ELDA: Extreme Limiting Dilution Analysis
Fit single-hit model to a dilution series using complementary log-log binomial regression.

Compare Groups of Growth Curves
Compare Groups of Growth Curves performs a permutation test of the difference between two groups of growth curves. It calculates all pairwise comparisons between two or more groups of growth curves.

Gene Mapping and Linkage

Linkdatagen *updated July 2011*
Performs QC and generates output formats from many common Affymetrix and Illumina SNP chips, as well as NGS/MPS data. Output formats include MERLIN, ALLEGRO, PLINK, MORGAN, FEstim and PREST. Different HAPMAP populations can be chosen as the source of marker allele frequencies.

XIBD *updated Oct 2015*
XIBD (X chromosome Identity by Descent) detects identity by descent using dense SNP chip data on the X chromosome.

Gene Prioritisation for candidate genes from linkage, association or NGS studies, specifically for brain disorders using the Allen Humna Brain Atlas data.

Age of mutation estimation
R Shiny app, also available as the original R script which performs the calculations required to produce mutation age estimates and confidence intervals using the method described in Gandolfo, L. C., Bahlo, M., and Speed, T. P. (2014). Dating rare mutations from small samples with dense marker data. Genetics, 197(4): 1315-27.

Creating LINKAGE style .pre and .dat files from AGRF style data. This creates standard format input files for linkage analysis software from human genotyping data.

Performs genome linkage disequilibrium (LD) mapping with case and control haplotype data with both microsatellite and SNP markers.

Genotype-Based Identification of Relative Pairs - identifies pairs of individuals who may be related to each other by comparing their genotypes.

A script that calculates two measures of the efficiency of a genome- wide mutation screen for recessive phenotypes and performs simulations to confirm results

EffiSim Web Interface
This is a web interface to the EffiSim script above.

Quantitative Trait Haplotype Analysis
A program to test whether a quantitative trait loci is in the vicinity of a number of markers that are fully linked with each other.


An R Library for Linear Models for Microarray Data. Uses linear models for analysing designed microarray experiments and for assessing differential expression.

MSigDB Gene Sets
Pure mouse and pure human versions of the MSigDB gene set collections as R lists.

Gender Gene Sets
R version of the Gender gene sets.

An R Library for Statistical Modelling and biostatistical analysis including comparison of growth curves and the analysis of randomized block designs.

An R Library for preprocessing Illumina Whole Genome Expression BeadChips.

Finding Isoforms with Robust Multichip Analysis. R code for analysing Affymetrix exon arrays. Estimates gene expression and calculates scores for alternative splicing detection.

Next-Gen Sequencing

An R package (empirical analysis of digital gene expression in R) for differential expression (DE) analysis of count data e.g. digital gene expression such as RNA-seq or SAGE data.

An R library for performing Gene Ontology (GO) and other category based tests on RNA-seq data, which corrects for selection bias.

Subread and Subjunc (R version C version)
Subread is a general-purpose read aligner (mapping both gDNA- and RNA-seq reads). It is espeically powerful in mapping RNA-seq reads for the purpose of expression analysis. Subjunc is designed to discover exon-exon junctions from using RNA-seq data. It performs full alignments for RNA-seq reads.

Rsubread annotation files
Annotation files in Subread SAF format or mm10, mm39, hg38 and T2T-CHM13v2.0

Sequence Analysis

Mungo python library
A python library supporting parsing, manipulation and visualisation of sequence analysis results (available via our Github repository).

Socrates is a pure split read-based breakpoint caller, which is designed to be fast and sensitive. It is a highly efficient for detecting genomic rearrangements in tumours, but requires significant downstream filtering by the user. SOCRATES is available via Github.
If you find SOCRATES useful, please cite the SOCRATES publication:
Schroeder J, Hsu A, Boyle SE, MacIntyre G, Cmero M, Tothill RW, Johnstone RW, Shackleton M, Papenfuss AT.
Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
Bioinformatics 2014, 30:8, 1064-1072.
Many of the ideas of SOCRATES have now been re-implemented and extended in GRIDSS.

GRIDSS - Genomic Rearrangement IDentification Software Suite
GRIDSS a modular software suite containing tools useful for the detection genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for i Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence. GRIDSS won the ICGC/TCGA Dream Mutation Calling Challenge #5 SV Sub-challenge in 2015 and is highest ranked as a late entry in the 2014 challenge.
GRIDSS is described in a preprint and currently under review.
GRIDSS is available from Github.

CLOVE - Classification of genomic fusions into structural variation events
CLOVE identifies groups of related breakpoints and classifies them as a particular type of structural variant, e.g. deletion or balanced translocation. CLOVE is available via Github. The CLOVE test data is available here.