Files in MPIIComputationalEpigenetics/epiRepeatR
epiRepeatR

DESCRIPTION
NAMESPACE
R/AnalysisManager-class.R R/GenomeAlignment-class.R R/GenomeMethylationCalls-class.R R/GenomeRepeatTrack-class.R R/RepeatAlignment-class.R R/RepeatEpigenomeCollection-class.R R/RepeatReference-class.R R/RepeatTree-class.R R/alignment.R R/config.R R/dendrogram_extension.R R/diagram_extension.R R/main.R R/methylationCalling.R R/plots.R R/preprocessing.R R/repeatAnnotation.R R/sandbox.R R/utils.R README.md
inst/extdata/curation/repeatFamilies.json
inst/extdata/curation/repeatTree.json
inst/extdata/curation/taxonomyAnnotation.json
inst/extdata/epiRepeatR.R
inst/extdata/exec/bamExtract.sh
inst/extdata/exec/chipQuantification.R inst/extdata/exec/exploratoryReport.R inst/extdata/exec/mergeChipInput.R inst/extdata/exec/methCalling.R inst/extdata/exec/plotRepeatGroupTreesMeth.R inst/extdata/exec/plotRepeatMarkTree.R inst/extdata/exec/repeatAlignmentStats.R
inst/extdata/exec/repeatAlignment_bowtie2_chip.sh
inst/extdata/exec/repeatAlignment_bsmap.sh
inst/extdata/exec/repeatAlignment_bwa_chip.sh
inst/extdata/exec/repeatEpigenomeCollection.R inst/extdata/exec/repeatReadCountsFromGenomeAlignment.R man/RepeatEpigenomeCollection-class.Rd man/filterRepRefChip-RepeatEpigenomeCollection-method.Rd man/filterRepRefMeth-RepeatEpigenomeCollection-method.Rd man/getAnnot-RepeatEpigenomeCollection-method.Rd man/getArgParser.Rd man/getConfigElement.Rd man/getMarks-RepeatEpigenomeCollection-method.Rd man/getRepRef-RepeatEpigenomeCollection-method.Rd man/getRepeatCovg-RepeatEpigenomeCollection-method.Rd man/getRepeatScores-RepeatEpigenomeCollection-method.Rd man/getSampleGroups.Rd man/getSampleMarkTable-RepeatEpigenomeCollection-method.Rd man/getSamples-RepeatEpigenomeCollection-method.Rd man/loadConfig.Rd man/loadConfigFromCommandLine.Rd man/logger.cmd.args.Rd man/normalizeMatrix.Rd man/plotRepeatAlignmentStats.Rd man/runAnalysis.Rd man/saveConfig.Rd man/setConfigElement.Rd vignettes/epiRepeatR.Rmd
vignettes/epiRepeatR.html
MPIIComputationalEpigenetics/epiRepeatR documentation built on May 10, 2017, 4:04 a.m.