Software
Check out https://github.com/markowetzlab
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.
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.
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.
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.
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.
lol - lots of lassos
Various optimization methods for matrix-to-matrix Lasso inference: cross-validation, randomised lasso, subsampling lasso and others.
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.
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.
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!
PANR - posterior association networks
The package implements methods to encode posteriori belief of functional association types on edges and phenotypic information on nodes.
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!
RTN - network reconstruction and analysis
Reconstruction of transcriptional networks including Master Regulator Analysis.
SANTA - Spatial ANalysis of NeTwork Associations
SANTA functionally annotates networks like standard enrichment methods annotate lists of genes.
VULCAN - VirtUaL ChIP-Seq data Analysis using Networks
VULCAN interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data.
Software hosted by collaborators
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.
CLOE: phylogenetic clonal deconvolution
Cloe (pronounced like the name Chloë) 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.