BioConductor
GOTHiC 1.16.0
Binomial test for Hi-C data analysis
Released Jun 7, 2013 by Borbala Mifsud
This package cannot yet be used with Renjin it depends on other packages which are not available: rtracklayer 1.40.5, BSgenome 1.48.0, data.table 1.11.4, and ShortRead 1.38.0
Dependencies
rtracklayer 1.40.5 data.table 1.11.4 ShortRead 1.38.0 BSgenome 1.48.0 ggplot2 3.0.0 Biostrings 2.48.0 GenomicRanges 1.32.6 BiocGenerics 0.26.0 IRanges 2.14.10 S4Vectors 0.18.3 Rsamtools 1.32.3
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.