Pinned Repositories
ampliconseq
Variant calling pipeline for amplicon sequencing data
camcAPP
shiny app to explore various prostate cancer datasets
clarityclient
A Java client for working with Genologics' REST API.
gatk-tools
Utilities for processing sequencing data and genomic variants using GATK
Genome_Biology_scripts
MGA
The original version of MGA has been archived - please see https://github.com/crukci-bioinformatics/mga2 instead.
mga2
Multi-genome alignment contaminant screen for high-throughput sequence data
multiqc_mga2_plugin
MultiQC Plugin for MGA 2
PlateLayout
Plate randomistation using R
rascal
R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.
CRUK Cambridge Institute - Bioinformatics Core's Repositories
crukci-bioinformatics/MGA
The original version of MGA has been archived - please see https://github.com/crukci-bioinformatics/mga2 instead.
crukci-bioinformatics/rascal
R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.
crukci-bioinformatics/clarityclient
A Java client for working with Genologics' REST API.
crukci-bioinformatics/PlateLayout
Plate randomistation using R
crukci-bioinformatics/ampliconseq
Variant calling pipeline for amplicon sequencing data
crukci-bioinformatics/mga2
Multi-genome alignment contaminant screen for high-throughput sequence data
crukci-bioinformatics/camcAPP
shiny app to explore various prostate cancer datasets
crukci-bioinformatics/BCaPE
R/Shiny app for Breast Cancer PDTX Encyclopaedia
crukci-bioinformatics/multiqc_mga2_plugin
MultiQC Plugin for MGA 2
crukci-bioinformatics/nf-alignment
Nextflow based alignment pipeline
crukci-bioinformatics/qPLEXanalyzer
qPLEXanalyzer: Tools for qPLEX-RIME data analysis
crukci-bioinformatics/shiny-base
Base Docker image for Shiny applications
crukci-bioinformatics/BamHeaderToRefflat
crukci-bioinformatics/bamMergeByScore
Merge BAM files, keeping the best hit for each read
crukci-bioinformatics/clarityclient-cache
Modularisation of the Clarity Client: separating the cache into its own project.
crukci-bioinformatics/clarityclient-recorder
A recording and playback wrapper around our ClarityClient for creating and executing unit tests.
crukci-bioinformatics/clarityclient2
EE10 and modularisation update to the Java Clarity Client.
crukci-bioinformatics/GreyListChIP
Bioconductor package: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
crukci-bioinformatics/htsjdk-tools
Command-line tools for processing high-throughput sequencing (HTS) data and genomic variants using the HTSJDK library.
crukci-bioinformatics/mga-referencebuilder
crukci-bioinformatics/multiqc_mga_plugin
Multi Genome Alignment plugin for MultiQC
crukci-bioinformatics/nextflow-support
Scripts and functions that are helpful in Nextflow pipelines.
crukci-bioinformatics/nf-referencebuilder
crukci-bioinformatics/nf-rnaseq
The Nextflow pipeline for quantifying RNAseq data using salmon
crukci-bioinformatics/permCheck
Report files and directories that do not follow permission rules.
crukci-bioinformatics/pod5split
Splitting tool for ONT Pod5 files
crukci-bioinformatics/redmine_common
Common code for CRUK-CI Bioinformatics Core Redmine plugins
crukci-bioinformatics/rnaseqRcode
R code for nf-rnaseq pipeline
crukci-bioinformatics/shinystats
Shiny app for one- and two-sample statistical tests
crukci-bioinformatics/struts2-jquery
Struts2 jQuery Plugin, converted for EE 10