diffloop
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see diffloop.
Identifying differential DNA loops from chromatin topology data
Bioconductor version: 3.9
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("diffloop")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("diffloop")
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("diffloop")| diffloop: Identifying differential DNA loops from chromatin topology data. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, GO, Preprocessing, QualityControl, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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 |
| System Requirements | |
| URL | https://github.com/aryeelab/diffloop |
| Bug Reports | https://github.com/aryeelab/diffloop/issues |
See More
| Suggests | DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | diffloop_1.12.0.tar.gz |
| Windows Binary | diffloop_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | diffloop_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/diffloop |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/diffloop |
| Bioc Package Browser | https://code.bioconductor.org/browse/diffloop/ |
| Package Short Url | https://bioconductor.org/packages/diffloop/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |