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# RStudio / R session files
.Rproj.user/
.Rhistory
.Rapp.history
.RData
.RDataTmp
.Ruserdata
.Renviron
# Example code in package build process
*-Ex.R
# Output files from R CMD build / check
/*.tar.gz
/*.Rcheck/
# intermediary files
intermediary_files/
# produced vignettes
vignettes/*.html
vignettes/*.pdf
# local job scripts (personal/one-off, not part of the pipeline)
LocalJob_File_*
# 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
# translation temp files
po/*~
# RStudio Connect folder
rsconnect/
# OS files
.DS_Store
# Python bytecode cache
__pycache__/
*.pyc
# Personal maintenance scripts / audit notes, not part of the pipeline
cleanup_unused_data.sh
optimize_data.R
STORAGE_AUDIT.md
# Big data - too large for git, kept locally and distributed via Zenodo
# (see README.md "Large data files" section for download links)
data/
data.zip
eCLIPSE/all_data_combined_38.txt
eCLIPSE/BigExon_events.txt
eCLIPSE/Exon_events_Rmats.txt
eCLIPSE/Intron_events.txt