Repositories list

• NanoSeq

  Public
  Analysis software for Nanorate Sequencing (NanoSeq) experiments

  C++

  •

  GNU Affero General Public License v3.0

  •1515 forks in cancerit/NanoSeq•3636 stars in cancerit/NanoSeq•2525 issues in cancerit/NanoSeq•44 pull requests in cancerit/NanoSeq•Updated Oct 14, 2026Oct 14, 2026

• hairpin2

  Public
  artefact flagging algorithm based on Ellis et al. 2020 (DOI: 10.1038/s41596-020-00437-6) for LCM sequencing

  Python

  •

  Other

  •00 forks in cancerit/hairpin2•33 stars in cancerit/hairpin2•22 issues in cancerit/hairpin2•88 pull requests in cancerit/hairpin2•Updated Jun 22, 2026Jun 22, 2026

• pyQUEST

  Public
  Python

  •

  GNU General Public License v3.0

  •22 forks in cancerit/pyQUEST•00 stars in cancerit/pyQUEST•00 issues in cancerit/pyQUEST•00 pull requests in cancerit/pyQUEST•Updated Apr 29, 2026Apr 29, 2026

• annotateVCF

  Public
  Annotate vcf file using user supplied data

  Python

  •

  GNU General Public License v3.0

  •00 forks in cancerit/annotateVCF•00 stars in cancerit/annotateVCF•00 issues in cancerit/annotateVCF•55 pull requests in cancerit/annotateVCF•Updated Apr 13, 2026Apr 13, 2026

• pileup-events

  Public
  modernised implementation of bam2R from the deepSNV R library. Standalone tool + R and Python bindings

  C++

  •

  MIT License

  •00 forks in cancerit/pileup-events•22 stars in cancerit/pileup-events•00 issues in cancerit/pileup-events•00 pull requests in cancerit/pileup-events•Updated Apr 4, 2026Apr 4, 2026

• LUCA

  Public
  Locus-based Universal CRISPR Aligner

  Python

  •

  GNU General Public License v3.0

  •00 forks in cancerit/LUCA•11 star in cancerit/LUCA•00 issues in cancerit/LUCA•00 pull requests in cancerit/LUCA•Updated Feb 27, 2026Feb 27, 2026

• pygas

  Public
  python Guide aligned Sequences

  bioinformaticsalignmentcrispr

  bioinformaticsalignmentcrispr

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks in cancerit/pygas•11 star in cancerit/pygas•00 issues in cancerit/pygas•22 pull requests in cancerit/pygas•Updated Dec 18, 2025Dec 18, 2025

• jbrowse-registry

  Public
  JBrowse Plugin Registry

  HTML

  •

  BSD 2-Clause "Simplified" License

  •88 forks in cancerit/jbrowse-registry•00 stars in cancerit/jbrowse-registry•00 issues in cancerit/jbrowse-registry•1010 pull requests in cancerit/jbrowse-registry•Updated Dec 6, 2025Dec 6, 2025

• parabam

  Public
  parabam

  Cython

  •

  Other

  •22 forks in cancerit/parabam•00 stars in cancerit/parabam•44 issues in cancerit/parabam•22 pull requests in cancerit/parabam•Updated Oct 23, 2025Oct 23, 2025

• swPipe

  Public
  Snakemake pipeline leveraging ultra-deep sequencing for low sub-clonal mutation calling

  00 forks in cancerit/swPipe•00 stars in cancerit/swPipe•00 issues in cancerit/swPipe•00 pull requests in cancerit/swPipe•Updated Sep 18, 2025Sep 18, 2025

• SComatic

  Public
  A tool for detecting somatic variants in single cell data

  Python

  •

  Other

  •3535 forks in cancerit/SComatic•11 star in cancerit/SComatic•00 issues in cancerit/SComatic•00 pull requests in cancerit/SComatic•Updated Sep 13, 2025Sep 13, 2025

• CRISPResso2

  Public
  Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

  Python

  •

  Other

  •120120 forks in cancerit/CRISPResso2•11 star in cancerit/CRISPResso2•00 issues in cancerit/CRISPResso2•00 pull requests in cancerit/CRISPResso2•Updated Sep 5, 2025Sep 5, 2025

• hairpin-wrapper

  Public archive
  Ease-of-use wrapper around Mathijs' Sanders AdditionalBamStatistics cruciform-DNA detection algorithm

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks in cancerit/hairpin-wrapper•00 stars in cancerit/hairpin-wrapper•00 issues in cancerit/hairpin-wrapper•00 pull requests in cancerit/hairpin-wrapper•Updated Jul 31, 2025Jul 31, 2025

• wgbs_tools

  Public
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

  Python

  •

  Other

  •5959 forks in cancerit/wgbs_tools•00 stars in cancerit/wgbs_tools•00 issues in cancerit/wgbs_tools•00 pull requests in cancerit/wgbs_tools•Updated Jun 18, 2025Jun 18, 2025

• pyCRISPRcleanR

  Public
  Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting

  Python

  •

  GNU General Public License v3.0

  •00 forks in cancerit/pyCRISPRcleanR•77 stars in cancerit/pyCRISPRcleanR•00 issues in cancerit/pyCRISPRcleanR•99 pull requests in cancerit/pyCRISPRcleanR•Updated Jun 11, 2025Jun 11, 2025

