GOTHiC
This is the released version of GOTHiC; for the devel version, see GOTHiC.
Binomial test for Hi-C data analysis
Bioconductor version: Release (3.23)
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
Maintainer: Borbala Mifsud <b.mifsud at qmul.ac.uk>
citation("GOTHiC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GOTHiC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GOTHiC")| package_vignettes.pdf | R Script | |
| Reference Manual |
Details
| biocViews | Epigenetics, HiC, ImmunoOncology, Preprocessing, Sequencing, Software |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table |
| Imports | BiocGenerics, S4Vectors(>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, Seqinfo |
| System Requirements | |
| URL |
See More
| Suggests | HiCDataLymphoblast |
| Linking To | |
| Enhances | parallel |
| Depends On Me | |
| Imports Me | OHCA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GOTHiC_1.48.0.tar.gz |
| Windows Binary (x86_64) | GOTHiC_1.48.0.zip |
| macOS Binary (big-sur-x86_64) | GOTHiC_1.48.0.tgz |
| macOS Binary (sonoma-arm64) | GOTHiC_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GOTHiC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GOTHiC |
| Bioc Package Browser | https://code.bioconductor.org/browse/GOTHiC/ |
| Package Short Url | https://bioconductor.org/packages/GOTHiC/ |
| Package Downloads Report | Download Stats |