Package: HicAggR 1.1.2
Olivier Cuvier
HicAggR: Set of 3D genomic interaction analysis tools
This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.
Authors:
HicAggR_1.1.2.tar.gz
HicAggR_1.1.2.zip(r-4.5)HicAggR_1.1.2.zip(r-4.4)HicAggR_1.1.2.zip(r-4.3)
HicAggR_1.1.2.tgz(r-4.4-any)HicAggR_1.1.2.tgz(r-4.3-any)
HicAggR_1.1.2.tar.gz(r-4.5-noble)HicAggR_1.1.2.tar.gz(r-4.4-noble)
HicAggR_1.1.2.tgz(r-4.4-emscripten)HicAggR_1.1.2.tgz(r-4.3-emscripten)
HicAggR.pdf |HicAggR.html✨
HicAggR/json (API)
NEWS
| # Install 'HicAggR' in R: |
| install.packages('HicAggR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cuvierlab/hicaggr/issues
- Beaf32_Peaks.gnr - D.melanogaster Beaf-32 ChIP-seq.
- HiC_Ctrl.cmx_lst - In situ Hi-C control.
- HiC_HS.cmx_lst - In situ Hi-C heat treated.
- TADs_Domains.gnr - D.melanogaster TADs.
- TSS_Peaks.gnr - D.melanogaster Transcription starting sites.
On BioConductor:HicAggR-1.1.2(bioc 3.20)HicAggR-1.0.2(bioc 3.19)
Last updated 2 months agofrom:527fc80ba8
Exports:AggregationBalanceHiCBinGRangesCompareToBackgroundCutHiCExtractSubmatrixFilterInteractionsGenomicSystemGetInfoGetQuantifggAPAHueICEnormImportHiCImportLoopsIndexFeaturesJoinHiCMergeGRangesOrientateMatrixOverExpectedHiCPlotAPAplotMultiAPAPrepareMtxListpreparePlotgardenerQtlThresholdSearchPairsSeqEndsStrToGRangesSwitchMatrixVCnormviridisYlGnBuYlOrRd
Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscheckmateclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpurrrR6RColorBrewerRcppRCurlreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
