Files in biobenkj/compartmap
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
.Rinstignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
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
data/datalist
data/hg19.gr.rda
data/hg38.gr.rda
data/k562_scatac_chr14.rda
data/k562_scrna_chr14.rda
data/k562_scrna_raw.rda
data/meth_array_450k_chr14.rda
data/mm10.gr.rda
data/mm9.gr.rda
data/openSeas.hg19.rda
data/openSeas.hg38.rda
data/openSeas.mm10.rda
data/openSeas.mm9.rda
data/ss3_umi_sce.rda
inst/extdata/grch38_91_hsapiens.gtf.gz
inst/extdata/k562_scrna_chr14_cell1.bw
inst/extdata/k562_scrna_chr14_cell2.bw
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/figures/compartmap_logo.png
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
