Files in davetgerrard/GenomicLayers

Simple, sequence-based simulation of epi-genomes.

R/af.factorSet.R R/assignListNodeByCharacter.R R/buildMutationSkeleton.R R/checkBfAgainstLayerSet.R R/confusionMatrix.GR.R R/createBindingFactor.DNA_consensus.R R/createBindingFactor.DNA_motif.R R/createBindingFactor.DNA_regexp.R R/createBindingFactor.layer_region.R R/createLayerList.DNAString.R R/createLayerSet.BSgenome.R R/createRandomBindingFactor.R R/data.R R/generateHitsCache.R R/getListNodeByCharacter.R R/keepBSgenomeSequences.R R/matchBindingFactor.BSgenome.R R/matchBindingFactor.R R/matchRegExp.BSgenome.R R/modifyLayerByBindingFactor.BSgenome.R R/modifyLayerByBindingFactor.Views.R R/mutateBindingFactor.R R/mutateFactorSet.R R/optimiseFactorSet.R R/plot.factorSet.R R/plot.layerBindingHistory.R R/plot.score.hits.R R/plotLayers.R R/print.bfSet.R R/randGranges.R R/randGrangesBigGenome.R R/recurseListNames.R R/removeGRangesBySize.R R/removeShortGRanges.R R/runLayerBinding.BSgenome.R R/runLayerBinding.R R/windowMean.R R/windowWidth.R README.md man/GSM1182890_d3.xist.mus.meanScores.Rd man/createBindingFactor.DNA_consensus.Rd man/createBindingFactor.DNA_motif.Rd man/createBindingFactor.DNA_regexp.Rd man/createBindingFactor.layer_region.Rd man/createLayerList.DNAstring.Rd man/createLayerSet.BSgenome.Rd man/createRandomBindingFactor.Rd man/generateHitsCache.Rd man/keepBSgenomeSequences.Rd man/matchBindingFactor.BSgenome.Rd man/matchBindingFactor.Rd man/modifyLayerByBindingFactor.BSgenome.Rd man/modifyLayerByBindingFactor.Views.Rd man/plot.factorSet.Rd man/print.bfSet.Rd man/randGrangesBigGenome.Rd man/runLayerBinding.BSgenome.Rd man/runLayerBinding.Rd tests/testthat.R tests/testthat/test-createBindingFactor.R tests/testthat/test-createBindingFactor.layer_region.R tests/testthat/test-createLayerSet.BSgenome.R tests/testthat/test-createRandomBindingFactor.R tests/testthat/test-matchBindingFactor.BSgenome.R tests/testthat/test-matchBindingFactor.R tests/testthat/test-modifyLayerByBindingFactor.BSgenome.R tests/testthat/test-runLayerBinding.BSgenome.R tests/testthat/test-runLayerBinding.R vignettes/GenomicLayersIntroduction.Rmd vignettes/sacCer.RIPmeth.Rmd vignettes/sacCer3_rap1_B2_plain.Rmd