Files in jianhong/ATACseqTFEA
Transcription Factor Enrichment Analysis for ATAC-seq
DESCRIPTION
NAMESPACE
NEWS.md
R/ATACseqTFEA.R
R/AllClasses.R
R/AllGenerics.R
R/DBscore.R
R/TFEA.R
R/calWeights.R
R/count5ends.R
R/countsNormalization.R
R/doTFEA.R
R/eventsFilter.R
R/expandBindingSites.R
R/extdata.R
R/getWeightedBindingScore.R
R/importFimoBindingSites.R
R/internal-utils.R
R/methods-TFEAresults.R
R/plotES.R
R/prepareBindingSites.R
R/volcanoplot.R
README.md
inst/extdata/KD.shift.rep1.bam
inst/extdata/KD.shift.rep1.bam.bai
inst/extdata/KD.shift.rep2.bam
inst/extdata/KD.shift.rep2.bam.bai
inst/extdata/PWMatrixList.rds
inst/extdata/README.md
inst/extdata/WT.shift.rep1.bam
inst/extdata/WT.shift.rep1.bam.bai
inst/extdata/WT.shift.rep2.bam
inst/extdata/WT.shift.rep2.bam.bai
inst/extdata/best_curated_Human.rds
inst/extdata/bindingSites.rds
inst/extdata/cluster_PWMs.rds
inst/extdata/fimo1.gff
inst/extdata/fimo2.gff
inst/extdata/res.rds
inst/extdata/sample_scripts.R
man/ATACseqTFEA-package.Rd
man/DBscore.Rd
man/ESvolcanoplot.Rd
man/TFEA.Rd
man/TFEAresults-class.Rd
man/TFEAresults-methods.Rd
man/calWeights.Rd
man/count5ends.Rd
man/countsNormalization.Rd
man/doTFEA.Rd
man/eventsFilter.Rd
man/expandBindingSites.Rd
man/extdata.Rd
man/getWeightedBindingScore.Rd
man/importFimoBindingSites.Rd
man/plotES.Rd
man/prepareBindingSites.Rd
man/reduceByPercentage.Rd
tests/runTests.R
tests/testthat/test_TFEA.R
tests/testthat/test_eventsFilter.R
tests/testthat/test_expandBindingSites.R
tests/testthat/test_prepareBindingSites.R
vignettes/ATACseqTFEA.Rmd
vignettes/ATACseqTFEA.png
vignettes/bibliography.bib
vignettes/nature.csl
