | 5 |\n", "| ENSG00000001629 | 1660 | 1251 | 2259 | 1079 | 2462 | 2514 | 1888 | 1660 |\n", "| ENSG00000001630 | 59 | 54 | 66 | 23 | 84 | 87 | 31 | 59 |\n", "| ENSG00000001631 | 729 | 692 | 943 | 475 | 1034 | 1163 | 731 | 744 |\n", "| ENSG00000002016 | 201 | 161 | 256 | 99 | 268 | 257 | 160 | 137 |\n", "| ENSG00000002079 | 3 | 0 | 3 | 1 | 4 | 0 | 0 | 1 |\n", "| ENSG00000002330 | 206 | 174 | 184 | 111 | 194 | 260 | 156 | 177 |\n", "| ENSG00000002549 | 1459 | 1294 | 1317 | 998 | 1451 | 1824 | 853 | 1031 |\n", "| ENSG00000002586 | 7507 | 7203 | 9501 | 6214 | 10973 | 12863 | 6834 | 7225 |\n", "| ENSG00000002587 | 2 | 0 | 1 | 0 | 0 | 2 | 0 | 0 |\n", "| ENSG00000002726 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000002745 | 4 | 6 | 22 | 10 | 2 | 1 | 5 | 3 |\n", "| ENSG00000002746 | 151 | 139 | 117 | 65 | 90 | 102 | 86 | 119 |\n", "| ENSG00000002822 | 411 | 303 | 446 | 195 | 445 | 523 | 295 | 300 |\n", "| ENSG00000002834 | 6314 | 6364 | 7831 | 5809 | 6677 | 11970 | 5766 | 7825 |\n", "| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |\n", "| LRG_70 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_71 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_715 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_717 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_72 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_73 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_74 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_75 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_76 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_77 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_78 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_79 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_80 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_81 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_83 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_84 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_85 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_86 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_88 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_89 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_90 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_91 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_92 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_93 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_94 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_96 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_97 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_98 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| LRG_99 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "\n" ], "text/plain": [ " SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516\n", "ENSG00000000003 679 448 873 408 1138 \n", "ENSG00000000005 0 0 0 0 0 \n", "ENSG00000000419 467 515 621 365 587 \n", "ENSG00000000457 260 211 263 164 245 \n", "ENSG00000000460 60 55 40 35 78 \n", "ENSG00000000938 0 0 2 0 1 \n", "ENSG00000000971 3251 3679 6177 4252 6721 \n", "ENSG00000001036 1433 1062 1733 881 1424 \n", "ENSG00000001084 519 380 595 493 820 \n", "ENSG00000001167 394 236 464 175 