Alternatives and similar repositories for CNApp:

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

• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• shbrief / CNVWorkflow_Code
  CNV analysis workflow code for the manuscript
  ☆13Updated 4 years ago
• markowetzlab / CINSignatureQuantification
  Quantifying copy number signatures from absolute copy number profiles
  ☆23Updated 3 weeks ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 3 years ago
• gxiaolab / REDITs
  RNA editing tests
  ☆16Updated 4 years ago
• quevedor2 / aneuploidy_score
  R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…
  ☆16Updated 3 years ago
• campbio / Manuscripts
  ☆14Updated 2 years ago
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated 2 weeks ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago
• AlexandrovLab / SigProfilerTopography
  SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…
  ☆19Updated last month
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 3 months ago
• amf71 / ECLIPSE
  ☆11Updated last year
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆28Updated 5 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• slagtermaarten / LOHHLA
  Fork of https://bitbucket.org/mcgranahanlab/lohhla
  ☆16Updated 4 years ago
• farkkilab / scarHRD
  Package for calculation of Homologous Recombination Deficiency
  ☆13Updated 4 years ago
• navinlabcode / ACT_paper
  Scripts used for the ACT paper
  ☆12Updated 3 years ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆28Updated 2 years ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆27Updated 2 years ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• getzlab / MutSig2CV
  MutSig2CV from Lawrence et al. 2014
  ☆30Updated 4 years ago
• raphael-group / decifer
  DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…
  ☆20Updated 7 months ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• jw156605 / SingleSplice
  Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: h…
  ☆21Updated 8 years ago
• gerstung-lab / PCAWG-11
  Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)
  ☆17Updated 5 years ago
• henssenlab / TreeShapedRearrangements
  Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)
  ☆15Updated 4 years ago
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆21Updated last year
• wenweixiong / MARVEL
  ☆45Updated 5 months ago
• sfu-compbio / citup
  Clonality Inference in Multiple Tumor Samples using Phylogeny
  ☆13Updated 9 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year