API for biobenkj/compartmap
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
| Global functions | |
|---|---|
| .arrayCompartments | Source code |
| .binarizeMatrix | Source code |
| .ebayes | Source code |
| .jse | Source code |
| .meanSmoother.internal | Source code |
| .meanSmoother.rcpp | Source code |
| .n_approx | Man page Source code |
| .p_approx | Man page Source code |
| .resampleMatrix | Source code |
| .squeezeit | Source code |
| .tfidf | Source code |
| .unitarize | Source code |
| .window.mean | Source code |
| .window.mean.rcpp | Source code |
| .z | Man page Source code |
| agrestiCoullCI | Man page Source code |
| array.data.chr14 | Man page |
| bootstrapCompartments | Man page Source code |
| checkAssayType | Man page Source code |
| cleanAssayCols | Man page Source code |
| cleanAssayRows | Man page Source code |
| condenseRE | Man page Source code |
| condenseSE | Man page Source code |
| estRMT | Man page Source code |
| extractOpenClosed | Man page Source code |
| fexpit | Man page Source code |
| filterCompartments | Man page Source code |
| filterOpenSea | Man page Source code |
| fisherZ | Man page Source code |
| fixCompartments | Man page Source code |
| flogit | Man page Source code |
| getABSignal | Man page Source code |
| getATACABsignal | Man page Source code |
| getArrayABsignal | Man page Source code |
| getAssayNames | Man page Source code |
| getBinMatrix | Man page Source code |
| getChrs | Man page Source code |
| getCorMatrix | Man page Source code |
| getDenoisedCorMatrix | Man page Source code |
| getDenoisedMatrix | Man page |
| getDomainInflections | Man page Source code |
| getGlobalMeans | Man page Source code |
| getMatrixBlocks | Man page Source code |
| getOpenSeas | Man page Source code |
| getRNAABsignal | Man page |
| getSVD | Man page |
| getSeqLengths | Man page Source code |
| getShrinkageTargets | Man page Source code |
| hdf5TFIDF | Man page Source code |
| hg19.gr | Man page |
| hg38.gr | Man page |
| ifisherZ | Man page Source code |
| importBigWig | Man page Source code |
| imputeKNN | Man page Source code |
| k562_scatac_chr14 | Man page |
| k562_scrna_chr14 | Man page |
| k562_scrna_se_chr14 | Man page |
| meanSmoother | Man page Source code |
| mm10.gr | Man page |
| mm9.gr | Man page |
| openSeas.hg19 | Man page |
| openSeas.hg38 | Man page |
| openSeas.mm10 | Man page |
| openSeas.mm9 | Man page |
| plotAB | Man page Source code |
| plotCorMatrix | Man page Source code |
| precomputeBootstrapMeans | Man page Source code |
| preprocessArrays | Man page Source code |
| removeEmptyBoots | Man page Source code |
| scCompartments | Man page Source code |
| shrinkBins | Man page Source code |
| sparseToDenseMatrix | Man page Source code |
| ss3_umi_sce | Man page |
| summarizeBootstraps | Man page Source code |
| transformTFIDF | Man page Source code |
