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ampliconseq

Variant calling pipeline for amplicon sequencing data

bamheadertorefflat

bammergebyscore

Merge BAM files, keeping the best hit for each read

bcape

R/Shiny app for Breast Cancer PDTX Encyclopaedia

camcapp

shiny app to explore various prostate cancer datasets

clarityclient

A Java client for working with Genologics' REST API.

clarityclient-cache

Modularisation of the Clarity Client: separating the cache into its own project.

clarityclient-recorder

A recording and playback wrapper around our ClarityClient for creating and executing unit tests.

data-champions

Repository for all data champions related activity

docker-crossmap

Docker image for conversion of genome coordinates between assemblies using CrossMap

docker-g4hunter

g4hunter

App related to G4Hunter published in Bedrat et al. NAR 2016

galaxy-annotatemyids

A generic tool to get genomic annotation for a generic set of IDs

galaxy-diffbind

galaxy-fgsea

A galaxy front-end to the Bioconductor fgsea package

galaxy-survival

gatk-tools

Utilities for processing sequencing data and genomic variants using GATK

genome_biology_scripts

greylistchip

Bioconductor package: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

htsjdk-tools

Command-line tools for processing high-throughput sequencing (HTS) data and genomic variants using the HTSJDK library.

mga

The original version of MGA has been archived - please see https://github.com/crukci-bioinformatics/mga2 instead.

mga-referencebuilder

mga2

Multi-genome alignment contaminant screen for high-throughput sequence data

multiqc_mga2_plugin

MultiQC Plugin for MGA 2

multiqc_mga_plugin

Multi Genome Alignment plugin for MultiQC

mutation-demo

nextflow-support

Scripts and functions that are helpful in Nextflow pipelines.

nf-alignment

Nextflow based alignment pipeline

nf-referencebuilder

nf-rnaseq

The Nextflow pipeline for quantifying RNAseq data using salmon