Man pages for robinweide/GENOVA
GENOVA: expore the Hi-C

APAAggegrate Peak Analysis
ATAAggegrate TAD Analysis
badBin.findFind all bad bins
badBin.plotPrint RCP_base versus RCP-test
centromere.telomere.analysiscentromere.telomere.analysis
chrom.comparison.plotplot.chrom.comparison
chromosomeMatrixchromosomeMatrix
chromosome.wide.insulationchromosome.wide.insulation
cis.compartment.plotcis.compartment.plot
cisTotal.perChromcisTotal.perChrom
cisTotal.scorescisTotal.scores
compartment.scoreGet compartment-scores
construct.experimentConstruct a HiC-experiment.
cov2dcov2d
differential.TAD.dotplotdifferential.TAD.dotplot
differential.TAD.scatterplotdifferential.TAD.scatterplot
draw.centromere.telomeredraw.centromere.telomere
fastDIGet DI-scores for a specific region
fields.interp.surfacefields.interp.surface
frequency.from.matrixPlot pyramid-style HiC-regions.
genome.wide.insulationgenome.wide.insulation
hic.matrixplothic.matrixplot
insulation.callTADinsulation.callTAD
insulation.domainograminsulation.domainogram
insulation.heatmapPlot insulation-heatmaps.
insulation.plot.dualplot.insulation.dual
insulation.plot.singleplot.insulation.single
insulation.polygoninsulation.polygon
insulation.scoreinsulation.score
intra.inter.TAD.contactsintra.inter.TAD.contacts
matrix.insulationchromosome.wide.insulation
PESCAnPE-SCAn
PESCAn_covertPESCAn_covert
quantifyAPAGet statistics from the centers of APA-results
RCPRelative Contact Probabilities
read.bedpeLoad, parse and check BEDPE.
read.hicpro.matrixRead hicpro three column matrix format.
rescaleRescale a vector.
resize.matRescale a matrix.
saddleCompute compartment-v-compartment scores
select.subA quick lookup of square region from a HiC matrix.
select.sub.2DA quick lookup of square region from a HiC matrix.
select.subsetGet matrix from a BED-like entry.
shuffleHiCShuffle a symmetric matrix
trans.compartment.plottrans.compartment.plot
virtual.4CGet an average virtual 4C of 2D-regions (e.g. loops).
visualise.APA.basevisualise.APA.ggplot
visualise.APA.ggplotvisualise.APA.ggplot
visualise.ATA.ggplotvisualise.ATA.ggplot
visualise.compartmentStrengthPlot compartment-strengths
visualise.PESCAn.ggplotvisualise.PESCAn.ggplot
visualise.RCP.ggplotPlot the RCP results
visualise.saddlePlot saddle-plots
visualise.virtual.4CPlot the virtual 4C results.
robinweide/GENOVA documentation built on Sept. 18, 2019, 4:24 a.m.