REDseq
This is the development version of REDseq; for the stable release version, see REDseq.
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Bioconductor version: Development (3.24)
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")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("REDseq")
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("REDseq")| REDseq Vignette | R Script | |
| Reference Manual |
Details
| biocViews | Preprocessing, SequenceMatching, Sequencing, Software |
| Version | 1.59.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 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
| Suggests | |
| 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 | REDseq_1.59.0.tar.gz |
| Windows Binary (x86_64) | REDseq_1.59.0.zip |
| macOS Binary (big-sur-x86_64) | REDseq_1.59.0.tgz |
| macOS Binary (sonoma-arm64) | REDseq_1.59.0.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 |