TCGAbiolinks - TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
The aim of TCGAbiolinks is : i) facilitate the GDC 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) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
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dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksequencingsurvivalsoftwarebiocbioconductorgdcintegrative-analysistcgatcga-datatcgabiolinks
14.91 score 355 stars 8 dependents 2.9k scripts 9.9k downloadsTCGAWorkflowData - Data for TCGA Workflow
This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages".
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experimentdatahomo_sapiens_datamicroarraydatacancerdatabioconductortcgatcgabiolinksdatapkg
6.10 score 53 stars 24 scriptsELMER - Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.
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dnamethylationgeneexpressionmotifannotationsoftwaregeneregulationtranscriptionnetwork
5.43 score 135 scripts 570 downloads