.gitignore

# Pipeline data
proteomics/data


# 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

# macOS
.DS_Store

# misc files
Misc/

# plots
mutational_analysis/plots/

# NMF raw data
cohort_summary/NMF/Data/
Analysis/NMF/Data/
util/differential_expression_helper_dev.R
cohort_summary/cytogenetics_and_clusters.Rmd
cohort_summary/data_sample_summary_circos.png

# NMF prediction signature analysis
cohort_summary/NMF/individual_models_elastic_net/enet_binomial_data
cohort_summary/NMF/multinomial_models_elastic_net/enet_multinomial_data
cohort_summary/NMF/multinomial_models_k_4_elastic_net/enet_multinomial_data


# Validation folder
Validations

# mutational analysis
mutational_analysis/raw_tables

# networks
mutational_analysis/network_analysis/networks

# PeCorA
mutational_analysis/PeCorA/pecora_presentation
mutational_analysis/PeCorA/pecora_scripts/pecora_example.R
cohort_summary/data_sample_summary_circos.pdf
cohort_summary/NMF/multinomial_models_elastic_net/k_5_alpha_notes.txt
cohort_summary/NMF/multinomial_models_k_4_elastic_net/k_4_alpha_notes.txt
cohort_summary/NMF/NMF_differential_markers_enrichment.Rmd
cohort_summary/NMF/peptide_subtype_interaction/Data/


# Drug story
Drug Story/
cohort_summary/NMF/multinomial_models_k_4_elastic_net/cell_line_data_notes.txt
5-31 next.txt
cohort_summary/NMF/peptide_subtype_interaction/Protein peptide deviation Vlad.pptx
cohort_summary/NMF/peptide_subtype_interaction/Protein Peptide Deviation PTRC tuesday.pptx
cohort_summary/supplemental_table_1.txt