BaalChIP - Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP stands for Bayesian Analysis of Allelic imbalances from ChIP-seq data.
BaalChIP is a rigorous statistical method to identify allele-specific binding of transcription factors, which is important, for example, to understand the functional consequences of the many disease-risk associated SNPs occurring in non-coding DNA.
BaalChIP combines a strict filtering and quality-control pipeline for quality control with a Bayesian statistical model that corrects for biases introduced by overdispersion, biases towards the reference allele, and most importantly, differences in allele frequencies due to copy number changes
Download and Installation
You can download BaalChIP R package from Bioconductor
To install this package directly in R type:
## from github library(devtools) install_github("inesdesantiago/BaalChIP") ## from BioC ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("BaalChIP")
BaalChIP: A probabilistic framework for reconstructing intra-tumor phylogenies
I. de Santiago*, W. Liu*, K. Yuan, M. O'Reilly, CS. Chilamakuri, B. Ponder, K. Meyer, F. Markowetz
in preparation, 2016