@cancerit

Cancer IT

Bioinformatic support for Cancer, Ageing and Somatic Mutation group at the Wellcome Trust Sanger Institute

Pinned repositories

  1. ascatNgs

    Somatic copy number analysis using paired end wholegenome sequencing

    Perl 29 8

  2. BRASS

    Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.

    Perl 22 8

  3. cgpPindel

    Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

    Perl 11 5

  4. cgpCaVEManWrapper

    Reference implementation of CGP workflow for CaVEMan SNV analysis

    Perl 2 1

  5. proportionalmultibw

    JBrowse plugin to display multiple BigWig tracks as a stacked proportion

    JavaScript 4 1

  6. VAGrENT

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

    Perl 5 3

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

    Perl 11 5 AGPL-3.0 Updated Sep 21, 2018
  • 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 28 6 AGPL-3.0 Updated Sep 21, 2018
  • Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting

    Python GPL-3.0 Updated Sep 20, 2018
  • NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)

    Perl 2 6 GPL-2.0 Updated Sep 20, 2018
  • Flagging add on to CaVEMan

    Perl 3 AGPL-3.0 Updated Sep 11, 2018
  • WDL descriptor for BRASS

    wdl AGPL-3.0 Updated Sep 10, 2018
  • Holds publicly useful scripts and tools for JBrowse users and admins

    JavaScript 1 1 AGPL-3.0 Updated Aug 24, 2018
  • Dockstore implementation of CGP core WGS analysis

    Shell 3 7 AGPL-3.0 Updated Aug 16, 2018
  • The tools is used to extract PPCG defined QC metrics from Sanger variant calling pipeline results.

    Python AGPL-3.0 Updated Aug 10, 2018
  • Compares pair of archives, files and folders using user configured tools

    Python Updated Aug 10, 2018
  • dockstore tool for running GRIDSS

    Shell GPL-3.0 Updated Aug 8, 2018
  • Pipeline for processing inDrops sequencing data

    Python 20 Updated Aug 7, 2018
  • Reference implementation of CGP workflow for CaVEMan SNV analysis

    Perl 2 1 AGPL-3.0 Updated Jul 31, 2018
  • Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.

    Perl 22 8 AGPL-3.0 Updated Jul 25, 2018
  • Calculates the Variant Allele Fraction of variants in VCF files

    Perl 3 3 AGPL-3.0 Updated Jul 13, 2018
  • JBrowse plugin to display multiple BigWig tracks as a stacked proportion

    JavaScript 4 1 AGPL-3.0 Updated Jul 6, 2018
  • Gossamer bioinformatics suite

    C++ 6 Updated Jun 5, 2018
  • Dockersised pyCRISPRcleanR

    Common Workflow Language AGPL-3.0 Updated May 21, 2018
  • Dockstore implementation of CGP core WXS analysis

    Shell 2 2 AGPL-3.0 Updated May 4, 2018
  • Mapping using PCAP

    Visual Basic 2 7 AGPL-3.0 Updated May 4, 2018
  • Dockstore implementation of cgpBigWig utility

    Common Workflow Language GPL-3.0 Updated May 4, 2018
  • Dockstore workflows to import sequencing files

    Common Workflow Language GPL-3.0 Updated May 3, 2018
  • cgp-chksum produces md5sum and sha512sum of a file, and optionally POST results

    Shell AGPL-3.0 Updated Apr 25, 2018
  • BigWig manpulation tools using libBigWig and htslib

    C 15 3 AGPL-3.0 Updated Apr 20, 2018
  • Object-oriented Perl library for somatic rearrangement analysis

    Perl AGPL-3.0 Updated Apr 16, 2018
  • Contains scripts and packer builds for cgp-dockstore and Openstack builds

    Shell 1 1 AGPL-3.0 Updated Apr 13, 2018
  • A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

    Perl 5 3 AGPL-3.0 Updated Apr 9, 2018
  • Somatic copy number analysis using paired end wholegenome sequencing

    Perl 29 8 AGPL-3.0 Updated Mar 27, 2018
  • Gene Rearrangement AnalySiS

    Perl 5 1 AGPL-3.0 Updated Mar 27, 2018
  • Perl 3 3 AGPL-3.0 Updated Mar 26, 2018