Files in BaalChIP

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

README.md

NEWS

NAMESPACE

DESCRIPTION

mixcr_align_txt_2_fastq_pairedEnd.py

build/vignette.rds

data/blacklist_hg19.RData

data/datalist

data/FAIREexample.RData

data/ENCODEexample.RData

data/pickrell2011cov1_hg19.RData

data/UniqueMappability50bp_hg19.RData

data/baalObject.RData

R/allplots.R R/QCIntBias.R R/QCmerged.R R/allASBbias.R R/alleleCounts.R R/BaalChIP-generics.R R/BaalChIP-class.R R/Bayes_report.R R/QCperBam.R R/allsummary.R R/applyBayes.R R/BaalChIP-methods.R R/BaalChIP-checks.R

vignettes/baal.png

vignettes/BaalChIP.Rmd

vignettes/BaalChIP-vignette.bib

vignettes/biomed-central.csl

man/QCfilter.Rd man/blacklist_hg19.Rd man/BaalChIP.run.Rd man/plotQC.Rd man/adjustmentBaalPlot.Rd man/filterIntbias.Rd man/pickrell2011cov1_hg19.Rd man/getASB.Rd man/ENCODEexample.Rd man/BaalChIP.Rd man/BaalChIP.get.Rd man/plotSimul.Rd man/filter1allele.Rd man/FAIREexample.Rd man/mergePerGroup.Rd man/alleleCounts.Rd man/summaryASB.Rd man/BaalObject.Rd man/summaryQC.Rd man/BaalChIP.report.Rd man/UniqueMappability50bp_hg19.Rd tests/runTests.R inst/doc/BaalChIP.Rmd inst/doc/BaalChIP.R

inst/doc/BaalChIP.html

inst/extra/get.overlaps.v2_chrXY.perl

inst/extra/run_simulations.sh

inst/test/GM12891_hetSNP.txt

inst/test/TaT1_hetSNP.txt

inst/test/AMOVC_hetSNP.txt

inst/test/MCF7_hetSNP.txt

inst/test/exampleChIP2.tsv

inst/test/exampleChIP1.tsv

inst/test/exampleChIP.tsv

inst/test/bamFiles/MCF7_cMYC_Rep1.bam

inst/test/bamFiles/TaT1_2.test.bam.bai

inst/test/bamFiles/GM12891_POL2_Rep1.bam

inst/test/bamFiles/GM12891_PU1_Rep2.bam

inst/test/bamFiles/MCF7_POL2_Rep1.bam.bai

inst/test/bamFiles/MCF7_cMYC_Rep2.bam.bai

inst/test/bamFiles/GM12891_POL2_Rep2.bam.bai

inst/test/bamFiles/MCF7_cMYC_Rep2.bam

inst/test/bamFiles/TaT1_1_gDNA.test.bam.bai

inst/test/bamFiles/AMOVC_1_gDNA.test.bam

inst/test/bamFiles/GM12891_TAF1_Rep1.bam

inst/test/bamFiles/GM12891_POL2_Rep2.bam

inst/test/bamFiles/AMOVC_1_gDNA.test.bam.bai

inst/test/bamFiles/AMOVC_2_gDNA.test.bam

inst/test/bamFiles/MCF7_cFOS_Rep2.bam.bai

inst/test/bamFiles/GM12891_TAF1_Rep1.bam.bai

inst/test/bamFiles/MCF7_cMYC_Rep1.bam.bai

inst/test/bamFiles/MCF7_STAT3_Rep1.bam.bai

inst/test/bamFiles/MCF7_POL2_Rep1.bam

inst/test/bamFiles/AMOVC_2_gDNA.test.bam.bai

inst/test/bamFiles/AMOVC_2.test.bam.bai

inst/test/bamFiles/GM12891_PU1_Rep1.bam.bai

inst/test/bamFiles/TaT1_1.test.bam.bai

inst/test/bamFiles/GM12891_PAX5_Rep1.bam.bai

inst/test/bamFiles/AMOVC_1.test.bam

inst/test/bamFiles/AMOVC_1.test.bam.bai

inst/test/bamFiles/MCF7_POL2_Rep2.bam.bai

inst/test/bamFiles/MCF7_POL2_Rep2.bam

inst/test/bamFiles/GM12891_PU1_Rep1.bam

inst/test/bamFiles/GM12891_TAF1_Rep2.bam

inst/test/bamFiles/GM12891_POL2_Rep1.bam.bai

inst/test/bamFiles/TaT1_2_gDNA.test.bam

inst/test/bamFiles/MCF7_STAT3_Rep2.bam.bai

inst/test/bamFiles/AMOVC_2.test.bam

inst/test/bamFiles/GM12891_PU1_Rep2.bam.bai

inst/test/bamFiles/TaT1_2.test.bam

inst/test/bamFiles/MCF7_cFOS_Rep1.bam.bai

inst/test/bamFiles/MCF7_cFOS_Rep2.bam

inst/test/bamFiles/MCF7_cFOS_Rep1.bam

inst/test/bamFiles/GM12891_TAF1_Rep2.bam.bai

inst/test/bamFiles/MCF7_STAT3_Rep2.bam

inst/test/bamFiles/MCF7_STAT3_Rep1.bam

inst/test/bamFiles/TaT1_2_gDNA.test.bam.bai

inst/test/bamFiles/GM12891_PAX5_Rep2.bam

inst/test/bamFiles/TaT1_1_gDNA.test.bam

inst/test/bamFiles/GM12891_PAX5_Rep1.bam

inst/test/bamFiles/TaT1_1.test.bam

inst/test/bamFiles/GM12891_PAX5_Rep2.bam.bai

inst/test/bedFiles/GM12891_TAF1.bed

inst/test/bedFiles/GM12891_YY1.bed

inst/test/bedFiles/GM12891_POU2F2.bed

inst/test/bedFiles/MCF7_POL2.bed

inst/test/bedFiles/AMOVC_peaks_example.bed

inst/test/bedFiles/MCF7_cFOS.bed

inst/test/bedFiles/GM12891_PAX5.bed

inst/test/bedFiles/MCF7_cMYC.bed

inst/test/bedFiles/MCF7_STAT3.bed

inst/test/bedFiles/TaT1_peaks_example.bed

inst/test/bedFiles/GM12891_PU1.bed

inst/test/bedFiles/GM12891_POL2.bed

inst/test/simuloutput/c67c6ec6c433_aln32.bam

inst/test/simuloutput/c67c6ec6c433_aln34.fasta.sam

inst/test/simuloutput/c67c6ec6c433_aln34.bam.bai

inst/test/simuloutput/c67c6ec6c433_aln32.fasta.sam

inst/test/simuloutput/c67c6ec6c433_aln32.bam.bai

inst/test/simuloutput/c67c6ec6c433_aln32_snplist.txt

inst/test/simuloutput/c67c6ec6c433_aln34.fasta

inst/test/simuloutput/c67c6ec6c433_aln32.fasta

inst/test/simuloutput/c67c6ec6c433_aln36.fasta.sam

inst/test/simuloutput/c67c6ec6c433_aln36.fasta

inst/test/simuloutput/c67c6ec6c433_aln36.bam.bai

inst/test/simuloutput/c67c6ec6c433_aln34.bam

inst/test/simuloutput/c67c6ec6c433_snplist.txt

inst/test/simuloutput/c67c6ec6c433_aln36.bam

inst/unitTests/test_get_allele_counts.R

BaalChIP documentation built on Nov. 8, 2020, 5:23 p.m.