REDseq
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Bioconductor version: 2.10
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 and Thomas Fazzio
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("REDseq")
To cite this package in a publication, start R and enter:
citation("REDseq")
Documentation
| R Script | REDseq Vignette | |
| Reference Manual |
Details
| biocViews | Preprocessing, SequenceMatching, Sequencing, Software |
| Depends | R (>= 2.14.0), BiocGenerics(>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno |
| Imports | BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges(>= 1.13.5), multtest, stats, utils |
| Suggests | |
| System Requirements | |
| License | GPL (>=2) |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 1.2.0 |
| Since | Bioconductor 2.9 (R-2.14) |
Package Downloads
| Package Source | REDseq_1.2.0.tar.gz |
| Windows Binary | REDseq_1.2.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | REDseq_1.2.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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