.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# User-specific files
.Ruserdata

# 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

# R Environment Variables
.Renviron

############################
markdowns
markdowns/*.html
markdowns/*.tsv
markdowns/*.csv
markdowns/*.xlsx
markdowns/*.png
.Rproj.user

renv


##############################
## FOLDERS TO EXCLUDE

results
knockdown_analysis
paper_figures
database

dependencies/ENCORI/*
!dependencies/ENCORI/encori-rbp.sh

natcomms_review
ENCODE_LR
SAI-10k-calc
ENCODE_SR
logs

#############################
## FILES TO EXCLUDE

thesis.R
thesis_corrections.R
splicing_accuracy_manuscript_natcomms_review.R