SOPA and SIMPA: Normalized single sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers

This repository contains all raw data obtained from The Cancer Genome Atlas, through the custom search criteria used in the single-omic single-sample pathway anaylsis pipeline (SOPA) and its integrated multiomics extension, SIMPA. .rar files: CNV.rar: Contains copy number variation data. RNAseq.rar: Contains transcriptomics data. Meth.rar: Contains DNA methylation data. SOPA_SIMPA_res.rar: Contains results for SOPA and SIMPA obtained through running the pipeline on the rankings obtained from the custom ranking metrics calculated from the raw data. ssGSEA_GDC_res.rar: Results from running ssGSEA on GDC samples (n = 1,968). GSVA_GDC_res.rar: Results from running GSVA on GDC samples (n = 1,968). Datasets.rar: Contains various results from the analyses made for SOPA/ SIMPA validation and testing. Each of these files was generated from the jupyter notebooks in the linked GitHub repository. The results are as follows: clin.csv: - contains clinical information for the integrated multiomics population p2preinteg_raw_rnaseq_counts.csv: - raw counts for differential expression analysis pre-integration p2preinteg_tpm_rnaseq_counts.csv: - tpm counts pre-integration p2preinteg_cnv_counts.csv: - CNVs pre-integration pre-imputation p2preinteg_cnvs.csv: - CNVs pre-integration post-imputation p2preinteg_mcounts.csv: - DNAm beta values sites pre-integration pre-imputation p2preinteg_dnam_sites.csv: - DNAm beta values sites pre-integration post-imputation p2preinteg_dnam_dma.csv: - DNAm OLS regression results for weighted average of gene methylation p2preinteg_dnam_genes.csv: - DNAm beta values genes pre-integration post-imputation p2postinteg_genename_ensembleid_template.csv: - contains annotations for gene names and ensemble ids for integrated data p2postinteg_cnvs_template.csv: - contains annotations for gene names and ensemble ids, as well as for chromosome location, start location, and end location for each gene p2postinteg_raw_rnaseq_counts.csv: - raw counts for differential expression analysis post-integration p2postinteg_tpm_rnaseq_counts.csv: - TPM counts for SOPA post-integration p2postinteg_cnvs.csv: - CNVs post-integration p2postinteg_dnam_genes.csv: - DNAm beta values genes post-integration p2postinteg_rnaseq_dea.csv: - results of differential expression analysis using log2FC p2postinteg_cnv_da.csv: - results of mutation frequency and significance using Fisher's Exact p2postinteg_dnam_dma.csv: - results of DNAm differential methylation analysis using odds least square regression The GitHub repository connected to these datasets can be found at https://github.com/hasanalsharoh/SIMPA. For utilizing the SOPA/SIMPA tool python package can be found at https://pypi.org/project/SIMPApy/ and the homepage for project at https://github.com/hasanalsharoh/SIMPApy/.