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

The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BaalChIP")
AuthorInes de Santiago, Wei Liu, Ke Yuan, Bruce Ponder, Kerstin Meyer, Florian Markowetz
Bioconductor views Bayesian ChIPSeq Sequencing Software
Date of publicationNone
MaintainerInes de Santiago <ines.deSantiago@cruk.cam.ac.uk>
LicenseArtistic-2.0
Version1.0.0

View on Bioconductor

Functions

adjustmentBaalPlot Man page
adjustmentBaalPlot,BaalChIP-method Man page
alleleCounts Man page
alleleCounts,BaalChIP-method Man page
BaalChIP Man page
BaalChIP.get Man page
BaalChIP.get,BaalChIP-method Man page
BaalChIP.report Man page
BaalChIP.report,BaalChIP-method Man page
BaalChIP.run Man page
BaalChIP.run,BaalChIP-method Man page
BaalObject Man page
blacklist_hg19 Man page
ENCODEexample Man page
FAIREexample Man page
filter1allele Man page
filter1allele,BaalChIP-method Man page
filterIntbias Man page
filterIntbias,BaalChIP-method Man page
getASB Man page
getASB,BaalChIP-method Man page
mergePerGroup Man page
mergePerGroup,BaalChIP-method Man page
pickrell2011cov1_hg19 Man page
plotQC Man page
plotQC,BaalChIP-method Man page
plotSimul Man page
plotSimul,BaalChIP-method Man page
QCfilter Man page
QCfilter,BaalChIP-method Man page
summaryASB Man page
summaryASB,BaalChIP-method Man page
summaryQC Man page
summaryQC,BaalChIP-method Man page
UniqueMappability50bp_hg19 Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BaalChIP-checks.R R/BaalChIP-class.R R/BaalChIP-generics.R R/BaalChIP-methods.R R/Bayes_report.R R/QCIntBias.R R/QCmerged.R R/QCperBam.R R/allASBbias.R R/alleleCounts.R R/allplots.R R/allsummary.R R/applyBayes.R
README.md
build
build/vignette.rds
data
data/ENCODEexample.RData
data/FAIREexample.RData
data/UniqueMappability50bp_hg19.RData
data/baalObject.RData
data/blacklist_hg19.RData
data/datalist
data/pickrell2011cov1_hg19.RData
inst
inst/doc
inst/doc/BaalChIP.R
inst/doc/BaalChIP.Rmd
inst/doc/BaalChIP.html
inst/extra
inst/extra/get.overlaps.v2_chrXY.perl
inst/extra/run_simulations.sh
inst/test
inst/test/AMOVC_hetSNP.txt
inst/test/GM12891_hetSNP.txt
inst/test/MCF7_hetSNP.txt
inst/test/TaT1_hetSNP.txt
inst/test/bamFiles
inst/test/bamFiles/AMOVC_1.test.bam
inst/test/bamFiles/AMOVC_1.test.bam.bai
inst/test/bamFiles/AMOVC_1_gDNA.test.bam
inst/test/bamFiles/AMOVC_1_gDNA.test.bam.bai
inst/test/bamFiles/AMOVC_2.test.bam
inst/test/bamFiles/AMOVC_2.test.bam.bai
inst/test/bamFiles/AMOVC_2_gDNA.test.bam
inst/test/bamFiles/AMOVC_2_gDNA.test.bam.bai
inst/test/bamFiles/GM12891_PAX5_Rep1.bam
inst/test/bamFiles/GM12891_PAX5_Rep1.bam.bai
inst/test/bamFiles/GM12891_PAX5_Rep2.bam
inst/test/bamFiles/GM12891_PAX5_Rep2.bam.bai
inst/test/bamFiles/GM12891_POL2_Rep1.bam
inst/test/bamFiles/GM12891_POL2_Rep1.bam.bai
inst/test/bamFiles/GM12891_POL2_Rep2.bam
inst/test/bamFiles/GM12891_POL2_Rep2.bam.bai
inst/test/bamFiles/GM12891_PU1_Rep1.bam
inst/test/bamFiles/GM12891_PU1_Rep1.bam.bai
inst/test/bamFiles/GM12891_PU1_Rep2.bam
inst/test/bamFiles/GM12891_PU1_Rep2.bam.bai
