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.

AuthorNicolas Servant
Date of publicationNone
MaintainerNicolas Servant <nicolas.servant@curie.fr>
LicenseArtistic-2.0
Version1.18.0

View on Bioconductor

Functions

addImageTracks Man page
as.list,HTClist-method Man page
binningC Man page
c,HTCexp-method Man page
c,HTClist-method Man page
colorC Man page
CQC Man page
detail Man page
detail,HTCexp-method Man page
detail,HTClist-method Man page
detail-methods Man page
directionalityIndex Man page
discretize Man page
divide Man page
divide,HTCexp,HTCexp-method Man page
divide-methods Man page
E14 Man page
exportC Man page
export-defunct Man page
export.my5C Man page
extractRegion Man page
forcePairwise Man page
forcePairwise,HTClist-method Man page
forceSymmetric,HTCexp,character-method Man page
forceSymmetric,HTCexp,missing-method Man page
forceSymmetric,HTClist,character-method Man page
forceSymmetric,HTClist,missing-method Man page
forceTriangular Man page
forceTriangular,HTCexp-method Man page
forceTriangular-method Man page
gdiag Man page
getAnnotatedRestrictionSites Man page
getCombinedContacts Man page
getCombinedContacts,HTClist-method Man page
getCombinedContacts-method Man page
getCombinedIntervals Man page
getCombinedIntervals,HTClist-method Man page
getCombinedIntervals-method Man page
getData2Map Man page
getDeltaRange Man page
getExpectedCounts Man page
getPearsonMap Man page
getRestrictionFragmentsPerChromosome Man page
heatmapC Man page
HTCexp Man page
HTCexp-class Man page
HTClist Man page
[,HTClist,ANY,ANY,ANY-method Man page
[,HTClist,ANY,ANY-method Man page
HTClist-class Man page
id Man page
id,GRanges-method Man page
id-methods Man page
importC Man page
import.my5C Man page
intdata Man page
intdata<- Man page
intdata<-,HTCexp,Matrix-method Man page
intdata,HTCexp-method Man page
intdata-method Man page
intdata<--methods Man page
intervalsDist Man page
isBinned Man page
isBinned,HTCexp-method Man page
isBinned,HTClist-method Man page
isBinned-methods Man page
isComplete Man page
isComplete,HTClist-method Man page
isComplete-methods Man page
isIntraChrom Man page
isIntraChrom,HTCexp-method Man page
isIntraChrom,HTClist-method Man page
isIntraChrom-methods Man page
isPairwise Man page
isPairwise,HTClist-method Man page
isPairwise-method Man page
isSymmetric Man page
isSymmetric,HTCexp-method Man page
isSymmetric-methods Man page
isTriangular,HTCexp-method Man page
isTriangular-methods Man page
mapC Man page
mapC,HTCexp,ANY-method Man page
mapC,HTCexp,HTCexp-method Man page
mapC,HTClist,ANY-method Man page
mapC-methods Man page
MEF Man page
my5C2gr Man page
Nora_5C Man page
normICE Man page
normLGF Man page
normPerExpected Man page
normPerExpected,HTCexp-method Man page
normPerExpected,HTClist-method Man page
normPerExpected-methods Man page
normPerReads Man page
normPerReads,HTCexp-method Man page
normPerReads-methods Man page
normPerTrans Man page
normPerTrans,HTCexp,HTCexp,HTCexp-method Man page
normPerTrans-methods Man page
normPerZscore-defunct Man page
pair.chrom Man page
pca.hic Man page
plot,HTCexp,ANY-method Man page
plot,HTCexp,HTCexp-method Man page
plot,HTClist,ANY-method Man page
range Man page
range,HTCexp-method Man page
range,HTClist-method Man page
range-method Man page
ranges Man page
ranges,HTClist-method Man page
ranges-methods Man page
reduce Man page
reduce,HTClist-method Man page
reduce-methods Man page
removeIntervals Man page
seqlevels Man page
seqlevels,HTCexp-method Man page
seqlevels,HTClist-method Man page
seqlevels-method Man page
seq_name-deprecated Man page
setGenomicFeatures Man page
setIntervalScale Man page
show,HTCexp-method Man page
show,HTClist-method Man page
substract Man page
substract,HTCexp,HTCexp-method Man page
substract-methods Man page
summary,HTCexp-method Man page
summary,HTClist-method Man page
tricube Man page
triViewC Man page
x_intervals Man page
x_intervals<- Man page
x_intervals<-,HTCexp,GRanges-method Man page
x_intervals,HTCexp-method Man page
x_intervals<--methods Man page
x_intervals-methods Man page
xy_intervals Man page
xy_intervals,HTCexp-method Man page
xy_intervals-methods Man page
y_intervals Man page
y_intervals<- Man page
y_intervals<-,HTCexp,GRanges-method Man page
y_intervals,HTCexp-method Man page
y_intervals,HTCexp-method Man page
y_intervals<--methods Man page
y_intervals-methods Man page

