.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# Example code in package build process
*-Ex.R

# 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

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
/*_cache/
/cache/

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

# .RDS and .Rdata files of all recount samples
recount2/data
recount2/recount_experiments_rse-gene.tar.gz
recount2/recount_rpkm.RDS
recount2/recount_data_prep_PLIER.RDS
recount2/recount_PLIER_model.RDS

# Ignore hidden metadata files
._*

Rplots\.pdf

## Files related to RNA-seq processing

# ignore raw data
rituximab/fastq/

# transcripts fasta
rituximab/hsapiens.fa.gz

# transcriptome index itself
rituximab/transcriptome_index

# the output of salmon quant
rituximab/quants/

# H sapiens GTF & ensembldb derivative
rituximab/Homo_sapiens.GRCh38.92.gtf
rituximab/Homo_sapiens.GRCh38.92.sqlite

# rituximab files
rituximab/sample_list.txt
rituximab/tximport.RDS
rituximab/select_covariates.tsv
rituximab/VST_design.pcl
rituximab/VST_blind.pcl

# glomeruli clinical data before cleaning
glomeruli/Neptune_ERCB_GE_Clinical_Data_2016-08-24_15-11-58-1.txt