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.
|Date of publication||None|
|Maintainer||Nicolas Servant <firstname.lastname@example.org>|
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
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