Files

HiTC/DESCRIPTION
HiTC/NAMESPACE
HiTC/NEWS
HiTC/R
HiTC/R/AllGenerics.R HiTC/R/HTCexp-class.R HiTC/R/HTClist-class.R HiTC/R/binningC.R HiTC/R/deprecated.R HiTC/R/export.R HiTC/R/import.R HiTC/R/mapC.R HiTC/R/mapC_tracks.R HiTC/R/normalize_5C.R HiTC/R/normalize_hiC.R HiTC/R/pca.R HiTC/R/qualityControl.R HiTC/R/tads.R
HiTC/build
HiTC/build/vignette.rds
HiTC/data
HiTC/data/Nora_5C.RData
HiTC/inst
HiTC/inst/CITATION
HiTC/inst/doc
HiTC/inst/doc/HiC_analysis.R
HiTC/inst/doc/HiC_analysis.Rnw
HiTC/inst/doc/HiC_analysis.pdf
HiTC/inst/doc/HiTC.R
HiTC/inst/doc/HiTC.Rnw
HiTC/inst/doc/HiTC.pdf
HiTC/inst/extdata
HiTC/inst/extdata/CTCF_chrX_98892125_102969775.bed
HiTC/inst/extdata/HIC_gm06690_chr12_chr12_1000000_obs.txt
HiTC/inst/extdata/HIC_gm06690_chr12_chr13_1000000_obs.txt
HiTC/inst/extdata/HIC_gm06690_chr12_chr14_1000000_obs.txt
HiTC/inst/extdata/HIC_gm06690_chr13_chr13_1000000_obs.txt
HiTC/inst/extdata/HIC_gm06690_chr13_chr14_1000000_obs.txt
HiTC/inst/extdata/HIC_gm06690_chr14_chr14_1000000_obs.txt
HiTC/inst/extdata/refseq_mm9_chrX_98831149_103425150.bed
HiTC/man
HiTC/man/CQC.Rd HiTC/man/HTCexp-class.Rd HiTC/man/HTClist-class.Rd HiTC/man/HiTC-internal.Rd HiTC/man/Nora_5C.Rd HiTC/man/binningC.Rd HiTC/man/directionalityIndex.Rd HiTC/man/discretize.Rd HiTC/man/export.my5C.Rd HiTC/man/exportC.Rd HiTC/man/extractRegion.Rd HiTC/man/getAnnotatedRestrictionSites.Rd HiTC/man/getExpectedCounts.Rd HiTC/man/getPearsonMap.Rd HiTC/man/getRestrictionFragmentsPerChromosome.Rd HiTC/man/import.my5C.Rd HiTC/man/importC.Rd HiTC/man/intervalsDist.Rd HiTC/man/mapC.Rd HiTC/man/normICE.Rd HiTC/man/normLGF.Rd HiTC/man/pca.hic.Rd HiTC/man/removeIntervals.Rd HiTC/man/setGenomicFeatures.Rd HiTC/man/setIntervalScale.Rd
HiTC/vignettes
HiTC/vignettes/HiC_analysis.Rnw
HiTC/vignettes/HiTC.Rnw
HiTC/vignettes/HiTC.bib
HiTC/vignettes/HiTC_memory_usage.png

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