Files in korkutlab/imogimap
What the Package Does (One Line, Title Case)
.Rapp.history
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/Get_quantile_rank.R
R/calculate_syng_score.R
R/data.R
R/find_a_synergy.R
R/get_TCI_score.R
R/get_angio_score.R
R/get_emt_score.R
R/get_features.R
R/get_ifng_score.R
R/get_select_features.R
R/get_sensitivity.R
R/get_specificity.R
R/im_boxplot.R
R/im_boxplot_tcga.R
R/im_boxplot_tcga_plot.R
R/im_cor.R
R/im_cor_tcga.R
R/im_netplot.R
R/im_syng.R
R/im_syng_tcga.R
R/im_syng_tcga_shiny.R
R/imogimap.R
R/round_df.R
README.html
README.md
data/.Rapp.history
data/AG_gene_list.rda
data/EMT_gene_list.rda
data/TCGA_IMCell_fraction.rda
data/TCGA_Leukocyte_fraction.rda
data/TCGA_TMB.rda
data/TCGA_disease_list.rda
data/TCGA_immune_features_list.rda
data/icp_gene_list.rda
data/lgn_receptor_ligand.rda
data/lgn_tcell_tnbc.rda
data/sample_Leukocyte_fraction_data.rda
data/sample_immune_cell_fraction_data.rda
data/sample_mRNA_data.rda
data/tcell_inflamed_gene_list.rda
imogimap.Rproj
inst/CITATION
inst/Tcell_dysfunction_analysis/GSE114725_rna_imputed.csv
inst/Tcell_dysfunction_analysis/GSE148673_rna_raw.csv
inst/Tcell_dysfunction_analysis/TCGA_PFIsurvival_UCEC.csv
inst/Tcell_dysfunction_analysis/TCellDys_scores_Basal.csv
inst/Tcell_dysfunction_analysis/TCell_dys_genes_brca.csv
inst/Tcell_dysfunction_analysis/TCell_dys_genes_ucec.csv
inst/Tcell_dysfunction_analysis/TCell_dys_scores_ucec.csv
inst/Tcell_dysfunction_analysis/analysis.R
inst/Tcell_dysfunction_analysis/samples_BRCA_basal.csv
inst/Tcell_dysfunction_analysis/~$ARID3B.txt
inst/extdata/ICP_interactions.csv
inst/extdata/ICT_fractions.csv
inst/extdata/Pan-Cancer-EMT-Signature-Genes.csv
inst/extdata/TCGA_all_leuk_estimate.masked.20170107.tsv
inst/extdata/TCGA_disease.csv
inst/extdata/TCGA_immune_features.csv
inst/extdata/cellphoneDB_gene_name.xlsx
inst/extdata/cellphoneDB_interaction_input.xlsx
inst/extdata/gene_list.txt
inst/extdata/genes_Immune_checkpoints.txt
inst/extdata/genes_angiogenesis.txt
inst/extdata/ligand_receptor_curated.csv
inst/extdata/mutation-load_updated.txt
inst/extdata/mydataset.R
inst/extdata/sample_Leukocyte_fraction.csv
inst/extdata/sample_immune_cell_fraction.csv
inst/extdata/sample_mRNA_data.csv
inst/extdata/significant_dysfunction_scores.xlsx
inst/extdata/t_inflamed_gene_expr.tsv
inst/shiny/about.md
inst/shiny/global.R
inst/shiny/interpretation.html
inst/shiny/interpretation.md
inst/shiny/introduction.html
inst/shiny/introduction.md
inst/shiny/server.R
inst/shiny/ui.R
inst/shiny/www/__rectSitelogo__MDA SITE LOGO - Thumbnail.png
inst/shiny/www/networjk_guide.pdf
inst/shiny/www/network_guide.png
man/AG_gene_list.Rd
man/EMT_gene_list.Rd
man/TCGA_IMCell_fraction.Rd
man/TCGA_Leukocyte_fraction.Rd
man/TCGA_TMB.Rd
man/TCGA_disease_list.Rd
man/TCGA_immune_features_list.Rd
man/calculate_syng_score.Rd
man/find_a_synergy.Rd
man/get_TCI_score.Rd
man/get_angio_score.Rd
man/get_emt_score.Rd
man/get_features.Rd
man/get_ifng_score.Rd
man/get_quantile_rank.Rd
man/get_selected_features.Rd
man/get_sensitivity.Rd
man/get_specificity.Rd
man/icp_gene_list.Rd
man/im_boxplot.Rd
man/im_boxplot_tcga.Rd
man/im_boxplot_tcga_plot.Rd
man/im_cor.Rd
man/im_cor_tcga.Rd
man/im_netplot.Rd
man/im_syng.Rd
man/im_syng_tcga.Rd
man/im_syng_tcga_shiny.Rd
man/imogimap.Rd
man/round_df.Rd
man/sample_Leukocyte_fraction_data.Rd
man/sample_immune_cell_fraction_data.Rd
man/sample_mRNA_data.Rd
references.bib
vignettes/imogimap-vignette.Rmd
vignettes/syng_network.jpeg
