Bioinformatics tools

  • bpipe - A tool for running and managing bioinformatics pipelines

Transcriptomics

  • 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.

Cancer

  • 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

Genomics

  • 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.

Methylation

  • missMethyl - Bioconductor package for analysing data from Illumina‚Äôs methylation arrays