• cgpPindel

  Public
  Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

  Perl

  •

  GNU Affero General Public License v3.0

  •66 forks in cancerit/cgpPindel•2828 stars in cancerit/cgpPindel•1010 issues in cancerit/cgpPindel•22 pull requests in cancerit/cgpPindel•Updated May 14, 2025May 14, 2025

• QUANTS

  Public
  Python

  •

  MIT License

  •66 forks in cancerit/QUANTS•11 star in cancerit/QUANTS•33 issues in cancerit/QUANTS•00 pull requests in cancerit/QUANTS•Updated May 12, 2025May 12, 2025

• CASM-Smart-Phase

  Public
  Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks in cancerit/CASM-Smart-Phase•11 star in cancerit/CASM-Smart-Phase•00 issues in cancerit/CASM-Smart-Phase•44 pull requests in cancerit/CASM-Smart-Phase•Updated May 3, 2025May 3, 2025

• CaVEMan

  Public
  SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam a…

  C

  •

  GNU Affero General Public License v3.0

  •1818 forks in cancerit/CaVEMan•8585 stars in cancerit/CaVEMan•2222 issues in cancerit/CaVEMan•11 pull request in cancerit/CaVEMan•Updated Apr 24, 2025Apr 24, 2025

• vafCorrect

  Public
  Calculates the Variant Allele Fraction of variants in VCF files

  Perl

  •

  GNU Affero General Public License v3.0

  •33 forks in cancerit/vafCorrect•1919 stars in cancerit/vafCorrect•66 issues in cancerit/vafCorrect•00 pull requests in cancerit/vafCorrect•Updated Nov 28, 2024Nov 28, 2024

• cgp-methpipe

  Public
  CGP implementation of Nextflow methylseq

  Shell

  •11 fork in cancerit/cgp-methpipe•00 stars in cancerit/cgp-methpipe•11 issue in cancerit/cgp-methpipe•00 pull requests in cancerit/cgp-methpipe•Updated Nov 18, 2024Nov 18, 2024

• cgpCaVEManWrapper

  Public
  Reference implementation of CGP workflow for CaVEMan SNV analysis

  Perl

  •

  GNU Affero General Public License v3.0

  •44 forks in cancerit/cgpCaVEManWrapper•99 stars in cancerit/cgpCaVEManWrapper•99 issues in cancerit/cgpCaVEManWrapper•00 pull requests in cancerit/cgpCaVEManWrapper•Updated Nov 15, 2024Nov 15, 2024

• lowinputtrees

  Public
  Python

  •

  MIT License

  •22 forks in cancerit/lowinputtrees•00 stars in cancerit/lowinputtrees•11 issue in cancerit/lowinputtrees•00 pull requests in cancerit/lowinputtrees•Updated Oct 30, 2024Oct 30, 2024

• cgpRna

  Public
  Perl

  •

  GNU Affero General Public License v3.0

  •44 forks in cancerit/cgpRna•55 stars in cancerit/cgpRna•77 issues in cancerit/cgpRna•11 pull request in cancerit/cgpRna•Updated Aug 30, 2024Aug 30, 2024

• ta_analyser

  Public
  script to analyse ta repeats coverage calculated using samtools bedcov

  Python

  •

  GNU General Public License v3.0

  •00 forks in cancerit/ta_analyser•00 stars in cancerit/ta_analyser•00 issues in cancerit/ta_analyser•44 pull requests in cancerit/ta_analyser•Updated Aug 26, 2024Aug 26, 2024

• dockstore-cgpmap

  Public
  Mapping using PCAP

  bwa-membiobambam2

  bwa-membiobambam2

  Common Workflow Language

  •

  GNU Affero General Public License v3.0

  •1010 forks in cancerit/dockstore-cgpmap•55 stars in cancerit/dockstore-cgpmap•77 issues in cancerit/dockstore-cgpmap•00 pull requests in cancerit/dockstore-cgpmap•Updated Aug 19, 2024Aug 19, 2024

• PCAP-core

  Public
  NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)

  Perl

  •

  GNU General Public License v2.0

  •99 forks in cancerit/PCAP-core•99 stars in cancerit/PCAP-core•1010 issues in cancerit/PCAP-core•22 pull requests in cancerit/PCAP-core•Updated Aug 9, 2024Aug 9, 2024

• cgpBigWig

  Public
  BigWig manpulation tools using libBigWig and htslib

  coveragebioinformaticsbigwig+ 3

  coveragebioinformaticsbigwightslibbioinformatics-analysislibbigwig

  C

  •

  GNU Affero General Public License v3.0

  •77 forks in cancerit/cgpBigWig•3030 stars in cancerit/cgpBigWig•77 issues in cancerit/cgpBigWig•22 pull requests in cancerit/cgpBigWig•Updated Aug 8, 2024Aug 8, 2024

• BRASS

  Public
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

  Perl

  •

  GNU Affero General Public License v3.0

  •1919 forks in cancerit/BRASS•6161 stars in cancerit/BRASS•1717 issues in cancerit/BRASS•00 pull requests in cancerit/BRASS•Updated Jul 19, 2024Jul 19, 2024

• C-SAR

  Public archive
  Data will be added ahead of poster/conference

  Nextflow

  •

  GNU Affero General Public License v3.0

  •00 forks in cancerit/C-SAR•11 star in cancerit/C-SAR•22 issues in cancerit/C-SAR•55 pull requests in cancerit/C-SAR•Updated Jul 16, 2024Jul 16, 2024