.gitignore

# History files
.Rhistory
.Rapp.history
.Rprofile

# 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/
*.Rproj

# 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

# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
rsconnect/

# other extensions
.png
.rds
.csv
.tsv
.html
.pdf
*_misc.Rmd
*.html

# other directories and files
packrat/
output/
src/ebits/
src/run_bedtools.sh
analyses/dorothea_benchmark/tfbs_analysis.Rmd
*processed/
*raw/
*yaml/
*mmus_exp_from_bence/
*bences_benchmark_exps.rds
*progeny_benchmark_data.rds
*progeny_training_accession.rds
*disease_expr.rds
*Remap2_adnp_nrPeaks.bed.closest
*tss_merged.gencode.v26.annotation.bed
*all_tfbs.bed
*dorothea_benchmark_data.rds

packrat/lib*/
packrat/src/
.Rproj.user