Files in biobenkj/compartmap

Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

NEWS.md R/RMT.R R/agrestiCoullCI.R R/bootstrapCompartments.R R/condenseRE.R R/data.R R/filterCompartments.R R/fisherTransform.R R/fixCompartments.R R/getABSignal.R R/getATACABsignal.R R/getArrayABsignal.R R/getBinMatrix.R R/getCorMatrix.R R/getDomainInflections.R R/getGlobalMeans.R R/getSVD.R R/getShrinkageTargets.R R/granges.R R/imputeKNN.R R/meanSmoother.R R/plotAB.R R/scCompartments.R R/shrinkBins.R R/summarizeBootstraps.R R/transformTFIDF.R R/utils.R README.md inst/scripts/create_species_seqlengths_granges.R man/agrestiCoullCI.Rd man/array.data.chr14.Rd man/bootstrapCompartments.Rd man/checkAssayType.Rd man/cleanAssayCols.Rd man/cleanAssayRows.Rd man/condenseRE.Rd man/condenseSE.Rd man/dot-n_approx.Rd man/dot-p_approx.Rd man/dot-z.Rd man/estRMT.Rd man/extractOpenClosed.Rd man/fexpit.Rd man/filterCompartments.Rd man/filterOpenSea.Rd man/fisherZ.Rd man/fixCompartments.Rd man/flogit.Rd man/getABSignal.Rd man/getATACABsignal.Rd man/getArrayABsignal.Rd man/getAssayNames.Rd man/getBinMatrix.Rd man/getChrs.Rd man/getCorMatrix.Rd man/getDenoisedMatrix.Rd man/getDomainInflections.Rd man/getGlobalMeans.Rd man/getMatrixBlocks.Rd man/getSVD.Rd man/getSeqLengths.Rd man/getShrinkageTargets.Rd man/hdf5TFIDF.Rd man/hg19.gr.Rd man/hg38.gr.Rd man/ifisherZ.Rd man/importBigWig.Rd man/imputeKNN.Rd man/k562_scatac_chr14.Rd man/k562_scrna_chr14.Rd man/k562_scrna_se_chr14.Rd man/meanSmoother.Rd man/mm10.gr.Rd man/mm9.gr.Rd man/openSeas.hg19.Rd man/openSeas.hg38.Rd man/openSeas.mm10.Rd man/openSeas.mm9.Rd man/plotAB.Rd man/plotCorMatrix.Rd man/precomputeBootstrapMeans.Rd man/preprocessArrays.Rd man/removeEmptyBoots.Rd man/scCompartments.Rd man/shrinkBins.Rd man/sparseToDenseMatrix.Rd man/ss3_umi_sce.Rd man/summarizeBootstraps.Rd man/transformTFIDF.Rd vignettes/compartmap_vignette.Rmd