BaalChIP - Bayesian analysis of allele-specific transcription factor binding in cancer genomes

BaalChIP

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")

References:

R

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You can download from Bioconductor.

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Other packages

Software
  • BaalChIP - allele-specific TF binding
  • BitPhylogeny - infer intra-tumor phylogenies
  • CRImage - tumor image analysis
  • DANCE - subtype specific drivers of cancer
  • GoIFISH - single cell IFISH analysis
  • HTSanalyzeR - functional annotation
  • lol - lots of lassos
  • MEDICC - intra-patient copy number comparison
  • nem - nested effects models
  • OncoNEM - oncogenetic NEMs
  • PAN - posterior associa- tion networks
  • RedeR - graph visualiza- tion and analysis
  • RTN - network recon- struction and analysis
  • SANTA - spatial analysis of network associations
  • VULCAN - co-factors from CHiP-seq data
Data @ Bioconductor