Alternatives and similar repositories for TCGA:

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

• JEFworks-Lab / MERmaid
  WebGL-based viewer for spatially-resolved transcriptomics data
  ☆26Updated 2 years ago
• hbc / NGS-Data-Analysis-long-course
  ☆11Updated 7 years ago
• MaayanLab / biojupies-plugins
  User-submitted RNA-seq data analysis tools for BioJupies.
  ☆19Updated 3 years ago
• ding-lab / hotspot3d
  3D hotspot mutation proximity analysis tool
  ☆46Updated last year
• jpiper / pyDNase
  Python module for the easy handling and analysis of DNase-seq data
  ☆37Updated 5 years ago
• SnakeChunks / SnakeChunks
  Modular blocks to build Snakemake workflows for reproducible NGS analyses
  ☆22Updated 5 years ago
• aboyle / F-seq
  A Feature Density Estimator for High-Throughput Sequence Tags
  ☆23Updated 3 years ago
• mikelove / alpine
  Modeling and correcting fragment sequence bias for RNA-seq
  ☆24Updated 7 months ago
• HumanCellAtlas / table-testing
  requirements, examples, and tests for expression matrix file formats
  ☆22Updated 6 years ago
• epigen / cll-chromatin
  Data analysis scripts for Rendeiro et. al, 2016 (doi:10.1038/ncomms11938)
  ☆9Updated 7 years ago
• tgen / MMRF_CoMMpass
  A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.
  ☆18Updated last year
• YosefLab / FastProject
  Dimensionality reduction for single cell RNA-seq data
  ☆35Updated 4 years ago
• rthurman / hotspot
  Hotspot is a program for identifying genomic regions of local enrichment of short-read sequence tags.
  ☆14Updated 10 years ago
• jmschrei / rambutan
  Prediction of the 3D structure of the genome through statistically significant Hi-C contacts.
  ☆21Updated 6 years ago
• csoneson / NativeRNAseqComplexTranscriptome
  Code for the paper "A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes"
  ☆19Updated 5 years ago
• lucapinello / Haystack
  Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
  ☆30Updated 7 years ago
• shenlab-sinai / diffreps
  Differential analysis for ChIP-seq with biological replicates
  ☆35Updated 3 years ago
• FertigLab / CancerInSilico
  An R package for running cell-based models
  ☆8Updated 5 years ago
• mandricigor / imrep
  ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
  ☆28Updated 5 years ago
• mnsmar / clipseqtools
  A suite for the analysis of CLIP-Seq datasets.
  ☆12Updated 3 years ago
• stracquadaniolab / pygna
  A Python package for gene network analysis
  ☆32Updated 2 years ago
• Neurosurgery-Brain-Tumor-Center-DiazLab / scell
  Single-CELL rna-seq analysis software
  ☆38Updated 7 years ago
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 8 years ago
• KarchinLab / SCHISM
  Subclonal Hierarchy Inference from Somatic Mutations
  ☆21Updated 5 years ago
• ma-compbio / PEP
  ☆14Updated 4 years ago
• songlab / chance
  Download binary executables and sample data here:
  ☆18Updated 8 years ago
• seandavi / ci4cc-informatics-resources
  Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are d…
  ☆22Updated 6 years ago
• raphael-group / wext
  A Weighted Exact Test for Mutually Exclusive Mutations in Cancer
  ☆21Updated 6 years ago
• klarman-cell-observatory / scPlot
  Single cell interactive plotting tools
  ☆23Updated 4 years ago
• BenLangmead / qtip
  Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
  ☆25Updated 5 years ago