DOI: 10.5281/zenodo.14909793
title: SOPA and SIMPA: Normalized single sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers

description: 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-alignment


    p2preinteg_tpm_rnaseq_counts.csv:

    - tpm counts pre-alignment


    p2preinteg_cnv_counts.csv:

    - CNVs pre-alignment pre-imputation


    p2preinteg_cnvs.csv:

    - CNVs pre-alignment post-imputation


    p2preinteg_mcounts.csv:

    - DNAm beta values sites pre-alignment pre-imputation


    p2preinteg_dnam_sites.csv:

    - DNAm beta values sites pre-alignment 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-alignment 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-alignment


    p2postinteg_tpm_rnaseq_counts.csv:

    - TPM counts for SOPA post-alignment


    p2postinteg_cnvs.csv:

    - CNVs post-alignment


    p2postinteg_dnam_genes.csv:

    - DNAm beta values genes post-alignment


    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/.
description: This updated version contains SOPA_SIMPA_res.rar with corrected column names for smoother code execution.