Files in oriolarques/GEGVIC
A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.
.Rbuildignore
.gitignore
DESCRIPTION
GEGVIC.Rproj
LICENSE
NAMESPACE
R/auto_rep.R
R/ge_annot.R
R/ge_data_preprocess.R
R/ge_diff_exp.R
R/ge_gsea.R
R/ge_pca.R
R/ge_single.R
R/ge_volcano.R
R/gv_extr_mut_sig.R
R/gv_mut_load.R
R/gv_mut_signatures.R
R/gv_mut_summary.R
R/ic_deconv.R
R/ic_plot_comp_celltypes.R
R/ic_plot_comp_samples.R
R/ic_raw_to_tpm.R
R/ic_score.R
R/module_ge.R
R/module_gv.R
R/module_ic.R
R/sysdata.rda
README.Rmd
README.md
data/COSMIC_v2_SBS_GRCh37.rda
data/COSMIC_v2_SBS_GRCh38.rda
data/COSMIC_v2_SBS_mm10.rda
data/COSMIC_v2_SBS_mm9.rda
data/COSMIC_v3.2_DBS_GRCh37.rda
data/COSMIC_v3.2_DBS_GRCh38.rda
data/COSMIC_v3.2_DBS_mm10.rda
data/COSMIC_v3.2_DBS_mm9.rda
data/COSMIC_v3.2_SBS_GRCh37.rda
data/COSMIC_v3.2_SBS_GRCh38.rda
data/COSMIC_v3.2_SBS_mm10.rda
data/COSMIC_v3.2_SBS_mm9.rda
data/IPS_genes.rda
data/c2.cp.reactome.v7.5.1.symbols.gmt.rda
data/c7.all.v7.2.symbols.gmt.rda
data/ensembl_biomart_GRCh37.rda
data/ensembl_biomart_GRCh38_p13.rda
data/ensembl_biomart_GRCm38_p6.rda
data/ensembl_biomart_GRCm39.rda
data/gmt_diverse_v72_symbol.rda
data/hallmark.gmt.rda
data/ic_grouping.rda
data/input_ge_module.rda
data/input_gv_module.rda
data/metadata_ge_module.rda
data/sample_counts.rda
data/sample_metadata.rda
data/sample_mutations.rda
inst/extdata/GEGVIC_auto_flexreport.Rmd
inst/extdata/GEGVIC_auto_report.Rmd
inst/extdata/c2.cp.reactome.v7.5.1.symbols.gmt
inst/extdata/sample_counts.csv
inst/extdata/sample_metadata.csv
inst/extdata/sample_mutations.csv
man/auto_rep.Rd
man/ge_annot.Rd
man/ge_diff_exp.Rd
man/ge_gsea.Rd
man/ge_pca.Rd
man/ge_single.Rd
man/ge_volcano.Rd
man/gv_extr_mut_sig.Rd
man/gv_mut_load.Rd
man/gv_mut_signatures.Rd
man/gv_mut_summary.Rd
man/ic_deconv.Rd
man/ic_plot_comp_celltypes.Rd
man/ic_plot_comp_samples.Rd
man/ic_raw_to_tpm.Rd
man/ic_score.Rd
man/module_ge.Rd
man/module_gv.Rd
man/module_ic.Rd
man/preprocess_ge_counts.Rd
man/preprocess_ge_meta.Rd
rmarkdown/.DS_Store
rmarkdown/.gitignore
rmarkdown/GEGVIC-NGS.Rmd
vignettes/.gitignore
vignettes/01_pca.png
vignettes/02_volcano.png
vignettes/03_bubble_plot.png
vignettes/03_gsea_clust.png
vignettes/03_gsea_leading_edge.png
vignettes/03_gsea_wordclouds.png
vignettes/03_gsva.png
vignettes/04_gv_oncoplot.png
vignettes/04_gv_summary.png
vignettes/05_gv_mutload.png
vignettes/06_gv_heatmap.png
vignettes/06_gv_mutsig.png
vignettes/07_ic_samples.png
vignettes/07_ic_types.png
vignettes/08_ic_ipg.png
vignettes/08_ic_ips.png
vignettes/GEGVIC.Rmd
vignettes/GEGVIC_outline.png
vignettes/input_counts.png
vignettes/input_metadata.png
vignettes/input_muts.png