658 \n", "ENSG00000001460 172 168 264 118 241 \n", "ENSG00000001461 2112 1867 5137 2657 2735 \n", "ENSG00000001497 524 488 638 357 676 \n", "ENSG00000001561 71 51 211 156 23 \n", "ENSG00000001617 555 394 905 415 727 \n", "ENSG00000001626 10 2 9 2 10 \n", "ENSG00000001629 1660 1251 2259 1079 2462 \n", "ENSG00000001630 59 54 66 23 84 \n", "ENSG00000001631 729 692 943 475 1034 \n", "ENSG00000002016 201 161 256 99 268 \n", "ENSG00000002079 3 0 3 1 4 \n", "ENSG00000002330 206 174 184 111 194 \n", "ENSG00000002549 1459 1294 1317 998 1451 \n", "ENSG00000002586 7507 7203 9501 6214 10973 \n", "ENSG00000002587 2 0 1 0 0 \n", "ENSG00000002726 0 0 1 0 0 \n", "ENSG00000002745 4 6 22 10 2 \n", "ENSG00000002746 151 139 117 65 90 \n", "ENSG00000002822 411 303 446 195 445 \n", "ENSG00000002834 6314 6364 7831 5809 6677 \n", "⋮ ⋮ ⋮ ⋮ ⋮ ⋮ \n", "LRG_70 0 0 0 0 0 \n", "LRG_71 0 0 0 0 0 \n", "LRG_715 0 0 0 0 0 \n", "LRG_717 0 0 0 0 0 \n", "LRG_72 0 0 0 0 0 \n", "LRG_73 0 0 0 0 0 \n", "LRG_74 0 0 0 0 0 \n", "LRG_75 0 0 0 0 0 \n", "LRG_76 0 0 0 0 0 \n", "LRG_77 0 0 0 0 0 \n", "LRG_78 0 0 0 0 0 \n", "LRG_79 0 0 0 0 0 \n", "LRG_8 0 0 0 0 0 \n", "LRG_80 0 0 0 0 0 \n", "LRG_81 0 0 0 0 0 \n", "LRG_83 0 0 0 0 0 \n", "LRG_84 0 0 0 0 0 \n", "LRG_85 0 0 0 0 0 \n", "LRG_86 0 0 0 0 0 \n", "LRG_88 0 0 0 0 0 \n", "LRG_89 0 0 0 0 0 \n", "LRG_90 0 0 0 0 0 \n", "LRG_91 0 0 0 0 0 \n", "LRG_92 0 0 0 0 0 \n", "LRG_93 0 0 0 0 0 \n", "LRG_94 0 0 0 0 0 \n", "LRG_96 0 0 0 0 0 \n", "LRG_97 0 0 0 0 0 \n", "LRG_98 0 0 0 0 0 \n", "LRG_99 0 0 0 0 0 \n", " SRR1039517 SRR1039520 SRR1039521\n", "ENSG00000000003 1047 770 572 \n", "ENSG00000000005 0 0 0 \n", "ENSG00000000419 799 417 508 \n", "ENSG00000000457 331 233 229 \n", "ENSG00000000460 63 76 60 \n", "ENSG00000000938 0 0 0 \n", "ENSG00000000971 11027 5176 7995 \n", "ENSG00000001036 1439 1359 1109 \n", "ENSG00000001084 714 696 704 \n", "ENSG00000001167 584 360 269 \n", "ENSG00000001460 210 155 177 \n", "ENSG00000001461 2751 2467 2905 \n", "ENSG00000001497 806 493 475 \n", "ENSG00000001561 38 134 172 \n", "ENSG00000001617 697 618 599 \n", "ENSG00000001626 6 5 5 \n", "ENSG00000001629 2514 1888 1660 \n", "ENSG00000001630 87 31 59 \n", "ENSG00000001631 1163 731 744 \n", "ENSG00000002016 257 160 137 \n", "ENSG00000002079 0 0 1 \n", "ENSG00000002330 260 156 177 \n", "ENSG00000002549 1824 853 1031 \n", "ENSG00000002586 12863 6834 7225 \n", "ENSG00000002587 2 0 0 \n", "ENSG00000002726 0 0 0 \n", "ENSG00000002745 1 5 3 \n", "ENSG00000002746 102 86 119 \n", "ENSG00000002822 523 295 300 \n", "ENSG00000002834 11970 5766 7825 \n", "⋮ ⋮ ⋮ ⋮ \n", "LRG_70 0 0 0 \n", "LRG_71 0 0 0 \n", "LRG_715 0 0 0 \n", "LRG_717 0 0 0 \n", "LRG_72 0 0 0 \n", "LRG_73 0 0 0 \n", "LRG_74 0 0 0 \n", "LRG_75 0 0 0 \n", "LRG_76 0 0 0 \n", "LRG_77 0 0 0 \n", "LRG_78 0 0 0 \n", "LRG_79 0 0 0 \n", "LRG_8 0 0 0 \n", "LRG_80 0 0 0 \n", "LRG_81 0 0 0 \n", "LRG_83 0 0 0 \n", "LRG_84 0 0 0 \n", "LRG_85 0 0 0 \n", "LRG_86 0 0 0 \n", "LRG_88 0 0 0 \n", "LRG_89 0 0 0 \n", "LRG_90 0 0 0 \n", "LRG_91 0 0 0 \n", "LRG_92 0 0 0 \n", "LRG_93 0 0 0 \n", "LRG_94 0 0 0 \n", "LRG_96 0 0 0 \n", "LRG_97 0 0 0 \n", "LRG_98 0 0 0 \n", "LRG_99 0 0 0 