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/differential.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/atacQuantification.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/filterRepRefAcc-RepeatEpigenomeCollection-method.Rd
man/filterRepRefChip-RepeatEpigenomeCollection-method.Rd
man/filterRepRefMeth-RepeatEpigenomeCollection-method.Rd
man/getAnnot-RepeatEpigenomeCollection-method.Rd
man/getArgParser.Rd
man/getComparisonInfo-RepeatEpigenomeCollection-method.Rd
man/getComparisons-RepeatEpigenomeCollection-method.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/getRepeatScoresDiff-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
