REDseq
This is thereleased version of REDseq; for the devel version, seeREDseq.
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Bioconductor version: Release (3.22)
The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
Author: Lihua Julie Zhu, Junhui Li and Thomas Fazzio
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>
citation("REDseq")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("REDseq")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("REDseq")| REDseq Vignette | R Script | |
| Reference Manual |
Details
| biocViews | Preprocessing,SequenceMatching,Sequencing,Software |
| Version | 1.56.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.5.0),BiocGenerics,BSgenome.Celegans.UCSC.ce2,multtest,Biostrings,BSgenome,ChIPpeakAnno |
| Imports | AnnotationDbi, graphics,IRanges(>= 1.13.5), stats, utils |
| System Requirements | |
| URL |
See More
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| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | REDseq_1.56.0.tar.gz |
| Windows Binary (x86_64) | REDseq_1.56.0.zip (64-bit only) |
| macOS Binary (x86_64) | REDseq_1.56.0.tgz |
| macOS Binary (arm64) | REDseq_1.56.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/REDseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/REDseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/REDseq/ |
| Package Short Url | https://bioconductor.org/packages/REDseq/ |
| Package Downloads Report | Download Stats |