The cancer genome atlas data processing software tools | Genome annotation
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Due to the complexity of this collection, numerous software tools have been developed for retrieving, exploring, visualizing, and analyzing TCGA data.
Provides a web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. cBioPortal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface, combined with customized data storage, enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes.
Automatically generates, testes and deploys such clients for rapid response to API changes. Firebrowse provides a raw construct of an R function including all the comments, which will be rendered as the documentation when the final package is built. Firebrowse can be integrated into existing analysis workflows. Using such API clients over the download of flat files has several advantages, including having the latest data available, making the process of data importing obsolete and avoiding data re-formatting, which often serves as an additional source of errors.
Assesses the effect of genes on survival using cancer samples. KM plotter is a web application, developed for meta-analysis-based biomarker assessment, that can be used for breast, ovarian, lung, gastric, and liver cancer. The software includes patients with a mean follow-up of 69 / 40/ 49 /33 months. The subtool miRpower enables the validation of the prognostic relevance of microRNAs (miRNAs) in breast and liver cancer.
Aids in querying, downloading, analyzing and integrating The Cancer Genome Atlas (TCGA) data. TCGAbiolinks can: i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) allow user to download a specific version of the data and thus to easily reproduce earlier research results. It provides multiple methods for analysis and methods for visualization in order to easily develop complete analysis pipelines.
Performs secure analyses and visualization of users’ private functional genomics data set in the context of public and shared genomic/phenotypic data sets. UCSC Xena is a Functional Genomics Browser that provides analytics, visualization and Galaxy integration for analyzing and viewing the public data hubs. It gives access to public databases (Xena Public Data Hubs) and allows users to mix in and compare private data (Xena Private Data Hubs).
Authorizes to retrieve, assemble and process public data from The Cancer Genome Atlas (TCGA). TCGA-assembler is an open source software which is composed of two modules: (i) the first module earns the public data including TCGA somatic mutation and proteomics data and gathers the individual files into local data tables, and (ii) the second module furnishes multiple features for preparing information for downstream analysis such as a way for separating different types of measurements into their own data tables.
Enables users to perform a diverse range of gene expression analyses. GEPIA is an interactive web application that analyzes the RNA sequencing expression data of more than 9,000 tumors and 8,000 normal samples from The Cancer Genome Atlas (TCGA) and the GTEx projects. It provides customizable functions such as tumor/normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.