Alternatives and similar repositories for rascal:

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

• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated 8 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 8 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆61Updated 4 years ago
• asntech / QDNAseq.hg38
  QDNAseq bin annotation for hg38
  ☆14Updated this week
• RahmanTeam / DECoN
  ☆53Updated 2 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆70Updated 10 months ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated last month
• shahcompbio / hmmcopy_utils
  Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
  ☆39Updated 3 years ago
• tgac-vumc / ACE
  Absolute Copy Number Estimation using low-coverage whole genome sequencing data
  ☆15Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 3 years ago
• broadinstitute / PhylogicNDT
  ☆72Updated 11 months ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• hartwigmedical / pipeline5
  ☆21Updated last week
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆86Updated last week
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• girirajanlab / CN_Learn
  CN-Learn
  ☆29Updated 5 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• ShixiangWang / copynumber
  The "copynumber" R package with support for hg38
  ☆19Updated last year
• mskcc / facets-suite
  Utility functions for FACETS
  ☆34Updated last year
• AlexandrovLab / SigProfilerSingleSample
  SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity…
  ☆23Updated 2 months ago
• niu-lab / msisensor-ct
  Microsatellite instability (MSI) detection for cfDNA samples.
  ☆19Updated 4 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆44Updated 2 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• amcpherson / citup
  Clonality inference in multiple tumor samples using phylogeny
  ☆13Updated 7 years ago
• babelomics / SMAca
  SMN1 copy-number and sequence variant analysis from next generation sequencing data
  ☆22Updated last year
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year
• hw538 / cfDNAPro
  cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
  ☆29Updated this week
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆66Updated 5 years ago