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    98 repositories

    • parabam

      Public
      parabam
      Cython
      •1•0•4•2•Updated Oct 14, 2025Oct 14, 2025

    • hairpin2

      Public
      artefact flagging algorithm based on Ellis et al. 2020 (DOI: 10.1038/s41596-020-00437-6) for LCM sequencing
      Python
      •
      Other
      •0•3•2•2•Updated Oct 13, 2025Oct 13, 2025

    • NanoSeq

      Public
      Analysis software for Nanorate Sequencing (NanoSeq) experiments
      C++
      •
      GNU Affero General Public License v3.0
      •15•28•20•3•Updated Sep 19, 2025Sep 19, 2025

    • swPipe

      Public
      Snakemake pipeline leveraging ultra-deep sequencing for low sub-clonal mutation calling
      0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • SComatic

      Public
      A tool for detecting somatic variants in single cell data
      Python
      •
      Other
      •32•1•0•0•Updated Sep 13, 2025Sep 13, 2025

    • CRISPResso2

      Public
      Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
      Python
      •
      Other
      •107•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • annotateVCF

      Public
      Annotate vcf file using user supplied data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•4•Updated Aug 22, 2025Aug 22, 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
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

    • LUCA

      Public
      Locus-based Universal CRISPR Aligner
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • wgbs_tools

      Public
      tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
      Python
      •
      Other
      •48•0•0•0•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
      •0•6•0•9•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
      •5•28•10•2•Updated May 14, 2025May 14, 2025

    • QUANTS

      Public
      Python
      •
      MIT License
      •5•1•3•0•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
      •0•1•0•4•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 and cram format via htslib
      C
      •
      GNU Affero General Public License v3.0
      •13•63•22•1•Updated Apr 24, 2025Apr 24, 2025

    • jbrowse-registry

      Public
      JBrowse Plugin Registry
      HTML
      •
      BSD 2-Clause "Simplified" License
      •8•0•0•9•Updated Jan 16, 2025Jan 16, 2025

    • vafCorrect

      Public
      Calculates the Variant Allele Fraction of variants in VCF files
      Perl
      •
      GNU Affero General Public License v3.0
      •3•19•6•0•Updated Nov 28, 2024Nov 28, 2024

    • cgp-methpipe

      Public
      CGP implementation of Nextflow methylseq
      Shell
      •1•0•1•0•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
      •3•7•9•0•Updated Nov 15, 2024Nov 15, 2024

    • lowinputtrees

      Public
      Python
      •
      MIT License
      •2•0•1•0•Updated Oct 30, 2024Oct 30, 2024

    • cgpRna

      Public
      Perl
      •
      GNU Affero General Public License v3.0
      •4•5•7•1•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
      •0•0•0•4•Updated Aug 26, 2024Aug 26, 2024

    • dockstore-cgpmap

      Public
      Mapping using PCAP
      bwa-membiobambam2
      Common Workflow Language
      •
      GNU Affero General Public License v3.0
      •11•6•7•0•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
      •9•9•10•2•Updated Aug 9, 2024Aug 9, 2024

    • cgpBigWig

      Public
      BigWig manpulation tools using libBigWig and htslib
      coveragebioinformaticsbigwightslibbioinformatics-analysislibbigwig
      C
      •
      GNU Affero General Public License v3.0
      •7•29•7•2•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
      •20•57•17•0•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
      •0•1•2•5•Updated Jul 16, 2024Jul 16, 2024

    • dockstore-pyCRISPRcleanR

      Public archive
      Dockersised pyCRISPRcleanR
      Common Workflow Language
      •
      GNU Affero General Public License v3.0
      •1•0•0•6•Updated Jul 16, 2024Jul 16, 2024

    • cgp_seq_input_val

      Public
      Sequence data and manifest validation code.
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•0•3•Updated Jul 16, 2024Jul 16, 2024

    • pycroquet

      Public
      python Crispr Read to Oligo QUantification and Evaluation Tool
      bioinformaticscrisprquantification
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •1•2•1•2•Updated Jul 10, 2024Jul 10, 2024