Alternatives and similar repositories for ClonEvol

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

• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆62Updated 4 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated 2 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated 2 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• hellbelly / BS-Snper
  ☆38Updated 4 years ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 6 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆40Updated 3 years ago
• hartwigmedical / pipeline5
  ☆21Updated this week
• raphael-group / decifer
  DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…
  ☆21Updated last year
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆29Updated 7 months ago
• amcpherson / citup
  Clonality inference in multiple tumor samples using phylogeny
  ☆13Updated 8 years ago
• mskcc / facets-suite
  Utility functions for FACETS
  ☆39Updated last year
• francois-a / fastqtl
  Enhanced version of the FastQTL QTL mapper
  ☆68Updated 2 years ago
• nloyfer / UXM_deconv
  ☆46Updated 2 years ago
• gxiaolab / REDITs
  RNA editing tests
  ☆17Updated 4 years ago
• rcavalcante / annotatr
  Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post…
  ☆27Updated 2 months ago
• mskilab-org / dryclean
  Irons out wrinkles in noisy coverage data using robust PCA
  ☆15Updated 4 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• 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
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 7 years ago
• SGDDNB / translational_regulation
  Detection of differential translated genes using Ribo-seq
  ☆16Updated 4 years ago
• shahcompbio / hmmcopy_utils
  Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
  ☆41Updated 4 years ago
• ait5 / CNApp
  CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…
  ☆20Updated 5 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 last year
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆59Updated 3 months ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆56Updated 5 years ago
• eyzhao / hrdetect-pipeline
  ☆36Updated 6 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago