GOTHiC: Binomial test for Hi-C data analysis
Version 1.12.0

This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

AuthorBorbala Mifsud and Robert Sugar
Bioconductor views Epigenetics HiC Preprocessing Sequencing
Date of publicationNone
MaintainerBorbala Mifsud <b.mifsud@qmul.ac.uk>
LicenseGPL-3
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GOTHiC")

Popular man pages

filtered: A GenomicRangesList object used as an example in the GOTHiC...
GOTHiC: Genome Organisation Through HiC
GOTHiChicup: Genome Organisation Through HiC from HiCUP output
mapReadsToRestrictionSites: Function to map aligned and paired reads to the restriction...
pairReads: Function pairs aligned paired NGS reads
See all...

All man pages Function index File listing

Man pages

filtered: A GenomicRangesList object used as an example in the GOTHiC...
GOTHiC: Genome Organisation Through HiC
GOTHiChicup: Genome Organisation Through HiC from HiCUP output
mapReadsToRestrictionSites: Function to map aligned and paired reads to the restriction...
pairReads: Function pairs aligned paired NGS reads

Functions

GOTHiC Man page Source code
GOTHiChicup Man page Source code
binInteractions Source code
binomialHiC Source code
binomialHiChicup Source code
countDuplicates Source code
countDuplicatesOfRaw Source code
exportCoverage Source code
filterOutDuplicates Source code
filtered Man page
findOverlaps.circle Source code
findOverlaps.parallel Source code
fixChromosomeNames Source code
getHindIIIsitesFromHicup Source code
getRestrictionSitesFromBSgenome Source code
lymphoid_chr20_paired_filtered Man page
mapHicupToRestrictionFragment Source code
mapReadsToRestrictionSites Man page Source code
mportHicup Source code
onlyPairing Source code
pairReads Man page Source code
putRangesOnFirstCircle Source code
strandAsSignedNumber Source code

Files

DESCRIPTION
NAMESPACE
R
R/GOTHiC.R
build
build/vignette.rds
data
data/datalist
data/lymphoid_chr20_paired_filtered.rdata
inst
inst/doc
inst/doc/package_vignettes.R
inst/doc/package_vignettes.Snw
inst/doc/package_vignettes.pdf
man
man/GOTHiC.Rd
man/GOTHiChicup.Rd
man/filtered.Rd
man/mapReadsToRestrictionSites.Rd
man/pairReads.Rd
vignettes
vignettes/lymphoid_chr20_pvalue_distribution.pdf
vignettes/package_vignettes.Snw
GOTHiC documentation built on May 20, 2017, 10:02 p.m.

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