HBP: Hi-C BED File Analysis Pipeline

Hi-C dataset processing algorithm introduced by Chao He (2016) <doi.org/10.1101/083576>. The optimized and flexible pipeline for analyzing the folding of whole chromosome and interactions between some specific sites from the Hi-C raw sequencing reads to the partially processed datasets. The other complex genetic and epigenetic datasets from public sources such as GWAS, ENCODE consortiums etc. will also easily be integrated into HBP, hence the final output results of HBP could provide a comprehensive in-depth understanding for the specific chromatin interactions, potential molecular mechanisms and biological significance. We believe that HBP is a reliable tool for the rapidly analysis of Hi-C data and will be very useful for a wide range of researchers, particularly those who lack of background in computational biology.

Version: 0.1.2
Depends: R (≥ 3.0.0)
Imports: grid, lattice, BiocInstaller, rtracklayer, OmicCircos, ggplot2, igraph, reshape2, pgirmess, coin, multcomp, flexclust, HiTC, gplots
Suggests: BSgenome.Hsapiens.UCSC.hg19
Published: 2017-07-07
Author: Chao He
Maintainer: Chao He <hechao2010 at tsinghua.org.cn>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: HBP results

Downloads:

Reference manual: HBP.pdf
Package source: HBP_0.1.2.tar.gz
Windows binaries: r-devel: HBP_0.1.2.zip, r-release: HBP_0.1.2.zip, r-oldrel: HBP_0.1.2.zip
OS X binaries: r-release: HBP_0.1.2.tgz, r-oldrel: not available

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