Files in ytakemon/GINIR
Genetic inteRaction and EssenTiality neTwork mApper
.Rbuildignore
._.DS_Store
.gitattributes
.github/ISSUE_TEMPLATE/recommendations-.md
.gitignore
DESCRIPTION
DepMap_data_versions/20Q1/README.txt
DepMap_data_versions/20Q1/pre-processing/Data_formatting.R
DepMap_data_versions/20Q1/pre-processing/Pancan_coessential_precomputing.R
DepMap_data_versions/21Q4/README.txt
DepMap_data_versions/21Q4/pre-processing/Data_formatting.R
DepMap_data_versions/21Q4/pre-processing/Data_retreival.R
DepMap_data_versions/21Q4/pre-processing/Pancan_coessential_precomputing.R
DepMap_data_versions/22Q1/README.txt
DepMap_data_versions/22Q1/pre-processing/Data_formatting.R
DepMap_data_versions/22Q1/pre-processing/Data_retreival.R
DepMap_data_versions/22Q1/pre-processing/Pancan_coessential_precomputing.R
DepMap_data_versions/23Q2/README.txt
DepMap_data_versions/23Q2/pre-processing/Data_formatting.R
DepMap_data_versions/23Q2/pre-processing/Data_retreival.R
DepMap_data_versions/23Q2/pre-processing/Pancan_coessential_precomputing.R
GRETTA_hex_logo-02.png
LICENSE.md
NAMESPACE
NEWS.md
R/Append_perm_pval.R
R/GI_screen.R
R/GI_screen_perms.R
R/Pval_perm_adjust.R
R/annotate_df.R
R/coessential_map.R
R/common_coefs_coess.R
R/common_coefs_prot.R
R/common_coefs_rna.R
R/download_example_data.R
R/extract_prot.R
R/extract_rna.R
R/get_inflection_points.R
R/get_names.R
R/list_cancer_type.R
R/list_mutations.R
R/plot_coess.R
R/plot_screen.R
R/protein_coexpress.R
R/rna_coexpress.R
R/select_cell_lines.R
R/utils-pipe.R
R/zzz.R
README.Rmd
README.md
Singularity/ARID1A_tutorial.R
Singularity/README
inst/CITATION
inst/figures/README-Check_expression_rna_stats-1.png
inst/figures/README-combine_n_visualize-1.png
inst/figures/README-plot-1.png
man/Append_perm_pval.Rd
man/GI_screen.Rd
man/GI_screen_perms.Rd
man/Pval_perm_adjust.Rd
man/annotate_df.Rd
man/coessential_map.Rd
man/common_coefs_coess.Rd
man/common_coefs_prot.Rd
man/common_coefs_rna.Rd
man/download_example_data.Rd
man/extract_prot.Rd
man/extract_rna.Rd
man/get_GeneNameID.Rd
man/get_inflection_points.Rd
man/list_cancer_types.Rd
man/list_mutations.Rd
man/pipe.Rd
man/plot_coess.Rd
man/plot_screen.Rd
man/protein_coexpress.Rd
man/rna_coexpress.Rd
man/select_cell_lines.Rd
tests/testdata/GRETTA_example/CCLE_exp.rda
tests/testdata/GRETTA_example/CCLE_exp_annot.rda
tests/testdata/GRETTA_example/copy_num.rda
tests/testdata/GRETTA_example/copy_num_annot.rda
tests/testdata/GRETTA_example/dep.rda
tests/testdata/GRETTA_example/dep_annot.rda
tests/testdata/GRETTA_example/gene_effect.rda
tests/testdata/GRETTA_example/mut_calls.rda
tests/testdata/GRETTA_example/protein_annot.rda
tests/testdata/GRETTA_example/protein_nodup.rda
tests/testdata/GRETTA_example/sample_22Q2_ARID1A_KO_screen.rda
tests/testdata/GRETTA_example/sample_22Q2_ARID1A_coessential_inflection.rda
tests/testdata/GRETTA_example/sample_22Q2_ARID1A_coessential_result.rda
tests/testdata/GRETTA_example/sample_annot.rda
tests/testthat.R
tests/testthat/GRETTA_GI_screen_results.csv
tests/testthat/test-GI_screen.R
tests/testthat/test-extract_prot.R
tests/testthat/test-extract_rna.R
tests/testthat/test-get_DepMapID.R
tests/testthat/test-get_GeneNameID.R
tests/testthat/test-list_cancer_types.R
tests/testthat/test-list_mutations.R
tests/testthat/test-select_cell_lines.R
vignettes/.gitignore
vignettes/GRETTA_vignette.Rmd
