Software
Transcriptomics
Lace
A tool for constructing superTranscripts, a single linear representation of a gene built from constituent transcripts, retaining all exonic sequence in transcriptional order
Cancer
JAFFA
A multi-step pipeline that takes either raw RNA-Seq reads or pre-assembled transcripts, then searches for gene fusions
Single Cell
scRNA-tools
A database of tools for the analysis of single-cell RNA-sequencing data
clustree
An R package for creating clustering trees, a visualisation for interrogating clusterings at increasing resolutions
Genomics
Cpipe
An exome sequencing pipeline developed for analysis of exome and targeted sequencing data that is specialised for clinical purposes
https://melbournegenomics.github.io/
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 repeat expansions
Methylation
missMethyl
Bioconductor package for analysing data from Illumina's methylation arrays
Other tools
bpipe
A tool for running and managing bioinformatics pipelines
Bazam
A tool to extract paired reads in FASTQ format from coordinate sorted BAM files
