.gitignore

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# Generic .gitignore #
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# OS generated files #
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*.DS_Store

# R generated files #
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*.Rhistory

# Output files from R CMD build
/*.tar.gz
# Output files from R CMD check
/*.Rcheck/
# RStudio files
.Rproj.user/
# produced vignettes
vignettes/*.html
vignettes/*.pdf

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# R Environment Variables
.Renviron

# pkgdown testing doc build
/docs

/nogit

# tmp runtime files
*.png
*.html
*.txt
*.pdf

# Big data files #
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#data/Avner.counts.matrix.txt
#data/Avner_Target.txt
#data/*.combineExprData*
#data/ref_cohorts_all*
#data/Datasets_list_digestive_system_group.txt
#data/Datasets_list_gastrointestinal_group.txt
#data/Datasets_list_hematologic_lymphatic_lung_group.txt
#data/Datasets_list_neuroendocrine_glioma_group.txt
#data/Datasets_list_breast_head_and_neck_group.txt
#data/ref_data/UMCCR_samples_*.xlsx
#data/ref_data/~$UMCCR_samples_*.xlsx
#data/ref_data/UMCCR_samples_*.csv
#img/*.pptx
#processing/.gitignore
#processing/*.html
#data/clinker/*
#data/pizzly/*
#data/kallisto/*
#data/test_data/final/test_sample_WTS/RNAsum/*
#data/test_data/stratus/test_sample_WTS*/RNAsum/*
#data/test_data/final/test_sample_WTS/clinker/*.png
#data/2018-02-16_PMCC_Panel_Regions.bed
#data/2018-02-16_PMCC_Panel_Genes.txt
#data/2018-02-16_PMCC_Panel_Genes.xls
#merged_sample_quality_annotations.tsv
#merged_sample_quality_annotations_RNAseq.xlsx
#mmc3.xlsx
#mmc4.xlsx
#Notes.txt
#TCGA-CDR-SupplementalTableS1.xlsx
#TCGA_samples_to_combine.xlsx
#UMCCR Samples_Avner_for_RNAseq_test.xlsx
#docs/RNA-seq_single_sample_analyses.txt
#RNA-seq_report_installation*.txt
#RNA-seq_report_generation_workflow*.txt

# Google drive files #
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#output/*