.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/
*.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

# R Environment Variables
.Renviron

# data
data/*

# temporary material
temp/*

# output
*/*.results
*/*.png
*/*.html
*/*.log
*/*.ped
*/*.map
*/*.kinship
*/*.bim
*/*.bed
*/*.fam
*/*.vcf
*/*.gz
*/*.tped
*/*.tfam

*/*.hwe
*/*.frq
*/*.lmiss
*/*.imiss
*/*.log
*/*.frqx
*/*.het
*/*.nosex
*/*.strat
*/*.cc
*/*.irem
*/*.csv
*/*.counts
*/*.svg

# java files
*/*.jar

.Rproj.user

# snakefiles (temporary)
*/snakefile*
*/Snakefile*
*/.snakemake/*
*/.snakemake/metadata/*

# model extensions
model_extensions/gemma/rice/*
model_extensions/multi_trait/rice/*