Package: HiTC 1.51.0

Nicolas Servant

HiTC: High Throughput Chromosome Conformation Capture analysis

The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

Authors:Nicolas Servant

HiTC_1.51.0.tar.gz
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HiTC.pdf |HiTC.html
HiTC/json (API)
NEWS

# Install 'HiTC' in R:
install.packages('HiTC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • E14 - HiTC - 5C data
  • MEF - HiTC - 5C data

On BioConductor:HiTC-1.51.0(bioc 3.21)HiTC-1.50.0(bioc 3.20)

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

sequencinghighthroughputsequencinghic

5.40 score 42 scripts 461 downloads 21 mentions 54 exports 51 dependencies

Last updated 20 days agofrom:1718634982. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:as.listbinningCCQCdetaildirectionalityIndexdiscretizedivideexport.my5CexportCextractRegionforcePairwiseforceSymmetricforceTriangulargetAnnotatedRestrictionSitesgetCombinedContactsgetCombinedIntervalsgetExpectedCountsgetPearsonMapgetRestrictionFragmentsPerChromosomeHTCexpHTClistidimport.my5CimportCintdataintdata<-intervalsDistisBinnedisCompleteisIntraChromisPairwiseisSymmetricisTriangularmapCnormICEnormLGFnormPerExpectednormPerReadsnormPerTranspca.hicrangesreduceremoveIntervalsseqlevelssetGenomicFeaturessetIntervalScaleshowsubstractsummaryx_intervalsx_intervals<-xy_intervalsy_intervalsy_intervals<-

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

Hi-C data analysis using HiTC

Rendered fromHiC_analysis.Rnwusingutils::Sweaveon Nov 18 2024.

Last update: 2021-08-31
Started: 2015-03-13

Introduction to HiTC package

Rendered fromHiTC.Rnwusingutils::Sweaveon Nov 18 2024.

Last update: 2016-09-09
Started: 2013-10-23

Readme and manuals

Help Manual

Help pageTopics
Windowing of high-throughput 'C' contact matrixbinningC
Quality Control for high-throughput 'C' experimentCQC
Directionality index calculationdirectionalityIndex
Transform matrix of counts data into discrete matrixdiscretize
Export 'HTCexp' object to my5C website formatexport.my5C
Export 'HTCexp' objectexportC
Extract a subset of the HTCexp objectextractRegion
Annotation of restriction sitesgetAnnotatedRestrictionSites
Estimate expected interaction counts of a High-Throughput C intrachromsomal map based on the genomic distance between two locigetExpectedCounts
Pearson correlation mapgetPearsonMap
Get a list of DNA restriction fragmentsgetRestrictionFragmentsPerChromosome
Class 'HTCexp'c,HTCexp-method detail detail,HTCexp-method detail-methods divide divide,HTCexp,HTCexp-method divide-methods export-defunct forceSymmetric,HTCexp,character-method forceSymmetric,HTCexp,missing-method forceTriangular forceTriangular,HTCexp-method forceTriangular-method HTCexp HTCexp-class id id,GRanges-method id-methods intdata intdata,HTCexp-method intdata-method intdata<- intdata<-,HTCexp,Matrix-method intdata<--methods isBinned isBinned,HTCexp-method isBinned-methods isIntraChrom isIntraChrom,HTCexp-method isIntraChrom-methods isSymmetric isSymmetric,HTCexp-method isSymmetric-methods isTriangular,HTCexp-method isTriangular-methods normPerExpected normPerExpected,HTCexp-method normPerExpected-methods normPerReads normPerReads,HTCexp-method normPerReads-methods normPerTrans normPerTrans,HTCexp,HTCexp,HTCexp-method normPerTrans-methods normPerZscore-defunct plot,HTCexp,ANY-method plot,HTCexp,HTCexp-method range range,HTCexp-method range-method seqlevels seqlevels,HTCexp-method seqlevels-method seq_name-deprecated show,HTCexp-method substract substract,HTCexp,HTCexp-method substract-methods summary,HTCexp-method xy_intervals xy_intervals,HTCexp-method xy_intervals-methods x_intervals x_intervals,HTCexp-method x_intervals-methods x_intervals<- x_intervals<-,HTCexp,GRanges-method x_intervals<--methods y_intervals y_intervals,HTCexp-method y_intervals-methods y_intervals<- y_intervals<-,HTCexp,GRanges-method y_intervals<--methods
Class 'HTClist'as.list,HTClist-method c,HTClist-method detail,HTClist-method forcePairwise forcePairwise,HTClist-method forceSymmetric,HTClist,character-method forceSymmetric,HTClist,missing-method getCombinedContacts getCombinedContacts,HTClist-method getCombinedContacts-method getCombinedIntervals getCombinedIntervals,HTClist-method getCombinedIntervals-method HTClist HTClist-class isBinned,HTClist-method isComplete isComplete,HTClist-method isComplete-methods isIntraChrom,HTClist-method isPairwise isPairwise,HTClist-method isPairwise-method normPerExpected,HTClist-method plot,HTClist,ANY-method range,HTClist-method ranges ranges,HTClist-method ranges-methods reduce reduce,HTClist-method reduce-methods seqlevels,HTClist-method show,HTClist-method summary,HTClist-method [,HTClist,ANY,ANY,ANY-method [,HTClist,ANY,ANY-method
Import data from my5C webtoolimport.my5C
Import high-htroughput 'C' dataimportC
intervalsDistintervalsDist
Visualize 'C' ontact mapmapC mapC,HTCexp,ANY-method mapC,HTCexp,HTCexp-method mapC,HTClist,ANY-method mapC-methods
HiTC - 5C dataE14 MEF Nora_5C
Iterative Correction of Hi-C data (ICE)normICE
Local Genomic Feature (LGF) normalizationnormLGF
Perform Principle Component Analysis on Hi-C contact mappca.hic
Remove intervals from HTCexp objectremoveIntervals
Annotation of Hi-C contact mapsetGenomicFeatures
Set x and y interval of the HTCexp objectsetIntervalScale