Alternatives and similar repositories for web-TCGA

Users that are interested in web-TCGA are comparing it to the libraries listed below

• wkl1990 / Illumina450K-methylation
  From IDAT to beta.
  ☆25Updated 7 years ago
• icbi-lab / Immunophenogram
  ☆40Updated 7 years ago
• akoch8 / mexpress
  MEXPRESS is a data visualization tool designed for the visualization of TCGA expression, DNA methylation and clinical data.
  ☆13Updated 4 years ago
• ajitjohnson / imsig
  Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
  ☆27Updated 4 years ago
• icbi-lab / immune_deconvolution_benchmark
  Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…
  ☆43Updated 5 years ago
• hammerlab / multi-omic-urothelial-anti-pdl1
  Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis
  ☆23Updated 7 years ago
• BioinformaticsFMRP / TCGAWorkflow
  TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
  ☆45Updated 2 years ago
• zhiyhu / NMD-paper
  A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay
  ☆15Updated 4 years ago
• ding-lab / PanCanAtlasGermline
  ☆44Updated 6 years ago
• dfci / pancanmet_analysis
  Software and analysis of metabolism studies across multiple cancer types
  ☆9Updated 7 years ago
• morrislab / TrackSig
  A framework to infer mutational signatures in cancer over time
  ☆53Updated 6 years ago
• mruffalo / sc-rna-seq-pipeline
  ☆22Updated 5 years ago
• XSLiuLab / tumor-immunogenicity-score
  TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
  ☆32Updated 3 years ago
• ICBI / neoantigeR
  a R package to identify neoantigens from NGS data
  ☆19Updated 8 years ago
• srp33 / TCGA_RNASeq_Clinical
  ☆61Updated 4 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• bhklab / Xeva
  XEnograft Visualization & Analysis
  ☆11Updated 3 months ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• greenelab / gbm_immune_validation
  Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors
  ☆14Updated 6 years ago
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 5 years ago
• Neurosurgery-Brain-Tumor-Center-DiazLab / CONICS
  CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
  ☆74Updated 2 years ago
• mxxdxxx / FirebrowseR
  An R client for broads firehose pipeline, providing TCGA data sets
  ☆61Updated 6 years ago
• caravagnalab / revolver
  REVOLVER - Repeated Evolution in Cancer
  ☆65Updated 2 years ago
• MD-Anderson-Bioinformatics / MBatch
  Superseded by https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage
  ☆13Updated 4 years ago
• foreverdream2 / dysfunction_interaction_test
  ☆29Updated 7 years ago
• epigen / crop-seq
  Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
  ☆31Updated 7 years ago
• Sidra-TBI-FCO / ISPC
  Code for the paper on the ICR immune signatures and prognostic significance pan-cancer (TCGA)
  ☆10Updated 4 years ago
• GreenleafLab / motifmatchr
  Fast motif matching in R
  ☆47Updated last year
• hemberg-lab / SC3-paper-figures
  Scripts to recreate figures from the SC3 paper
  ☆40Updated 8 years ago
• lagelab / quack
  Machine learning algorithm to predict biological pathway relationships based on functional genomics networks
  ☆20Updated 6 years ago