The following tools are developed by the Bioinformatics Core.
DiffBind
R/Bioconductor package for differential binding analysis of ChIP-seq data.
GreyListChIP
R/Bioconductor package for identifying genomic regions with spurious high signals in ChIP-seq experiments.
SigCheck
R/Bioconductor package for checking the prognostic performance of a gene signature.
survivalMPL
R package for analysis of survival data using a maximum penalized likelihood approach.
Statistics Shiny apps
Interactive web applications for demonstrating the central limit theorem and carrying out basic statistical tests.
BCAPE
Shiny web application and R processing scripts for the Breast Cancer PDTX Encyclopaedia (BCaPE).
ClarityClient
Java package providing a programmatic interface to the REST API for the Clarity LIMS.
Rascal
Shiny web application for estimating ploidy and cellularity from tumour copy number profiles.
Ampliconseq
Variant calling pipeline for amplicon sequencing data.
qPLEXanalyzer
R/Bioconductor package providing a toolkit for statistical analysis of qPLEX-RIME proteomics data.
MGA
Contaminant screen quality control tool for high-throughput sequencing data.
camcAPP
Shiny web application for exploring prostate cancer datasets.
