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    93 repositories

    • 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

    • QUANTS

      Public
      Python
      •
      MIT License
      •3•1•3•0•Updated Nov 28, 2024Nov 28, 2024

    • NanoSeq

      Public
      Analysis software for Nanorate Sequencing (NanoSeq) experiments
      C++
      •
      GNU Affero General Public License v3.0
      •9•16•11•4•Updated Nov 20, 2024Nov 20, 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•6•7•0•Updated Nov 15, 2024Nov 15, 2024

    • hairpin2

      Public
      artefact flagging algorithm based on Ellis et al. 2020 (DOI: 10.1038/s41596-020-00437-6) for LCM sequencing
      Python
      •
      Other
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • lowinputtrees

      Public
      Python
      •
      MIT License
      •2•0•1•0•Updated Oct 30, 2024Oct 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
      C
      •
      GNU Affero General Public License v3.0
      •13•60•18•1•Updated Oct 25, 2024Oct 25, 2024

    • 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 Sep 9, 2024Sep 9, 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•8•2•Updated Aug 9, 2024Aug 9, 2024

    • cgpBigWig

      Public
      BigWig manpulation tools using libBigWig and htslib
      bioinformaticsbioinformatics-analysislibbigwigcoveragebigwightslib
      C
      •
      GNU Affero General Public License v3.0
      •7•28•7•1•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•16•0•Updated Jul 19, 2024Jul 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
      Python
      •
      GNU General Public License v3.0
      •0•4•0•7•Updated Jul 16, 2024Jul 16, 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

    • 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•3•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

    • annotateVCF

      Public
      Annotate vcf file using user supplied data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•3•Updated Jul 10, 2024Jul 10, 2024

    • pycroquet

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

    • pygas

      Public
      python Guide aligned Sequences
      bioinformaticsalignmentcrispr
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•1•Updated Jul 10, 2024Jul 10, 2024

    • crisprReadCountsPy

      Public
      A tool to count reads for CRISPR.
      Python
      •
      GNU Affero General Public License v3.0
      •1•1•0•1•Updated Jul 10, 2024Jul 10, 2024

    • vcf_flag_modifier

      Public
      Python application to remove specific flags from VCF files
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•2•Updated Jul 10, 2024Jul 10, 2024

    • jbrowse-registry

      Public
      JBrowse Plugin Registry
      HTML
      •
      BSD 2-Clause "Simplified" License
      •8•0•0•7•Updated Jul 3, 2024Jul 3, 2024

    • cgpJBrowseToolkit

      Public
      Holds publicly useful scripts and tools for JBrowse users and admins
      nodegmodpuppeteerjbrowse
      JavaScript
      •
      GNU Affero General Public License v3.0
      •1•1•0•3•Updated Jun 17, 2024Jun 17, 2024

    • CMScallerWrapper

      Public
      This is docker image to run CMScaller from
      GNU General Public License v3.0
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • VaLiAnT

      Public
      Variant Library Annotation Tool (VaLiAnT) is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments
      Python
      •
      GNU Affero General Public License v3.0
      •3•5•0•2•Updated Apr 22, 2024Apr 22, 2024

    • vcfilter

      Public
      Shell
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 22, 2024Feb 22, 2024