- Home
- Bioconductor 3.4
- Software Packages
- diffloop
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
|
|
|
|
|
|
|
|
Identifying differential DNA loops from chromatin topology data
Bioconductor version: Release (3.4)
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 | 1.2.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| 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.
| Package Source | diffloop_1.2.2.tar.gz |
| Windows Binary | diffloop_1.2.2.zip |
| Mac OS X 10.9 (Mavericks) | diffloop_1.2.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/diffloop/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/diffloop/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
