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

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

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