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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("diffloop")
In most cases, you don't need to download the package archive at all.
diffloop
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Identifying differential DNA loops from chromatin topology data
Bioconductor version: Release (3.5)
A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.
Author: Caleb Lareau [aut, cre], Martin Aryee [aut]
Maintainer: Caleb Lareau <caleblareau at g.harvard.edu>
Citation (from within R,
enter citation("diffloop")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("diffloop")
Documentation
| HTML | R Script | diffloop: Identifying differential DNA loops from chromatin topology data. |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DataImport, DataRepresentation, GO, Preprocessing, QualityControl, Software, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | methods, GenomicRanges, foreach, plyr, dplyr, reshape2, ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt, GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats, utils, Biobase, readr, data.table, rtracklayer, pbapply, limma |
| LinkingTo | |
| Suggests | DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/aryeelab/diffloop |
| BugReports | https://github.com/aryeelab/diffloop/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | diffloop_1.4.0.tar.gz |
| Windows Binary | diffloop_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | diffloop_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/diffloop |
| Package Short Url | http://bioconductor.org/packages/diffloop/ |
| Package Downloads Report | Download Stats |
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