segmentSeq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see segmentSeq.
Methods for identifying small RNA loci from high-throughput sequencing data
Bioconductor version: 3.9
High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.
Author: Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48 at cam.ac.uk>
citation("segmentSeq")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("segmentSeq")
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("segmentSeq")| segmentSeq: small RNA locus detection | R Script | |
| segmentsSeq: Methylation locus identification | R Script | |
| Reference Manual |
Details
| biocViews | Alignment, DataImport, DifferentialExpression, MultipleComparison, QualityControl, Sequencing, Software |
| Version | 2.18.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (14 years) |
| License | GPL-3 |
| Depends | R (>= 3.0.0), methods, baySeq(>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats |
| Imports | Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, BiocGenerics |
| 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 | segmentSeq_2.18.0.tar.gz |
| Windows Binary | segmentSeq_2.18.0.zip |
| Mac OS X 10.11 (El Capitan) | segmentSeq_2.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/segmentSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/segmentSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/segmentSeq/ |
| Package Short Url | https://bioconductor.org/packages/segmentSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |