.gitignore

# Lorenzi et al sup data
1_external/15_lncRNA/Lorenzi_et_al/41587_2021_936_MOESM3_ESM.xlsx

# transcript features inc kmers (too large; run notebook 6 in parent directory)
3_rna/notebooks/1_dlorna/2_lorna/5_relocalisation/out/transcript_features.rds

# bandle res object
2_protein/notebooks/out/bandleres.rds
2_protein/notebooks/out/bandleres_reps.rds

# large xlxs sup table
lorna/shared_files/Lorenzi_et_al/41587_2021_936_MOESM3_ESM.xlsx

# ENCODE files
1_external/1_ENCORE_eCLIP/ENCODE_download/
1_external/4_ENCODE_Cyt_Nuc/ENCFF*tsv
1_external/13_CeFraSeq/ENCODE_download/

# libreoffice lockfile
.~lock.*

# emacs tmpfile
*~

# Very large combined dataset files
3_rna/notebooks/1_dlorna/2_lorna/1_data_processing/out/all_datasets.rds
3_rna/notebooks/1_dlorna/2_lorna/2_clustering/out/all_datasets_with_novel.rds
3_rna/notebooks/1_dlorna/2_lorna/3_proportional_localisation/results/all_datasets_final.rds
3_rna/notebooks/1_dlorna/2_lorna/5_relocalisation/out/proportions_annot.rds

# 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