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CASM IT

CASM IT provide bioinformatic support for Cancer, Ageing and Somatic Mutation group at the Wellcome Sanger Institute

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  1. ascatNgs ascatNgs Public

    Somatic copy number analysis using WGS paired end wholegenome sequencing

    Perl 69 17

  2. BRASS BRASS Public

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

    Perl 57 20

  3. cgpPindel cgpPindel Public

    Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

    Perl 28 5

  4. cgpCaVEManWrapper cgpCaVEManWrapper Public

    Reference implementation of CGP workflow for CaVEMan SNV analysis

    Perl 6 3

  5. proportionalmultibw proportionalmultibw Public

    JBrowse plugin to display multiple BigWig tracks as a stacked proportion

    JavaScript 3 1

  6. VAGrENT VAGrENT Public

    A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

    Perl 8 7

Repositories

Showing 10 of 93 repositories
  • jbrowse-registry Public Forked from GMOD/jbrowse-registry

    JBrowse Plugin Registry

    cancerit/jbrowse-registry’s past year of commit activity
    HTML 0 BSD-2-Clause 8 0 8 Updated Dec 4, 2024
  • vafCorrect Public

    Calculates the Variant Allele Fraction of variants in VCF files

    cancerit/vafCorrect’s past year of commit activity
    Perl 19 AGPL-3.0 3 6 0 Updated Nov 28, 2024
  • QUANTS Public
    cancerit/QUANTS’s past year of commit activity
    Python 1 MIT 3 3 0 Updated Nov 28, 2024
  • NanoSeq Public

    Analysis software for Nanorate Sequencing (NanoSeq) experiments

    cancerit/NanoSeq’s past year of commit activity
    C++ 16 AGPL-3.0 9 12 4 Updated Nov 20, 2024
  • cgp-methpipe Public

    CGP implementation of Nextflow methylseq

    cancerit/cgp-methpipe’s past year of commit activity
    Shell 0 1 1 0 Updated Nov 19, 2024
  • cgpCaVEManWrapper Public

    Reference implementation of CGP workflow for CaVEMan SNV analysis

    cancerit/cgpCaVEManWrapper’s past year of commit activity
    Perl 6 AGPL-3.0 3 7 0 Updated Nov 15, 2024
  • hairpin2 Public

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

    cancerit/hairpin2’s past year of commit activity
    Python 0 0 0 0 Updated Nov 5, 2024
  • lowinputtrees Public Forked from Phuong-Le/process_sanger_lcm-nf
    cancerit/lowinputtrees’s past year of commit activity
    Python 0 MIT 2 1 0 Updated Oct 30, 2024
  • 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

    cancerit/CaVEMan’s past year of commit activity
    C 60 AGPL-3.0 13 18 1 Updated Oct 25, 2024
  • cgpPindel Public

    Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

    cancerit/cgpPindel’s past year of commit activity
    Perl 28 AGPL-3.0 5 10 2 Updated Sep 9, 2024
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