Alternatives and similar repositories for SigMA

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

• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆62Updated 4 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• broadinstitute / gistic2
  Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
  ☆51Updated 3 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated 11 months ago
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆82Updated this week
• ding-lab / PanCanAtlasGermline
  ☆44Updated 6 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 4 months ago
• eyzhao / hrdetect-pipeline
  ☆35Updated 5 years ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆72Updated 9 months ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 4 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated last year
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated 2 years ago
• parklab / ShatterSeek
  ☆69Updated last year
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 3 years ago
• aryeelab / hichipper
  A preprocessing and QC pipeline for HiChIP data
  ☆39Updated 2 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆55Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• morrislab / qapa
  RNA-seq Quantification of Alternative Polyadenylation
  ☆46Updated 2 years ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆59Updated 4 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• pdiakumis / rock
  Rocking R at UMCCR
  ☆9Updated 4 years ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆20Updated 2 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated last year
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• getzlab / MutSig2CV
  MutSig2CV from Lawrence et al. 2014
  ☆31Updated 4 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆88Updated 3 weeks ago