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "assays(se)$counts" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "GRangesList object of length 64102:\n", "$ENSG00000000003 \n", "GRanges object with 17 ranges and 2 metadata columns:\n", " seqnames ranges strand | exon_id exon_name\n", " | \n", " [1] X 99883667-99884983 - | 667145 ENSE00001459322\n", " [2] X 99885756-99885863 - | 667146 ENSE00000868868\n", " [3] X 99887482-99887565 - | 667147 ENSE00000401072\n", " [4] X 99887538-99887565 - | 667148 ENSE00001849132\n", " [5] X 99888402-99888536 - | 667149 ENSE00003554016\n", " ... ... ... ... . ... ...\n", " [13] X 99890555-99890743 - | 667156 ENSE00003512331\n", " [14] X 99891188-99891686 - | 667158 ENSE00001886883\n", " [15] X 99891605-99891803 - | 667159 ENSE00001855382\n", " [16] X 99891790-99892101 - | 667160 ENSE00001863395\n", " [17] X 99894942-99894988 - | 667161 ENSE00001828996\n", "\n", "...\n", "<64101 more elements>\n", "-------\n", "seqinfo: 722 sequences (1 circular) from an unspecified genome" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "rowRanges(se)" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "DataFrame with 8 rows and 9 columns\n", " SampleName cell dex albut Run avgLength\n", " \n", "SRR1039508 GSM1275862 N61311 untrt untrt SRR1039508 126\n", "SRR1039509 GSM1275863 N61311 trt untrt SRR1039509 126\n", "SRR1039512 GSM1275866 N052611 untrt untrt SRR1039512 126\n", "SRR1039513 GSM1275867 N052611 trt untrt SRR1039513 87\n", "SRR1039516 GSM1275870 N080611 untrt untrt SRR1039516 120\n", "SRR1039517 GSM1275871 N080611 trt untrt SRR1039517 126\n", "SRR1039520 GSM1275874 N061011 untrt untrt SRR1039520 101\n", "SRR1039521 GSM1275875 N061011 trt untrt SRR1039521 98\n", " Experiment Sample BioSample\n", " \n", "SRR1039508 SRX384345 SRS508568 SAMN02422669\n", "SRR1039509 SRX384346 SRS508567 SAMN02422675\n", "SRR1039512 SRX384349 SRS508571 SAMN02422678\n", "SRR1039513 SRX384350 SRS508572 SAMN02422670\n", "SRR1039516 SRX384353 SRS508575 SAMN02422682\n", "SRR1039517 SRX384354 SRS508576 SAMN02422673\n", "SRR1039520 SRX384357 SRS508579 SAMN02422683\n", "SRR1039521 SRX384358 SRS508580 SAMN02422677" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "colData(se)" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[[1]]\n", "Experiment data\n", " Experimenter name: Himes BE \n", " Laboratory: NA \n", " Contact information: \n", " Title: RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. \n", " URL: http://www.ncbi.nlm.nih.gov/pubmed/24926665 \n", " PMIDs: 24926665 \n", "\n", " Abstract: A 226 word abstract is available. Use 'abstract' method.\n" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "metadata(se)" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[[1]]\n", "Experiment data\n", " Experimenter name: Himes BE \n", " Laboratory: NA \n", " Contact information: \n", " Title: RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. \n", " URL: http://www.ncbi.nlm.nih.gov/pubmed/24926665 \n", " PMIDs: 24926665 \n", "\n", " Abstract: A 226 word abstract is available. Use 'abstract' method.