REDseq
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Bioconductor version: 3.23 · Package version: 1.58.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("REDseq")Details
| Maintainer | Lihua Julie Zhu <julie.zhu@umassmed.edu> |
| Author | Lihua Julie Zhu, Junhui Li and Thomas Fazzio |
| License | GPL (>=2) |
| Downloads rank | 583 |
| Source branch | RELEASE_3_23 |
| biocViews | Preprocessing, SequenceMatching, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | REDseq_1.58.0.tar.gz |
| Windows binary (x86_64) | REDseq_1.58.0.zip |
| macOS binary (arm64) | REDseq_1.58.0.tgz |
| macOS binary (x86_64) | REDseq_1.58.0.tgz |
Dependencies
Depends: R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno
Imports: AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils