Alternatives and similar repositories for mc3

Users that are interested in mc3 are comparing it to the libraries listed below

• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆44Updated 3 years ago
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆50Updated last year
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆53Updated 3 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆36Updated 4 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 3 years ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆25Updated 2 years ago
• PeeperLab / CopywriteR
  DNA copy number detection from off-target sequence data
  ☆33Updated 7 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• gagneurlab / OUTRIDER
  OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
  ☆55Updated 2 months ago
• hellbelly / BS-Snper
  ☆39Updated 4 years ago
• Xinglab / rMATS-DVR
  ☆18Updated 7 years ago
• anbrooks / juncBASE
  Junction Based Analysis of Splicing Events for RNA-Seq
  ☆34Updated 4 months ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆77Updated this week
• sdchandra / CNAclinic
  ☆26Updated last year
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• costasilvati / consexpression
  Tool for RNA-Seq analysis.
  ☆39Updated 3 years ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆28Updated 7 months ago
• heathsc / gemBS
  gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…
  ☆32Updated 3 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• ndbrown6 / MSK-GRAIL-TECHVAL
  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
  ☆22Updated 5 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆32Updated 2 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• eyzhao / hrdetect-pipeline
  ☆36Updated 6 years ago
• mskcc / facets-suite
  Utility functions for FACETS
  ☆39Updated 2 months ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated last year