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@cancerit

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 68 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 91 repositories
  • NanoSeq Public

    Analysis software for Nanorate Sequencing (NanoSeq) experiments

    cancerit/NanoSeq’s past year of commit activity
    C++ 12 AGPL-3.0 8 11 2 Updated Sep 13, 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
  • cgpRna Public
    cancerit/cgpRna’s past year of commit activity
    Perl 5 AGPL-3.0 4 7 1 Updated Aug 30, 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 Aug 27, 2024
  • ta_analyser Public

    script to analyse ta repeats coverage calculated using samtools bedcov

    cancerit/ta_analyser’s past year of commit activity
    Python 0 GPL-3.0 0 0 4 Updated Aug 26, 2024
  • dockstore-cgpmap Public

    Mapping using PCAP

    cancerit/dockstore-cgpmap’s past year of commit activity
    Common Workflow Language 6 AGPL-3.0 11 7 0 Updated Aug 19, 2024
  • PCAP-core Public

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

    cancerit/PCAP-core’s past year of commit activity
    Perl 9 GPL-2.0 10 8 2 Updated Aug 9, 2024
  • cgpBigWig Public

    BigWig manpulation tools using libBigWig and htslib

    cancerit/cgpBigWig’s past year of commit activity
    C 28 AGPL-3.0 7 7 1 Updated Aug 8, 2024
  • BRASS Public

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

    cancerit/BRASS’s past year of commit activity
    Perl 57 AGPL-3.0 20 16 0 Updated Jul 19, 2024
  • pyCRISPRcleanR Public

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

    cancerit/pyCRISPRcleanR’s past year of commit activity
    Python 4 GPL-3.0 0 0 7 Updated Jul 16, 2024
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