├── .gitignore ├── README.md ├── README_Admin.md ├── Resources ├── RStudio_cheat_sheet.pdf ├── R_cheat_sheet.pdf ├── data-wrangling-cheatsheet.pdf ├── dplyr_cheat_sheet.pdf ├── ggplot2_cheat_sheet.pdf └── readr_and_tidyr_cheat_sheet.pdf ├── Syllabus.docx ├── week_eight ├── week_eight.R └── week_eight.Rproj ├── week_eleven ├── RNA-Seq_alignment.pptx ├── Salmon.out │ ├── SRR1039508 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ ├── SRR1039509 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ ├── SRR1039512 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ ├── SRR1039513 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ ├── SRR1039516 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ ├── SRR1039517 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ ├── SRR1039520 │ │ ├── aux_info │ │ │ ├── ambig_info.tsv │ │ │ ├── expected_bias.gz │ │ │ ├── fld.gz │ │ │ ├── meta_info.json │ │ │ ├── observed_bias.gz │ │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ │ └── salmon_quant.log │ │ └── quant.sf │ └── SRR1039521 │ │ ├── aux_info │ │ ├── ambig_info.tsv │ │ ├── expected_bias.gz │ │ ├── fld.gz │ │ ├── meta_info.json │ │ ├── observed_bias.gz │ │ └── observed_bias_3p.gz │ │ ├── cmd_info.json │ │ ├── libParams │ │ └── flenDist.txt │ │ ├── lib_format_counts.json │ │ ├── logs │ │ └── salmon_quant.log │ │ └── quant.sf ├── import_and_analyze.R ├── pipeline.sh └── week_eleven.Rproj ├── week_five ├── 06202020.txt ├── week_five_lecture.Rproj ├── week_five_lecture.pptx └── week_five_notes.R ├── week_four ├── week_four.Rproj ├── week_four_lecture.pptx ├── week_four_lecture_code.Rmd ├── week_four_notes.R ├── week_four_practice_problems.R └── week_four_practice_problems_solutions.R ├── week_nine ├── GSE101770_GeneLevel_Raw_data.csv ├── GSE122632_RAW.tar ├── GSE132762_RAW.tar ├── clinical.cart.2020-10-27 (1).tar.gz ├── gdc_download_20201027_201844.644029.tar.gz ├── gdc_sample_sheet.2020-10-27 (1).tsv ├── week_nine.R └── week_nine.Rproj ├── week_one ├── lecture_week_one.pptx └── week_one_lecture.Rmd ├── week_seven ├── ERP010786.rda ├── dr_bunnik_nice_ggplots_script.R ├── week_seven.Rproj └── week_seven_code.R ├── week_six ├── week_six.Rproj ├── week_six_lecture.Rmd ├── week_six_lecture_code.R ├── week_six_lecture_notes.pdf ├── week_six_lecture_slides.pptx └── week_six_practice_problems.R ├── week_ten ├── Log into the VMs (Windows).pptx ├── Uthscsa-Bioinfo-BootCam-Linux-[3].pptx ├── Uthscsa-Bioinformatics-BootCamp-Linux-commands[2].docx └── gwas-sumstat.txt ├── week_three ├── week_three.Rproj └── weeks_1_and_2_review.R ├── week_twelve ├── 130503.UNC9-SN296.0362.BC23UKACXX.CGATGT.L001.withRG.GATKRecalibrated.flagged.mini.bam ├── 130503.UNC9-SN296.0362.BC23UKACXX.CGATGT.L001.withRG.GATKRecalibrated.flagged.mini.bam.bai ├── Presentation 2020 Nov 17 Zheng.pptx ├── ddab9888-1618-4eed-81da-452c421443fb.withRG.GATKRecalibrated.flagged.mini.bam ├── ddab9888-1618-4eed-81da-452c421443fb.withRG.GATKRecalibrated.flagged.mini.bam.bai └── download.sh └── week_two ├── gene_id_to_symbol.csv ├── lecture_week_two.pptx ├── week_two.Rproj ├── week_two_practice_problems.R └── week_two_practice_problems_solutions.R /.gitignore: -------------------------------------------------------------------------------- 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