inst/test/bamFiles/GM12891_TAF1_Rep1.bam
inst/test/bamFiles/GM12891_TAF1_Rep1.bam.bai
inst/test/bamFiles/GM12891_TAF1_Rep2.bam
inst/test/bamFiles/GM12891_TAF1_Rep2.bam.bai
inst/test/bamFiles/MCF7_POL2_Rep1.bam
inst/test/bamFiles/MCF7_POL2_Rep1.bam.bai
inst/test/bamFiles/MCF7_POL2_Rep2.bam
inst/test/bamFiles/MCF7_POL2_Rep2.bam.bai
inst/test/bamFiles/MCF7_STAT3_Rep1.bam
inst/test/bamFiles/MCF7_STAT3_Rep1.bam.bai
inst/test/bamFiles/MCF7_STAT3_Rep2.bam
inst/test/bamFiles/MCF7_STAT3_Rep2.bam.bai
inst/test/bamFiles/MCF7_cFOS_Rep1.bam
inst/test/bamFiles/MCF7_cFOS_Rep1.bam.bai
inst/test/bamFiles/MCF7_cFOS_Rep2.bam
inst/test/bamFiles/MCF7_cFOS_Rep2.bam.bai
inst/test/bamFiles/MCF7_cMYC_Rep1.bam
inst/test/bamFiles/MCF7_cMYC_Rep1.bam.bai
inst/test/bamFiles/MCF7_cMYC_Rep2.bam
inst/test/bamFiles/MCF7_cMYC_Rep2.bam.bai
inst/test/bamFiles/TaT1_1.test.bam
inst/test/bamFiles/TaT1_1.test.bam.bai
inst/test/bamFiles/TaT1_1_gDNA.test.bam
inst/test/bamFiles/TaT1_1_gDNA.test.bam.bai
inst/test/bamFiles/TaT1_2.test.bam
inst/test/bamFiles/TaT1_2.test.bam.bai
inst/test/bamFiles/TaT1_2_gDNA.test.bam
inst/test/bamFiles/TaT1_2_gDNA.test.bam.bai
inst/test/bedFiles
inst/test/bedFiles/AMOVC_peaks_example.bed
inst/test/bedFiles/GM12891_PAX5.bed
inst/test/bedFiles/GM12891_POL2.bed
inst/test/bedFiles/GM12891_POU2F2.bed
inst/test/bedFiles/GM12891_PU1.bed
inst/test/bedFiles/GM12891_TAF1.bed
inst/test/bedFiles/GM12891_YY1.bed
inst/test/bedFiles/MCF7_POL2.bed
inst/test/bedFiles/MCF7_STAT3.bed
inst/test/bedFiles/MCF7_cFOS.bed
inst/test/bedFiles/MCF7_cMYC.bed
inst/test/bedFiles/TaT1_peaks_example.bed
inst/test/exampleChIP.tsv
inst/test/exampleChIP1.tsv
inst/test/exampleChIP2.tsv
inst/test/simuloutput
inst/test/simuloutput/c67c6ec6c433_aln32.bam
inst/test/simuloutput/c67c6ec6c433_aln32.bam.bai
inst/test/simuloutput/c67c6ec6c433_aln32.fasta
inst/test/simuloutput/c67c6ec6c433_aln32.fasta.sam
inst/test/simuloutput/c67c6ec6c433_aln32_snplist.txt
inst/test/simuloutput/c67c6ec6c433_aln34.bam
inst/test/simuloutput/c67c6ec6c433_aln34.bam.bai
inst/test/simuloutput/c67c6ec6c433_aln34.fasta
inst/test/simuloutput/c67c6ec6c433_aln34.fasta.sam
inst/test/simuloutput/c67c6ec6c433_aln36.bam
inst/test/simuloutput/c67c6ec6c433_aln36.bam.bai
inst/test/simuloutput/c67c6ec6c433_aln36.fasta
inst/test/simuloutput/c67c6ec6c433_aln36.fasta.sam
inst/test/simuloutput/c67c6ec6c433_snplist.txt
inst/unitTests
inst/unitTests/test_get_allele_counts.R
man
man/BaalChIP.Rd man/BaalChIP.get.Rd man/BaalChIP.report.Rd man/BaalChIP.run.Rd man/BaalObject.Rd man/ENCODEexample.Rd man/FAIREexample.Rd man/QCfilter.Rd man/UniqueMappability50bp_hg19.Rd man/adjustmentBaalPlot.Rd man/alleleCounts.Rd man/blacklist_hg19.Rd man/filter1allele.Rd man/filterIntbias.Rd man/getASB.Rd man/mergePerGroup.Rd man/pickrell2011cov1_hg19.Rd man/plotQC.Rd man/plotSimul.Rd man/summaryASB.Rd man/summaryQC.Rd
tests
tests/runTests.R
vignettes
vignettes/BaalChIP-vignette.bib
vignettes/BaalChIP.Rmd
vignettes/baal.png
vignettes/biomed-central.csl

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.