- bpipe - A tool for running and managing bioinformatics pipelines
- Corset - Go from a de novo transcriptome assembly to gene-level counts.
- Lace - A tool for constructing superTranscripts: a single linear representation of a gene built from constituent transcripts, retaining all exonic sequence in transcriptional order.
- Necklace - Combine reference and assembled transcriptomes for RNA-Seq analysis.
- GOseq - Bioconductor package: Gene Ontology analyser for RNA-seq and other length biased data
- Splatter - Bioconductor package for the simple simulation of single-cell RNA-seq count data.
- clinker - A gene fusion visualiser tool.
- JAFFA - A multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions.
- AllSorts - An Acute Lymphoblasitc Leukemia B-Cell classifier
- Cpipe - An exome sequencing pipeline developed for analysis of exome and targeted sequencing data that is specialised for clinical purposes.
- Ximmer - A tool for evaluating, running and viewing results of CNV callers for exome and targeted sequencing data
- Schism - A tool for discovering novel, complex, pathogenic structural variation in whole
genome sequencing data.
- STRetch - A method for detecting and discovering pathogenic short tandem repeats expansions.
- missMethyl - Bioconductor package for analysing data from Illumina’s methylation arrays