Transcriptomics

Corset

Go from a de novo transcriptome assembly to gene-level counts

Oshlack/Corset

Lace

A tool for constructing superTranscripts, a single linear representation of a gene built from constituent transcripts, retaining all exonic sequence in transcriptional order

Oshlack/Lace

Necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis

Oshlack/Necklace

GOseq

Gene Ontology analyser for RNA-seq and other length biased data

bioc/goseq

Splatter

Simple simulation of single-cell RNA-seq count data

bioc/splatter

Oshlack/splatter

Clinker

A gene fusion visualisation tool

Oshlack/Clinker

Cancer

JAFFA

A multi-step pipeline that takes either raw RNA-Seq reads or pre-assembled transcripts, then searches for gene fusions

Oshlack/JAFFA

AllSorts

An Acute Lymphoblasitc Leukemia B-Cell classifier

Oshlack/AllSorts

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/

MelbourneGenomics/cpipe

Ximmer

A tool for evaluating, running and viewing results of CNV callers for exome and targeted sequencing data

http://ximmer.org/

ssadedin/ximmer

Schism

A tool for discovering novel, complex, pathogenic structural variation in whole genome sequencing data

ssadedin/schism

STRetch

A method for detecting and discovering pathogenic short tandem repeat expansions

Oshlack/STRetch

Methylation

missMethyl

Bioconductor package for analysing data from Illumina's methylation arrays

bioc/missMethyl

Oshlack/missMethyl

Other tools

bpipe

A tool for running and managing bioinformatics pipelines

http://docs.bpipe.org/

ssadedin/bpipe

scRNA-tools

A database of tools for the analysis of single-cell RNA-sequencing data

https://www.scrna-tools.org/

Oshlack/scRNA-tools

clustree

An R package for creating clustering trees, a visualisation for interrogating clusterings at increasing resolutions

CRAN/clustree

lazappi/clustree