(Center for Systems Analysis of the Cancer Regulome)Ī web-based tool for identifying network-based biomarkers that correlate with patient survival data. Web-based interactive tools for visualizing and exploring associations between clinical and molecular TCGA data. (MD Anderson Cancer Center and Baylor College of Medicine) Mutation calling using a Markov Substitution model for Evolution (MuSE)Ī mutation caller that models the evolution of the reference allele to the allelic composition of the tumor and normal tissue at each genomic locus and accounts for tumor heterogeneity through a sample-specific error model. (Broad Institute)Ī web-based tool for identifying and quantifying batch effects present in processed TCGA data, utilizing hierarchical clustering and enhanced PCA plots. (Weill Cornell Medicine)Ī high-performance visualization tool for interactive exploration of large, integrated data sets. Uses a pre-built data context generated from multiple genomic and cancer resources that is regularly updated. (Broad Institute)Ī tool to prioritize and annotate somatic variants, particularly non-coding variants, from cancer whole genome sequencing. Provides graphical tools like viewGene to explore expression levels and iCoMutto explore a comprehensive mutation analysis of each TCGA disease and an API for programmers. (Broad Institute)Ī tool to explore and visualize cancer data generated by Broad GDAC Firehose. (MD Anderson Cancer Center)Ī suite of tools and pipelines developed for processing and analyzing various types of large-scale genomic and proteomic data. (MD Anderson Cancer Center)Īn integrative, analytic web platform for annotating the functional impacts of somatic mutations in human cancer. It provides both the mixture proportions and individual sample-specific and gene-specific expression levels for each component. (Broad Institute)Ī software package thatdeconvolutes transcriptome data from a mixture of two (tumor, stroma) or three components (tumor, stroma, immune). (Memorial Sloan-Kettering Cancer Center)Ī portal for exploring copy number alterations of TCGA data, including results of GISTIC analyses for identifying genes targeted by somatic copy number alterations that drive cancer growth. Provides visualization, analysis, and download of large-scale cancer genomics data sets. (National Cancer Institute)Īn integrative data portal for accessing, visualizing, and analyzing proteomic data. TCIA supports imaging phenotype-genotype research, in addition to other imaging data sets for cancer imaging analysis. The Cancer Genome Atlas (TCGA) catalyzed considerable growth and advancement in the computational biology field by supporting the development of high-throughput genomic characterization technologies, generating a massive quantity of data, and fielding teams of researchers to analyze the data. Below is a collection of some of the tools developed by TCGA network researchers and collaborators that were used to analyze TCGA data.Ī service providing access to radiological imaging data sets in DICOM format from TCGA cases.
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