B compartment inference from ATAC-seq and methylation array data

.Rbuildignore

.Rinstignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/agrestiCoullCI.R R/bootstrapCompartments.R R/condenseRE.R R/data.R R/filterCells.R R/filterCompartments.R R/fisherTransform.R R/fixCompartments.R R/getABSignal.R R/getATACABsignal.R R/getArrayABsignal.R R/getBSABsignal.R R/getBinMatrix.R R/getCorMatrix.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/smoothBSCounts.R R/summarizeBootstraps.R R/transformTFIDF.R R/utils.R README.md

data/bulkATAC_raw_filtered_chr14.rda

data/cell_cycle_hansen_chr22.rda

data/datalist

data/hg19.gr.rda

data/hg38.gr.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

docs/404.html

docs/LICENSE-text.html

docs/articles/compartmap_vignette.html

docs/articles/compartmap_vignette_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/images/ATAC_supervised_UMAP.png

docs/images/Compartmap_Logo.png

docs/images/chr1_AB_compartments.png

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/agrestiCoullCI.html

docs/reference/array.data.chr14.html

docs/reference/bootstrapCompartments.html

docs/reference/checkAssayType.html

docs/reference/cleanAssayCols.html

docs/reference/cleanAssayRows.html

docs/reference/condenseRE.html

docs/reference/condenseSE.html

docs/reference/dot-n_approx.html

docs/reference/dot-p_approx.html

docs/reference/dot-z.html

docs/reference/extractOpenClosed.html

docs/reference/fexpit.html

docs/reference/figures/ATAC_supervised_UMAP.png

docs/reference/figures/Compartmap_Logo.png

docs/reference/figures/chr1_AB_compartments.png

docs/reference/filterCells.html

docs/reference/filterCompartments.html

docs/reference/filterOpenSea.html

docs/reference/filtered.data.chr14.html

docs/reference/fisherZ.html

docs/reference/fixCompartments.html

docs/reference/flogit.html

docs/reference/getABSignal.html

docs/reference/getATACABsignal.html

docs/reference/getArrayABsignal.html

docs/reference/getAssayNames.html

docs/reference/getBSABsignal.html

docs/reference/getBinMatrix.html

docs/reference/getChrs.html

docs/reference/getCorMatrix.html

docs/reference/getGlobalMeans.html

docs/reference/getMatrixBlocks.html

docs/reference/getSVD.html

docs/reference/getSeqLengths.html

docs/reference/getShrinkageTargets.html

docs/reference/hdf5TFIDF.html

docs/reference/ifisherZ.html

docs/reference/imputeKNN.html

docs/reference/index.html

docs/reference/meanSmoother.html

docs/reference/plotAB.html

docs/reference/precomputeBootstrapMeans.html

docs/reference/preprocessArrays.html

docs/reference/preprocessBSseq.html

docs/reference/removeEmptyBoots.html

docs/reference/scCompartments.html

docs/reference/shrinkBins.html

docs/reference/smoothBSCounts.html

docs/reference/sparseToDenseMatrix.html

docs/reference/summarizeBootstraps.html

docs/reference/transformTFIDF.html

inst/extdata/mm10_cpgi.bed

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/extractOpenClosed.Rd man/fexpit.Rd

man/figures/ATAC_supervised_UMAP.png

man/figures/Compartmap_Logo.png

man/figures/chr1_AB_compartments.png

man/filterCells.Rd man/filterCompartments.Rd man/filterOpenSea.Rd man/filtered.data.chr14.Rd man/fisherZ.Rd man/fixCompartments.Rd man/flogit.Rd man/getABSignal.Rd man/getATACABsignal.Rd man/getArrayABsignal.Rd man/getAssayNames.Rd man/getBSABsignal.Rd man/getBinMatrix.Rd man/getChrs.Rd man/getCorMatrix.Rd man/getGlobalMeans.Rd man/getMatrixBlocks.Rd man/getSVD.Rd man/getSeqLengths.Rd man/getShrinkageTargets.Rd man/hdf5TFIDF.Rd man/ifisherZ.Rd man/imputeKNN.Rd man/meanSmoother.Rd man/plotAB.Rd man/precomputeBootstrapMeans.Rd man/preprocessArrays.Rd man/preprocessBSseq.Rd man/removeEmptyBoots.Rd man/scCompartments.Rd man/shrinkBins.Rd man/smoothBSCounts.Rd man/sparseToDenseMatrix.Rd man/summarizeBootstraps.Rd man/transformTFIDF.Rd vignettes/compartmap_vignette.Rmd

vignettes/compartmap_vignette.html

JordanVeldboom/compartmap documentation built on July 3, 2020, 6:32 p.m.

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JordanVeldboom/compartmap
A/B compartment inference from ATAC-seq and methylation array data

Files in JordanVeldboom/compartmap
A/B compartment inference from ATAC-seq and methylation array data

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JordanVeldboom/compartmap A/B compartment inference from ATAC-seq and methylation array data

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JordanVeldboom/compartmap
A/B compartment inference from ATAC-seq and methylation array data

Files in JordanVeldboom/compartmap
A/B compartment inference from ATAC-seq and methylation array data