Alternatives and similar repositories for RTCGAToolbox

Users that are interested in RTCGAToolbox are comparing it to the libraries listed below

• waldronlab / curatedTCGAData
  Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
  ☆44Updated last month
• gladkia / igvR
  An R Bioconductor package providing interactive connections to igv.js (the Integrative Genomics Viewer) in a web browser
  ☆46Updated 7 months ago
• waldronlab / MultiAssayExperiment
  Bioconductor package for management of multi-assay data
  ☆72Updated last month
• Bioconductor / bioconductor_full
  [DEPRECATED] Docker Images which include a complete installation of all software needed to build all Bioconductor packages
  ☆25Updated 2 years ago
• Shians / Glimma
  Glimma R package
  ☆50Updated 9 months ago
• Bioconductor / OrchestratingSingleCellAnalysis-release
  An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.
  ☆36Updated 2 years ago
• Bioconductor / BiocWorkshops2019
  The official repository of the Bioconductor 2019 Conference Workshops
  ☆25Updated 2 years ago
• cBioPortal / cgdsr
  R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS)
  ☆24Updated 4 years ago
• csoneson / ExploreModelMatrix
  Explore design matrices interactively with R/Shiny
  ☆37Updated 2 months ago
• gladkia / igvShiny
  An htmlwidget version of igv, for RStudio and Shiny apps
  ☆38Updated 7 months ago
• leekgroup / recount
  R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
  ☆41Updated 6 months ago
• LTLA / basilisk
  Clone of the Bioconductor repository for the basilisk package.
  ☆27Updated last month
• RTCGA / RTCGA
  Download, integration and visualizations of the variety & volume of TCGA data.
  ☆51Updated 2 years ago
• hansenlab / minfi
  Devel repository for minfi
  ☆59Updated last year
• lcolladotor / derfinder
  Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
  ☆43Updated 6 months ago
• andrewparkermorgan / argyle
  An R package for import, QC and analysis of Illumina Infinium genotyping arrays
  ☆34Updated 7 years ago
• zhanxw / seqminer
  Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
  ☆30Updated 8 months ago
• leekgroup / networks_correction
  Code to reproduce analysis in "Addressing confounding artifacts in reconstruction of gene co-expression networks"
  ☆16Updated 6 years ago
• montilab / hypeR
  An R Package for Geneset Enrichment Workflows
  ☆76Updated 3 weeks ago
• waldronlab / enrichOmics
  Functional enrichment analysis of high-throughput omics data
  ☆20Updated 5 months ago
• stemangiola / bioc_2020_tidytranscriptomics
  Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap
  ☆26Updated 4 years ago
• isb-cgc / examples-R
  Analysis examples based on the ISB-CGC hosted TCGA data, using R and R Markdown.
  ☆31Updated 7 years ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆31Updated last year
• Bioconductor / GenomicRanges
  Representation and manipulation of genomic intervals
  ☆46Updated this week
• csoneson / countsimQC
  countsimQC - Compare characteristic features of count data sets
  ☆27Updated 2 months ago
• randel / MIND
  Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
  ☆45Updated 2 years ago
• waldronlab / HGNChelper
  Identify and correct invalid gene symbols
  ☆58Updated 7 months ago
• MathOnco / EvoFreq
  Evolutionary frequency visualization tool of temporal data
  ☆22Updated 3 years ago
• mikelove / deseq2_or_edger
  DESeq2 or edgeR
  ☆22Updated 8 years ago
• macarthur-lab / exac_2015
  Companion repo for ExAC paper, 2015
  ☆33Updated 8 years ago