.. HTS2019 documentation master file, created by sphinx-quickstart on Fri Jun 21 16:20:47 2019. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. HTS2019 Source Materials =================================== Source materials can be cloned from the `HTS2019 GitLab Repository `_ The working environment can be built using the dockerfile from Dockerhub: `/dukehtscourse/jupyter-hts-2019 `_ .. toctree:: :maxdepth: 2 :caption: Slides slides.rst .. toctree:: :maxdepth: 2 :caption: Quick Intro of Analysis Tools janice/1_IntroToCompBoot.ipynb janice/2_Intro_to_Unix_and_bash.ipynb janice/3_IntroductionToR.ipynb janice/4_Rlibraries_and_bioconductor.ipynb janice/5_Tidyverse_HandsOn-Filled.ipynb janice/6_Statistical_Inference.ipynb janice/7_Statistical_Inference_Solutions.ipynb .. toctree:: :maxdepth: 2 :caption: Unix Shell cliburn/Unix01_File_And_Directory_Solutions.ipynb cliburn/Unix02_FileIO_Solutions.ipynb cliburn/Unix03_File_Storage_Solutions.ipynb cliburn/Unix04_Text_Manipulation_Solutinos.ipynb cliburn/Unix05_Variables_Solutions.ipynb cliburn/Unix06_Bash_Bioinformatics.ipynb cliburn/Unix07_Capstone_Exercise.ipynb cliburn/Unix07_Capstone_Exercise_Solutions.ipynb cliburn/Unix_Appendix01_Regular_Expressions.ipynb cliburn/Unix_Appendix02_Review.ipynb .. toctree:: :maxdepth: 2 :caption: R Graphics and Data Manipulation cliburn/R00_Review_Basics.ipynb cliburn/R00_Review_Basics.ipynb cliburn/R01_Data_Manipulation_Solutions.ipynb cliburn/R02_Tidying_Data_Solutions.ipynb cliburn/R03_FileIO.ipynb cliburn/R04_Unsupervised_Learning.ipynb cliburn/R05_Unsupervised_Learning_More_Examples.ipynb cliburn/R06_Graphics_Overview.ipynb cliburn/R07_Graphics_Base.ipynb cliburn/R08_Graphics_ggplot2.ipynb cliburn/R09_Graphics_Exercise.ipynb cliburn/R09_Graphics_Exercise_Solutions.ipynb .. toctree:: :maxdepth: 2 :caption: Bioinformatics (FASTQ, FASTQC, STAR, etc) bioinformatics/fastq_intro.ipynb bioinformatics/quality_scores.ipynb bioinformatics/fastqc.ipynb bioinformatics/fastq_trimming.ipynb bioinformatics/genome_prep.ipynb bioinformatics/counting.ipynb bioinformatics/mapping.ipynb bioinformatics/making_generic_commands.ipynb bioinformatics/making_a_pipeline.ipynb bioinformatics/loop_pipeline.ipynb bioinformatics/multifastq_loop_pipeline.ipynb bioinformatics/glob_loop.ipynb bioinformatics/prep_for_full_run.ipynb bioinformatics/igv_visualization.ipynb bioinformatics/igv_shorter_introns.ipynb .. toctree:: :maxdepth: 2 :caption: Analysis of Pilot Data (Gene Count, DESeq2 & DE Analysis) DESeq2/8_Pilot2019_getstarcounts-KO.ipynb DESeq2/00_deseq_prepare_data.ipynb DESeq2/01_deseq_dataobject.ipynb DESeq2/02_deseq_DE.ipynb DESeq2/03_deseq_interaction.ipynb DESeq2/04-deseq2-plots.ipynb .. toctree:: :maxdepth: 2 :caption: Reproducible Analysis (Git) computing/data_handling_demo.ipynb computing/git_lesson.ipynb computing/git_in_class.ipynb .. toctree:: :maxdepth: 2 :caption: After the course... (Docker & Singularity) computing/post_course_resources.ipynb Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`