\n", "\n", "$formula\n", "counts ~ dex + albut\n" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Just a list - we can add elements\n", "\n", "metadata(se)$formula <- counts ~ dex + albut\n", "\n", "metadata(se)" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "class: RangedSummarizedExperiment \n", "dim: 5 3 \n", "metadata(2): '' formula\n", "assays(1): counts\n", "rownames(5): ENSG00000000003 ENSG00000000005 ENSG00000000419\n", " ENSG00000000457 ENSG00000000460\n", "rowData names(0):\n", "colnames(3): SRR1039508 SRR1039509 SRR1039512\n", "colData names(9): SampleName cell ... Sample BioSample" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# subset the first five transcripts and first three samples\n", "se[1:5, 1:3]" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 5 × 3 of type int
SRR1039508SRR1039509SRR1039512
ENSG00000000003679448873
ENSG00000000005 0 0 0
ENSG00000000419467515621
ENSG00000000457260211263
ENSG00000000460 60 55 40
\n" ], "text/latex": [ "A matrix: 5 × 3 of type int\n", "\\begin{tabular}{r|lll}\n", " & SRR1039508 & SRR1039509 & SRR1039512\\\\\n", "\\hline\n", "\tENSG00000000003 & 679 & 448 & 873\\\\\n", "\tENSG00000000005 & 0 & 0 & 0\\\\\n", "\tENSG00000000419 & 467 & 515 & 621\\\\\n", "\tENSG00000000457 & 260 & 211 & 263\\\\\n", "\tENSG00000000460 & 60 & 55 & 40\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 5 × 3 of type int\n", "\n", "| | SRR1039508 | SRR1039509 | SRR1039512 |\n", "|---|---|---|---|\n", "| ENSG00000000003 | 679 | 448 | 873 |\n", "| ENSG00000000005 | 0 | 0 | 0 |\n", "| ENSG00000000419 | 467 | 515 | 621 |\n", "| ENSG00000000457 | 260 | 211 | 263 |\n", "| ENSG00000000460 | 60 | 55 | 40 |\n", "\n" ], "text/plain": [ " SRR1039508 SRR1039509 SRR1039512\n", "ENSG00000000003 679 448 873 \n", "ENSG00000000005 0 0 0 \n", "ENSG00000000419 467 515 621 \n", "ENSG00000000457 260 211 263 \n", "ENSG00000000460 60 55 40 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "assays(se[1:5,1:3])$counts\n" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Registered S3 methods overwritten by 'ggplot2':\n", " method from \n", " [.quosures rlang\n", " c.quosures rlang\n", " print.quosures rlang\n" ] }, { "data": { "text/plain": [ "class: DESeqDataSet \n", "dim: 64102 8 \n", "metadata(3): '' formula version\n", "assays(1): counts\n", "rownames(64102): ENSG00000000003 ENSG00000000005 ... LRG_98 LRG_99\n", "rowData names(0):\n", "colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521\n", "colData names(9): SampleName cell ... Sample BioSample" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "library(\"DESeq2\")\n", "\n", "\n", "dds <- DESeqDataSet(se, design = ~ cell + dex)\n", "dds\n", "\n" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "# remove rows with less than 10 total transcripts\n", "\n", "keep <- rowSums(counts(dds)) >= 10\n", "dds <- dds[keep,]" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "DataFrame with 8 rows and 9 columns\n", " SampleName cell dex albut Run avgLength\n", " \n", "SRR1039508 GSM1275862 N61311 untrt untrt SRR1039508 126\n", "SRR1039509 GSM1275863 N61311 trt untrt SRR1039509 126\n", "SRR1039512 GSM1275866 N052611 untrt untrt SRR1039512 126\n", "SRR1039513 GSM1275867 N052611 trt untrt SRR1039513 87\n", "SRR1039516 GSM1275870 N080611 untrt untrt SRR1039516 120\n", "SRR1039517 GSM1275871 N080611 trt untrt SRR1039517 126\n", "SRR1039520 GSM1275874 N061011 untrt