Man pages for Repitools
Epigenomic tools

abcdDNAA wrapper for fitting the offset-adjusted ABCD-DNA GLM
absoluteCNCalculate and Segment Absolute Copy Number from Sequencing...
AdjustedCopyEstimate-classContainer for results of GC adjusted copy number estimation.
AffymetrixCdfFile-classPlaceholder For AffymetrixCdfFile Documentation
AffymetrixCelSet-classPlaceholder For AffymetrixCelSet Documentation
annoDF2GRConvert a 'data.frame' to a 'GRanges'.
annoGR2DFConvert an annotated 'GRanges' to a 'data.frame'.
annotationBlocksCountsCounts the number of sequencing reads within supplied genomic...
annotationBlocksLookupForms a mapping between probe locations and chromosomal...
annotationCountsCounts the number of sequencing reads surrounding supplied...
annotationLookupForms a mapping between probes on a tiling array and windows...
BAM2GRangesRead in a (list of) BAM file(s) into a GRanges(List) object.
BayMethList-classClass '"BayMethList"'
binPlotsCreate line plots of averaged signal across a promoter
blocksStatsCalculate statistics for regions in the genome
checkProbesCheck Probe Specificity for Some Regions
chr21genesPositions of Genes on Human Chromosome 21
ChromaBlocksA function to find areas of enrichment in sequencing data
ChromaResults-classChromaResults class
chromosomeCNplotsPlot copy number by chromosome
ClusteredScoresList-classContainer for coverage matrices with clustering results.
clusterPlotsVisualisation of tables of feature coverages.
CopyEstimate-classContainer for results of fold change copy number estimation.
cpgBoxPlotsBoxplots of intensity, binned by Cpg Density
cpgDensityCalcCalculate CpG Density in a Window
cpgDensityPlotPlot the distribution of sequencing reads CpG densities.
determineOffsetFunction to determine the normalising offset f that accounts...
empBayesFunction to calculate prior parameters using empirical Bayes.
enrichmentCalcCalculate sequencing enrichment
enrichmentPlotPlot the distribution of sequencing enrichment.
exprVector of expression differences
FastQC-classFastQC and associated classes
featureBlocksMake windows for distances around a reference point.
featureScoresGet scores at regular sample points around genomic features.
findClustersFind Clusters Epigenetically Modified Genes
GCadjustCopyCalculate Absolute Copy Number from Sequencing Counts
GCAdjustParams-classContainer for parameters for mappability and GC content...
GCbiasPlotsPlot GC content vs. Read Counts Before Normalising, and GC...
gcContentCalcCalculate The gcContent of a Region
genomeBlocksCreates bins across a genome.
genQCPlot Quality Checking Information for Sequencing Data
getProbePositionsDfTranslate Affymetrix probe information in a table.
getSampleOffsetsCalculates the sample-specific offsets, using the neutral...
hcRegionsMasking files for hg19
hyperGaussian hypergeometric function for vectorial arguments
loadPairFileA routine to read Nimblegen tiling array intensities
loadSampleDirectoryA routine to read Nimblegen tiling array intensities
makeWindowLookupTableUsing the output of 'annotationLookup', create a tabular...
mappabilityCalcCalculate The Mappability of a Region
MappabilitySource-classSuperclass for datatypes that can refer to genome mappability...
maskOutFunction to mask suspicious regions.
mergeReplicatesMerge GRanges that are of replicate experiments.
methylEstFunction to derive regional methylation estimates.
multiHeatmapSuperfigure plots
plotClustersPlot Scores of Cluster Regions
plotQdnaByCNPlotting the response of qDNA-seq data by CNV
processNDFReads in a Nimblegen microarray design file (NDF)
profilePlotsCreate line plots of averaged signal across a promoter for...
QdnaDataA container for quantitative DNA sequencing data for ABCD-DNA...
regionStatsFind Regions of significance in microarray data
relativeCNCalculate and Segment Relative Copy Number From Sequencing...
samplesListShort Reads from Cancer and Normal
ScoresList-classContainer for 'featureScores()' output.
sequenceCalcFind occurences of a DNA pattern
setCNVOffsetsSet the CNVOffsets of a 'QdnaData' object
summarizeScoresSubtract scores of different samples.
writeWigWrites sequencing data out into wiggle files
Repitools documentation built on Nov. 8, 2020, 7:52 p.m.