Files in InesdeSantiago/BaalChIP
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
.gitignore
DESCRIPTION
NAMESPACE
NEWS
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
data/.DS_Store
data/ENCODEexample.RData
data/FAIREexample.RData
data/UniqueMappability50bp_hg19.RData
data/baalObject.RData
data/blacklist_hg19.RData
data/datalist
data/pickrell2011cov1_hg19.RData
inst/CITATION
inst/extra/get.overlaps.v2_chrXY.perl
inst/extra/run_simulations.sh
inst/test/.DS_Store
inst/test/AMOVC_hetSNP.txt
inst/test/GM12891_hetSNP.txt
inst/test/MCF7_hetSNP.txt
inst/test/TaT1_hetSNP.txt
inst/test/bamFiles/.DS_Store
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/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/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/test_get_allele_counts.R
man/.Rapp.history
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/runTests.R
vignettes/.DS_Store
vignettes/BaalChIP-vignette.bib
vignettes/BaalChIP.Rmd
vignettes/baal.png
vignettes/biomed-central.csl
