Files in sjdlabgroup/metaITH
A Tool for Analyzing Intratumor Heterogeneity at Multiple Levels

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/metaITH_analysis_function.R R/other_functions.R R/signature_analysis_function.R
R/sysdata.rda
README.md
data/DNA_S1_frequency_matrix.rda
data/DNA_distance_matrix_S1_SNV_frequency_matrix.rda
data/DNA_phylo_list.rda
data/RNA_expression_matrix.rda
data/anti_PD1_favor_geneset.rda
data/apoptosis_geneset.rda
data/epithelial_geneset.rda
genesets/anti-PD1_favor_geneset.txt
genesets/apoptosis_geneset.txt
genesets/epithelial_geneset.txt
genesets/hypoxia_geneset.txt
genesets/mesenchymal_geneset.txt
genesets/pemetrexed_resistance_geneset.txt
genesets/proliferation_geneset.txt
input_files/dendro_inputs/DNA_S1_frequency_matrix.txt
input_files/dendro_inputs/DNA_dendro_list.txt
input_files/dendro_inputs/Immune_dendro_list.txt
input_files/dendro_inputs/RNA_dendro_list.txt
input_files/dendro_inputs/S1_Immune_CIBERSORT_matrix.txt
input_files/dendro_inputs/S1_RNA_expression_matrix.txt
input_files/multiregion_inputs/DNA_S1_frequency_matrix.txt
input_files/multiregion_inputs/S1_Immune_CIBERSORT_matrix.txt
input_files/multiregion_inputs/S1_RNA_expression_matrix.txt
input_files/multiregion_inputs/sample_names.txt
input_files/sig_analysis_inputs/RNA_matrix.txt
man/anti_pd1_favor_signature.Rd man/apoptosis_signature.Rd man/dna_dendrograms.Rd man/drug_resistance_signature.Rd man/emt_signature.Rd man/hypoxia_signature.Rd man/immune_dendrograms.Rd man/metaITH_analysis.Rd man/multi_level_divergence_diversity.Rd man/proliferation_signature.Rd man/rna_dendrograms.Rd man/signature_analysis.Rd man/snv_heatmaps.Rd man/specified_geneset_signature.Rd man/z_score_calculations.Rd
metaITH.Rproj
output_files/dendro_outputs/DNA_distance_matrix_DNA_S1_frequency_matrix.txt
output_files/dendro_outputs/DNA_tree_DNA_S1_frequency_matrix.txt
output_files/dendro_outputs/DNA_unrooted_dendrogram_DNA_S1_frequency_matrix.txt.tiff
output_files/dendro_outputs/Immune_distance_matrix_S1_Immune_CIBERSORT_matrix.txt
output_files/dendro_outputs/Immune_tree_S1_Immune_CIBERSORT_matrix.txt
output_files/dendro_outputs/Immune_unrooted_dendrogram_S1_Immune_CIBERSORT_matrix.txt.tiff
output_files/dendro_outputs/RNA_distance_matrix_S1_RNA_expression_matrix.txt
output_files/dendro_outputs/RNA_tree_S1_RNA_expression_matrix.txt
output_files/dendro_outputs/RNA_unrooted_dendrogram_S1_RNA_expression_matrix.txt.tiff
output_files/dendro_outputs/SNV_heatmap_DNA_S1_frequency_matrix.txt.tiff
output_files/multiregion_outputs/png_multiomics_ITH_comparison.png
output_files/sig_analysis_outputs/Apoptosis_score.txt
output_files/sig_analysis_outputs/Apoptosis_scores_heatmap.tiff
output_files/sig_analysis_outputs/Epithelial_Mesenchymal_scores.txt
output_files/sig_analysis_outputs/Geneset_score.txt
output_files/sig_analysis_outputs/Geneset_scores_heatmap.tiff
output_files/sig_analysis_outputs/Hypoxia_score.txt
output_files/sig_analysis_outputs/Hypoxia_scores_heatmap.tiff
output_files/sig_analysis_outputs/Mesenchymal-Epithelial_score.txt
output_files/sig_analysis_outputs/Mesenchymal-Epithelial_score_heatmap.tiff
output_files/sig_analysis_outputs/Pemetrexed_resistance_score.txt
output_files/sig_analysis_outputs/Pemetrexed_resistance_scores_heatmap.tiff
output_files/sig_analysis_outputs/Proliferation_score.txt
output_files/sig_analysis_outputs/Proliferation_scores_heatmap.tiff
output_files/sig_analysis_outputs/anti-PD1_favor_score.txt
output_files/sig_analysis_outputs/anti-PD1_favor_scores_heatmap.tiff
output_files/sig_analysis_outputs/z-scores_matrix.txt
vignettes/.gitignore
vignettes/metaITH.Rmd vignettes/metaITH.pdf
sjdlabgroup/metaITH documentation built on Nov. 5, 2019, 8:58 a.m.