GOTHiC: Binomial test for Hi-C data analysis

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.

Author
Borbala Mifsud and Robert Sugar
Date of publication
None
Maintainer
Borbala Mifsud <Borbala.Mifsud@cancer.org.uk>
License
GPL-3
Version
1.10.0

View on Bioconductor

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

Files in this package

GOTHiC/DESCRIPTION
GOTHiC/NAMESPACE
GOTHiC/R
GOTHiC/R/GOTHiC.R
GOTHiC/build
GOTHiC/build/vignette.rds
GOTHiC/data
GOTHiC/data/datalist
GOTHiC/data/lymphoid_chr20_paired_filtered.rdata
GOTHiC/inst
GOTHiC/inst/doc
GOTHiC/inst/doc/package_vignettes.R
GOTHiC/inst/doc/package_vignettes.Snw
GOTHiC/inst/doc/package_vignettes.pdf
GOTHiC/man
GOTHiC/man/GOTHiC.Rd
GOTHiC/man/GOTHiChicup.Rd
GOTHiC/man/filtered.Rd
GOTHiC/man/mapReadsToRestrictionSites.Rd
GOTHiC/man/pairReads.Rd
GOTHiC/vignettes
GOTHiC/vignettes/lymphoid_chr20_pvalue_distribution.pdf
GOTHiC/vignettes/package_vignettes.Snw