Package: HiCDCPlus 1.13.0

Merve Sahin

HiCDCPlus: Hi-C Direct Caller Plus

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation.

Authors:Merve Sahin [cre, aut]

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HiCDCPlus.pdf |HiCDCPlus.html✨
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On BioConductor:HiCDCPlus-1.13.0(bioc 3.20)HiCDCPlus-1.12.0(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

32 exports 0.49 score 158 dependencies

Last updated 2 months agofrom:e39334549e

Exports:add_1D_featuresadd_2D_featuresadd_hic_countsadd_hicpro_allvalidpairs_countsadd_hicpro_matrix_countsconstruct_featuresconstruct_features_chrconstruct_features_parallelexpand_1D_featuresextract_hic_eigenvectorsgenerate_binned_gi_listgenerate_bintolen_gi_listgenerate_df_gi_listget_chr_sizesget_chrsget_enzyme_cutsitesgi_list_binsize_detectgi_list_Dthreshold.detectgi_list_readgi_list_topdomgi_list_validategi_list_writegi_list2HTClisthic2icenorm_gi_listhicdc2hichicdcdiffHiCDCPlusHiCDCPlus_chrHiCDCPlus_parallelHTClist2gi_liststrawstraw_dump

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encbbmlebdsmatrixBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetnumDerivopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspsclpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc