Alternatives and similar repositories for copykit:

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

• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• henssenlab / TreeShapedRearrangements
  Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)
  ☆15Updated 4 years ago
• gxiaolab / scAllele
  ☆33Updated last year
• AlexandrovLab / SigProfilerTopography
  SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…
  ☆19Updated 2 months ago
• Henikoff / scCUT-Tag
  ☆16Updated last year
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• seasoncloud / Alleloscope
  Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separ…
  ☆29Updated 2 years 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
• UPSUTER / GEMLI
  ☆30Updated 3 months ago
• wenweixiong / MARVEL
  ☆49Updated 9 months ago
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆24Updated last month
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆23Updated 4 months ago
• theislab / hadge
  Comprehensive pipeline for donor demultiplexing in single cell
  ☆24Updated 11 months ago
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆25Updated 6 months ago
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year
• lanagarmire / SSrGE
  ☆34Updated 5 years ago
• Mayrlab / scUTRquant
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification
  ☆22Updated 5 months ago
• lkmklsmn / MitoTrace
  ☆17Updated 10 months ago
• navinlabcode / ACT_paper
  Scripts used for the ACT paper
  ☆12Updated 3 years ago
• KChen-lab / MEDALT
  Inference of Minimal Event Distance Aneuploidy Lineage Tree based on single cell copy number profile
  ☆19Updated last year
• favilaco / deconv_matching_bulk_scnRNA
  Repository for "Effective methods for bulk RNA-seq deconvolution using scRNA-seq and snRNA-seq derived transcriptomes"
  ☆15Updated last year
• UMCUGenetics / primary-met-wgs-comparison
  Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.
  ☆15Updated last year
• yjzhang / split-seq-pipeline
  ☆21Updated 5 years ago
• nghiavtr / SCmut
  ☆32Updated 5 years ago
• aet21 / EpiSCORE
  Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
  ☆31Updated last month
• Teichlab / gene2probe
  Pipeline for designing custom probes against human genes
  ☆16Updated 5 months ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated last year
• 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