Alternatives and similar repositories for MutationTimeR:

Users that are interested in MutationTimeR 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.
  ☆71Updated 11 months ago
• broadinstitute / gistic2
  Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
  ☆51Updated 3 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 2 months ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated 9 months ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆57Updated last month
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• getzlab / MutSig2CV
  MutSig2CV from Lawrence et al. 2014
  ☆31Updated 4 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated last month
• McGranahanLab / TcellExTRECT
  ☆47Updated 3 months ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• pdiakumis / rock
  Rocking R at UMCCR
  ☆9Updated 4 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆86Updated last month
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆81Updated last week
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆27Updated 2 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆55Updated 4 years ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆21Updated 2 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆47Updated 9 months ago
• raphael-group / decifer
  DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…
  ☆20Updated 11 months ago
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆42Updated last year
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• parklab / SigMA
  Mutational signature analysis for low statistics SNV data
  ☆63Updated 8 months ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• ShixiangWang / DoAbsolute
  Automate Absolute Copy Number Calling using 'ABSOLUTE' package
  ☆40Updated last year
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 9 months ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago