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.

AuthorInes de Santiago, Wei Liu, Ke Yuan, Bruce Ponder, Kerstin Meyer, Florian Markowetz
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

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