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

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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.

Author
Ines de Santiago, Wei Liu, Ke Yuan, Bruce Ponder, Kerstin Meyer, Florian Markowetz
Date of publication
None
Maintainer
Ines de Santiago <ines.deSantiago@cruk.cam.ac.uk>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

adjustmentBaalPlot
Method adjustmentBaalPlot
alleleCounts
Method alleleCounts
BaalChIP
BaalChIP-class
BaalChIP.get
Method BaalChIP.get
BaalChIP.report
Method BaalChIP.report
BaalChIP.run
Method BaalChIP.run
BaalObject
BaalObject example dataset
blacklist_hg19
Blacklisted genomic regions
ENCODEexample
ENCODEexample example dataset
FAIREexample
FAIREexample example dataset
filter1allele
Method filter1allele
filterIntbias
Method filterIntbias
getASB
Method getASB
mergePerGroup
Method mergePerGroup
pickrell2011cov1_hg19
Genomic regions of collapsed repeats
plotQC
Method plotQC
plotSimul
Method plotSimul
QCfilter
Method QCfilter
summaryASB
Method summaryASB
summaryQC
Method summaryQC
UniqueMappability50bp_hg19
Genomic regions of unique mappability

Files in this package

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