Software

R

BaalChIP - allele specific binding

BaalChIP corrects for the effect of background allele frequency on the observed ChIP-seq read counts jointly analyses multiple ChIP-seq samples across a single variant.

... more about BaalChIP

R Python

BitPhylogeny - intra-tumor phylogenies

A probabilistic framework for reconstructing intra-tumor phylogenies. In a full Bayesian approach, we jointly estimate the number and composition of clones as well as the most likely tree connecting them.

... more about BitPhylogeny

R

CRImage - tumour image analysis

Image analysis of histopathologically stained tumour slides.

... more about CRImage

R

DANCE - deregulation of copy-number and expression

Coming soon! DANCE quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.

... more about DANCE

MATLAB

GoIFISH - semi-automated analysis of IFISH images

Analysis of IFISH (Immunofluorescence + Fluorescence in situ Hybridisation) images, performing nuclear, membrane and spot detection in order to quantify heterogeneity at the single cell level.

... more about GoIFISH

R

HTSanalyzeR - Network analysis of high throughput screens

The one stop shop for enrichment and network analyses of high-through- put RNAi screens. Turns cellHTS2 output into annotated tables and graphs.

... more about HTSanalyzeR

R

lol - lots of lassos

Various optimization methods for matrix-to-matrix Lasso inference: cross-validation, randomised lasso, subsampling lasso and others.

... more about lol

Python

MEDICC - intra-patient copy number comparisons

MEDICC harnesses the power of a finite-state automaton representation of genomic profiles to model genomic rearrangement events with horizontal dependencies.

... more about MEDICC

R

nem - Nested Effects Models

NEMs reconstruct features of pathways from the nested structure of perturbation effects. The package unites the software from several labs and represents the current state-of-the-art in Nested Effects Models.

... more about Nested Effects Models

R

oncoNEM - oncogenetic Nested Effects Models

OncoNEM is a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. Built on NEM technology!

... more about oncoNEMs

R

PANR - posterior association networks

The package implements methods to encode posteriori belief of functional association types on edges and phenotypic information on nodes.

... more about PANR

R Java

RedeR - network analysis and visualization

Network Data Integration, Analysis, and Visualization really in a Box. There is no better way to work with networks in R!

... more about RedeR

R

RTN - network reconstruction and analysis

Reconstruction of transcriptional networks including Master Regulator Analysis.

... more about RTN

R

SANTA - Spatial ANalysis of NeTwork Associations

SANTA functionally annotates networks like standard enrichment methods annotate lists of genes.

... more about SANTA

 

Software hosted by collaborators

MATLAB

Patient-specific data fusion

Richard Savage hosts a page to supplement our paper 'Patient-specific data fusion defines prognostic cancer subtypes' from where you can download MATLAB code implementing our clustering method.

... more about PSDF

R

CLOE: phylogenetic clonal deconvolution

Cloe (pronounced like the name Chloƫ) is a computational biology tool to infer the clonal structure of heterogeneous tumour samples. It implements a phylogenetic latent feature model which discovers hierarchically related patterns (clonal genotypes) in the samples, and with these describes the observed mutation data.

... more about CLOE

 

Quick links

Most of our software is written in R and available on Bioconductor:
 
Software @ Bioconductor Data @ Bioconductor Other Repositories