CRUK Cambridge Institute - Bioinformatics Core
The Bioinformatics Core of the Cancer Research UK Cambridge Institute. Part of the University of Cambridge.
Cambridge, UK
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The original version of MGA has been archived - please see https://github.com/crukci-bioinformatics/mga2 instead.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/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/ampliconseq
Variant calling pipeline for amplicon sequencing data
crukci-bioinformatics/PlateLayout
Plate randomistation using R
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/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/BamHeaderToRefflat
crukci-bioinformatics/bamMergeByScore
Merge BAM files, keeping the best hit for each read
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/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/nf_preprocess_scSeq_CRUKCI
Download single cell data from Genomics server and process with CellRanger - specific to CRUK CI infrastructure
crukci-bioinformatics/nf_trim_fastq
Trims fastq files for adapter content etc. using fastp
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/struts-annotations
Mirror of Apache Struts Annotations
crukci-bioinformatics/struts2-jquery
Struts2 jQuery Plugin, converted for EE 10