untrt SRR1039520 101\n", "SRR1039521 GSM1275875 N061011 trt untrt SRR1039521 98\n", " Experiment Sample BioSample\n", " \n", "SRR1039508 SRX384345 SRS508568 SAMN02422669\n", "SRR1039509 SRX384346 SRS508567 SAMN02422675\n", "SRR1039512 SRX384349 SRS508571 SAMN02422678\n", "SRR1039513 SRX384350 SRS508572 SAMN02422670\n", "SRR1039516 SRX384353 SRS508575 SAMN02422682\n", "SRR1039517 SRX384354 SRS508576 SAMN02422673\n", "SRR1039520 SRX384357 SRS508579 SAMN02422683\n", "SRR1039521 SRX384358 SRS508580 SAMN02422677" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "colData(dds)" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [], "source": [ "# Specify reference level\n", "\n", "dds$dex <- factor(dds$dex, levels = c(\"untrt\",\"trt\"))\n", "\n", "#alternative\n", "dds$dex <- relevel(dds$dex, ref = \"untrt\")\n" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "estimating size factors\n", "estimating dispersions\n", "gene-wise dispersion estimates\n", "mean-dispersion relationship\n", "final dispersion estimates\n", "fitting model and testing\n" ] }, { "data": { "text/plain": [ "log2 fold change (MLE): dex trt vs untrt \n", "Wald test p-value: dex trt vs untrt \n", "DataFrame with 22369 rows and 6 columns\n", " baseMean log2FoldChange lfcSE\n", " \n", "ENSG00000000003 708.597861536998 -0.381227063105246 0.100702281802452\n", "ENSG00000000419 520.296296925274 0.206840376248021 0.112107724670949\n", "ENSG00000000457 237.162103834464 0.037954335389843 0.142823085130162\n", "ENSG00000000460 57.9323803212894 -0.0885309218770955 0.284934403160848\n", "ENSG00000000971 5817.31081674539 0.42642455731918 0.0888056149171329\n", "... ... ... ...\n", "ENSG00000273483 2.68955174874763 0.84920766214805 1.25336471679961\n", "ENSG00000273485 1.28646279725438 -0.123613168835481 1.58825060361379\n", "ENSG00000273486 15.4524429107135 -0.150428542992948 0.482097671940096\n", "ENSG00000273487 8.16326862804303 1.04563935414612 0.693057045984001\n", "ENSG00000273488 8.58437098976254 0.108945615633239 0.632299687532417\n", " stat pvalue padj\n", " \n", "ENSG00000000003 -3.78568445800561 0.000153286080966785 0.0012892045764893\n", "ENSG00000000419 1.84501448811957 0.065035431092294 0.194929521562025\n", "ENSG00000000457 0.265743702114076 0.790436603689371 0.909899502487793\n", "ENSG00000000460 -0.310706327123015 0.756023886827025 0.89299357560032\n", "ENSG00000000971 4.80177472693691 1.57265558148175e-06 2.06391014885582e-05\n", "... ... ... ...\n", "ENSG00000273483 0.677542339245393 0.498061916323377 NA\n", "ENSG00000273485 -0.0778297634858257 0.937963470414454 NA\n", "ENSG00000273486 -0.312029183604188 0.755018344483373 0.892519390830221\n", "ENSG00000273487 1.50873490170137 0.131366542567104 0.323297597320869\n", "ENSG00000273488 0.172300600144854 0.863201212561737 0.943414817499248" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "ddsDE <- DESeq(dds)\n", "res <- results(ddsDE)\n", "res" ] } ], "metadata": { "kernelspec": { "display_name": "R", "language": "R", "name": "ir" }, "language_info": { "codemirror_mode": "r", "file_extension": ".r", "mimetype": "text/x-r-source", "name": "R", "pygments_lexer": "r", "version": "3.6.0" } }, "nbformat": 4, "nbformat_minor": 1 }