HiTC: High Throughput Chromosome Conformation Capture analysis

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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.

Author
Nicolas Servant
Date of publication
None
Maintainer
Nicolas Servant <nicolas.servant@curie.fr>
License
Artistic-2.0
Version
1.18.0

View on Bioconductor

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

Files in this package

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