Package: HiCDCPlus 1.15.0
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_1.15.0.tar.gz
HiCDCPlus_1.15.0.zip(r-4.5)HiCDCPlus_1.15.0.zip(r-4.4)HiCDCPlus_1.15.0.zip(r-4.3)
HiCDCPlus_1.15.0.tgz(r-4.4-x86_64)HiCDCPlus_1.15.0.tgz(r-4.4-arm64)HiCDCPlus_1.15.0.tgz(r-4.3-x86_64)HiCDCPlus_1.15.0.tgz(r-4.3-arm64)
HiCDCPlus_1.15.0.tar.gz(r-4.5-noble)HiCDCPlus_1.15.0.tar.gz(r-4.4-noble)
HiCDCPlus_1.15.0.tgz(r-4.4-emscripten)HiCDCPlus_1.15.0.tgz(r-4.3-emscripten)
HiCDCPlus.pdf |HiCDCPlus.html✨
HiCDCPlus/json (API)
NEWS
| # Install 'HiCDCPlus' in R: |
| install.packages('HiCDCPlus', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:HiCDCPlus-1.15.0(bioc 3.21)HiCDCPlus-1.14.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
hicdna3dstructuresoftwarenormalizationzlibcpp
Last updated 2 months agofrom:cd71b78b50. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 19 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 19 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 19 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 19 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 19 2024 |
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
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 |
