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:
HiTC_1.51.0.tar.gz
HiTC_1.51.0.zip(r-4.5)HiTC_1.51.0.zip(r-4.4)HiTC_1.51.0.zip(r-4.3)
HiTC_1.51.0.tgz(r-4.4-any)HiTC_1.51.0.tgz(r-4.3-any)
HiTC_1.51.0.tar.gz(r-4.5-noble)HiTC_1.51.0.tar.gz(r-4.4-noble)
HiTC_1.51.0.tgz(r-4.4-emscripten)HiTC_1.51.0.tgz(r-4.3-emscripten)
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')) |
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
Last updated 2 months agofrom:1718634982. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | WARNING | Dec 18 2024 |
| R-4.5-linux | WARNING | Dec 18 2024 |
| R-4.4-win | WARNING | Dec 18 2024 |
| R-4.4-mac | WARNING | Dec 18 2024 |
| R-4.3-win | WARNING | Dec 18 2024 |
| R-4.3-mac | WARNING | Dec 18 2024 |
Exports:as.listbinningCCQCdetaildirectionalityIndexdiscretizedivideexport.my5CexportCextractRegionforcePairwiseforceSymmetricforceTriangulargetAnnotatedRestrictionSitesgetCombinedContactsgetCombinedIntervalsgetExpectedCountsgetPearsonMapgetRestrictionFragmentsPerChromosomeHTCexpHTClistidimport.my5CimportCintdataintdata<-intervalsDistisBinnedisCompleteisIntraChromisPairwiseisSymmetricisTriangularmapCnormICEnormLGFnormPerExpectednormPerReadsnormPerTranspca.hicrangesreduceremoveIntervalsseqlevelssetGenomicFeaturessetIntervalScaleshowsubstractsummaryx_intervalsx_intervals<-xy_intervalsy_intervalsy_intervals<-
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Windowing of high-throughput 'C' contact matrix | binningC |
| Quality Control for high-throughput 'C' experiment | CQC |
| Directionality index calculation | directionalityIndex |
| Transform matrix of counts data into discrete matrix | discretize |
| Export 'HTCexp' object to my5C website format | export.my5C |
| Export 'HTCexp' object | exportC |
| Extract a subset of the HTCexp object | extractRegion |
| Annotation of restriction sites | getAnnotatedRestrictionSites |
| Estimate expected interaction counts of a High-Throughput C intrachromsomal map based on the genomic distance between two loci | getExpectedCounts |
| Pearson correlation map | getPearsonMap |
| Get a list of DNA restriction fragments | getRestrictionFragmentsPerChromosome |
| 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 webtool | import.my5C |
| Import high-htroughput 'C' data | importC |
| intervalsDist | intervalsDist |
| Visualize 'C' ontact map | mapC mapC,HTCexp,ANY-method mapC,HTCexp,HTCexp-method mapC,HTClist,ANY-method mapC-methods |
| HiTC - 5C data | E14 MEF Nora_5C |
| Iterative Correction of Hi-C data (ICE) | normICE |
| Local Genomic Feature (LGF) normalization | normLGF |
| Perform Principle Component Analysis on Hi-C contact map | pca.hic |
| Remove intervals from HTCexp object | removeIntervals |
| Annotation of Hi-C contact map | setGenomicFeatures |
| Set x and y interval of the HTCexp object | setIntervalScale |
