Package: spatzie 1.11.0

Jennifer Hammelman

spatzie: Identification of enriched motif pairs from chromatin interaction data

Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.

Authors:Jennifer Hammelman [aut, cre, cph], Konstantin Krismer [aut], David Gifford [ths, cph]

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On BioConductor:spatzie-1.11.0(bioc 3.20)spatzie-1.10.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

8 exports 0.61 score 174 dependencies

Last updated 2 months agofrom:dbb1e32b8b

Exports:anchor_pair_enrichcompare_motif_pairsfilter_motifsfilter_pair_motifsfind_ep_coenrichmentget_specific_interactionsplot_motif_occurrencescan_motifs

Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmateclicliprclusterCNErcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestDirichletMultinomialdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggplot2glueGO.dbgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemotifmatchrmunsellnlmennetopensslpillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogressProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc