Installation | Standard workflow | Overview | Quickstart | Finding Significant Interactions from Hi-C/HiChIP | Finding Differential Interactions | ICE normalization using HiTC | Finding TADs using TopDom | Finding A/B compartment using Juicer | Creating genomic feature files | The gi_list instance | Uniformly binned gi_list instance | Restriction enzyme binned gi_list instance | Generating gi_list instance from a bintolen file | Using custom features with HiCDCPlus | How to get help for HiCDCPlus | Session info
Package: HiCDCPlus 1.21.0
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:
HiCDCPlus_1.21.0.tar.gz
HiCDCPlus_1.21.0.zip(r-4.7)HiCDCPlus_1.21.0.zip(r-4.6)HiCDCPlus_1.21.0.zip(r-4.5)
HiCDCPlus_1.21.0.tgz(r-4.6-x86_64)HiCDCPlus_1.21.0.tgz(r-4.6-arm64)HiCDCPlus_1.21.0.tgz(r-4.5-x86_64)HiCDCPlus_1.21.0.tgz(r-4.5-arm64)
HiCDCPlus_1.21.0.tar.gz(r-4.7-arm64)HiCDCPlus_1.21.0.tar.gz(r-4.7-x86_64)HiCDCPlus_1.21.0.tar.gz(r-4.6-arm64)HiCDCPlus_1.21.0.tar.gz(r-4.6-x86_64)
HiCDCPlus_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HiCDCPlus/json (API)
| # Install 'HiCDCPlus' in R: |
| install.packages('HiCDCPlus', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:HiCDCPlus-1.21.0(bioc 3.24)HiCDCPlus-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
hicdna3dstructuresoftwarenormalizationzlibcpp
Last updated from:be86a097c5. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 429 | ||
| linux-devel-arm64 | NOTE | 562 | ||
| linux-devel-x86_64 | NOTE | 630 | ||
| source / vignettes | OK | 568 | ||
| linux-release-arm64 | NOTE | 524 | ||
| linux-release-x86_64 | NOTE | 662 | ||
| macos-release-arm64 | NOTE | 339 | ||
| macos-release-x86_64 | NOTE | 663 | ||
| macos-oldrel-arm64 | NOTE | 318 | ||
| macos-oldrel-x86_64 | NOTE | 730 | ||
| windows-devel | NOTE | 564 | ||
| windows-release | NOTE | 564 | ||
| windows-oldrel | NOTE | 527 | ||
| wasm-release | OK | 409 |
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:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormnnetnumDerivopensslpillarpkgconfigpngprettyunitsprogressProtGenericspsclpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add_1D_features | add_1D_features |
| add_2D_features | add_2D_features |
| add_hic_counts | add_hic_counts |
| add_hicpro_allvalidpairs_counts | add_hicpro_allvalidpairs_counts |
| add_hicpro_matrix.counts | add_hicpro_matrix_counts |
| construct_features | construct_features |
| construct_features_chr | construct_features_chr |
| construct_features_parallel | construct_features_parallel |
| expand_1D_features | expand_1D_features |
| extract_hic_eigenvectors | extract_hic_eigenvectors |
| generate_binned_gi_list | generate_binned_gi_list |
| generate_bintolen_gi_list | generate_bintolen_gi_list |
| generate_df_gi_list | generate_df_gi_list |
| get_chr_sizes | get_chr_sizes |
| get_chrs | get_chrs |
| get_enzyme_cutsites | get_enzyme_cutsites |
| gi_list_binsize_detect | gi_list_binsize_detect |
| gi_list_Dthreshold_detect | gi_list_Dthreshold.detect |
| gi_list_read | gi_list_read |
| gi_list_topdom | gi_list_topdom |
| gi_list_validate | gi_list_validate |
| gi_list_write | gi_list_write |
| gi_list2HTClist | gi_list2HTClist |
| hic2icenorm_gi_list | hic2icenorm_gi_list |
| hicdc2hic | hicdc2hic |
| hicdcdiff | hicdcdiff |
| HiCDCPlus | HiCDCPlus |
| HiCDCPlus_chr | HiCDCPlus_chr |
| HiCDCPlus_parallel | HiCDCPlus_parallel |
| HTClist2gi_list | HTClist2gi_list |
| straw | straw |
| straw_dump | straw_dump |
