HiTC: High Throughput Chromosome Conformation Capture analysis
Version 1.20.0

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
Bioconductor views HiC HighThroughputSequencing Sequencing
Date of publicationNone
MaintainerNicolas Servant <nicolas.servant@curie.fr>
LicenseArtistic-2.0
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HiTC")

Popular man pages

directionalityIndex: Directionality index calculation
getAnnotatedRestrictionSites: Annotation of restriction sites
HiTC-internal: Internal HiTC functions
HTCexp-class: Class 'HTCexp'
HTClist-class: Class 'HTClist'
normICE: Iterative Correction of Hi-C data (ICE)
pca.hic: Perform Principle Component Analysis on Hi-C contact map
See all...

All man pages Function index File listing

Man pages

binningC: Windowing of high-throughput 'C' contact matrix
CQC: Quality Control for high-throughput 'C' experiment
directionalityIndex: Directionality index calculation
discretize: Transform matrix of counts data into discrete matrix
exportC: Export 'HTCexp' object
export.my5C: Export 'HTCexp' object to my5C website format
extractRegion: Extract a subset of the HTCexp object
getAnnotatedRestrictionSites: Annotation of restriction sites
getExpectedCounts: Estimate expected interaction counts of a High-Throughput C...
getPearsonMap: Pearson correlation map
getRestrictionFragmentsPerChromosome: Get a list of DNA restriction fragments
HiTC-internal: Internal HiTC functions
HTCexp-class: Class 'HTCexp'
HTClist-class: Class 'HTClist'
importC: Import high-htroughput 'C' data
import.my5C: Import data from my5C webtool
intervalsDist: intervalsDist
mapC: Visualize 'C' ontact map
Nora_5C: HiTC - 5C data
normICE: Iterative Correction of Hi-C data (ICE)
normLGF: Local Genomic Feature (LGF) normalization
pca.hic: Perform Principle Component Analysis on Hi-C contact map
removeIntervals: Remove intervals from HTCexp object
setGenomicFeatures: Annotation of Hi-C contact map
setIntervalScale: Set x and y interval of the HTCexp object

Functions

CQC Man page Source code
E14 Man page
HTCexp Man page Source code
HTCexp-class Man page
HTClist Man page Source code
HTClist-class Man page
MEF Man page
Nora_5C Man page
[,HTClist,ANY,ANY,ANY-method Man page
[,HTClist,ANY,ANY-method Man page
addImageTracks Man page Source code
annotateIntervals Source code
as.list,HTClist-method Man page
balancingSK Source code
binningC Man page Source code
c,HTCexp-method Man page
c,HTClist-method Man page
colorC Man page Source code
detail Man page
detail,HTCexp-method Man page
detail,HTClist-method Man page
detail-methods Man page
dimnames2gr Source code
directionalityIndex Man page Source code
discretize Man page Source code
divide Man page
divide,HTCexp,HTCexp-method Man page
divide-methods Man page
export-defunct Man page
export.my5C Man page Source code
exportC Man page Source code
extractCounts Source code
extractRegion Man page Source code
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 Source code
getAnnotatedRestrictionSites Man page Source code
getBlocsIndex Source code
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 Source code
getDeltaRange Man page Source code
getExpectedCounts Man page Source code
getExpectedCountsLoess Source code
getExpectedCountsMean Source code
getPearsonMap Man page Source code
getRestrictionFragmentsPerChromosome Man page Source code
getRestrictionSitesPerChromosome Source code
heatmapC Man page Source code
id Man page
id,GRanges-method Man page
id-methods Man page
import.my5C Man page Source code
importC Man page Source code
intdata Man page
intdata,HTCexp-method Man page
intdata-method Man page
intdata<- Man page
intdata<-,HTCexp,Matrix-method Man page
intdata<--methods Man page
intervalsDist Man page Source code
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
logbins Source code
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
maskdiag Source code
my5C2gr Man page
normICE Man page Source code
normLGF Man page Source code
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 Source code
pca.hic Man page Source code
plot,HTCexp,ANY-method Man page
plot,HTCexp,HTCexp-method Man page
plot,HTClist,ANY-method Man page
plotHistCounts Source code
plotHistDist Source code
plotInterIntraRatio Source code
plotIntraDist Source code
plottingfunc Source code
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 Source code
saveContactMaps Source code
seq_name-deprecated Man page
seqlevels Man page
seqlevels,HTCexp-method Man page
seqlevels,HTClist-method Man page
seqlevels-method Man page
setEnvDisplay Source code
setGenomicFeatures Man page Source code
setIntervalScale Man page Source code
show,HTCexp-method Man page
show,HTClist-method Man page
slidingWindow Source code
sparseCor Source code
splitCombinedContacts Source code
substract Man page
substract,HTCexp,HTCexp-method Man page
substract-methods Man page
summary,HTCexp-method Man page
summary,HTClist-method Man page
triViewC Man page Source code
tricube Man page Source code
write.my5C Source code
writeC Source code
x_intervals Man page
x_intervals,HTCexp-method Man page
x_intervals-methods Man page
x_intervals<- Man page
x_intervals<-,HTCexp,GRanges-method 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,HTCexp-method Man page Man page
y_intervals-methods Man page
y_intervals<- Man page
y_intervals<-,HTCexp,GRanges-method Man page
y_intervals<--methods Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/HTCexp-class.R
R/HTClist-class.R
R/binningC.R
R/deprecated.R
R/export.R
R/import.R
R/mapC.R
R/mapC_tracks.R
R/normalize_5C.R
R/normalize_hiC.R
R/pca.R
R/qualityControl.R
R/tads.R
build
build/vignette.rds
data
data/Nora_5C.RData
inst
inst/CITATION
inst/doc
inst/doc/HiC_analysis.R
inst/doc/HiC_analysis.Rnw
inst/doc/HiC_analysis.pdf
inst/doc/HiTC.R
inst/doc/HiTC.Rnw
inst/doc/HiTC.pdf
inst/extdata
inst/extdata/CTCF_chrX_98892125_102969775.bed
inst/extdata/HIC_gm06690_chr12_chr12_1000000_obs.txt
inst/extdata/HIC_gm06690_chr12_chr13_1000000_obs.txt
inst/extdata/HIC_gm06690_chr12_chr14_1000000_obs.txt
inst/extdata/HIC_gm06690_chr13_chr13_1000000_obs.txt
inst/extdata/HIC_gm06690_chr13_chr14_1000000_obs.txt
inst/extdata/HIC_gm06690_chr14_chr14_1000000_obs.txt
inst/extdata/refseq_mm9_chrX_98831149_103425150.bed
man
man/CQC.Rd
man/HTCexp-class.Rd
man/HTClist-class.Rd
man/HiTC-internal.Rd
man/Nora_5C.Rd
man/binningC.Rd
man/directionalityIndex.Rd
man/discretize.Rd
man/export.my5C.Rd
man/exportC.Rd
man/extractRegion.Rd
man/getAnnotatedRestrictionSites.Rd
man/getExpectedCounts.Rd
man/getPearsonMap.Rd
man/getRestrictionFragmentsPerChromosome.Rd
man/import.my5C.Rd
man/importC.Rd
man/intervalsDist.Rd
man/mapC.Rd
man/normICE.Rd
man/normLGF.Rd
man/pca.hic.Rd
man/removeIntervals.Rd
man/setGenomicFeatures.Rd
man/setIntervalScale.Rd
vignettes
vignettes/HiC_analysis.Rnw
vignettes/HiTC.Rnw
vignettes/HiTC.bib
vignettes/HiTC_memory_usage.png
HiTC documentation built on May 20, 2017, 9:44 p.m.

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