segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing data
Bioconductor version: Release (3.17)
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 "4.3") 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
| Reference Manual |
Details
| biocViews | Alignment, DataImport, DifferentialExpression, MultipleComparison, QualityControl, Sequencing, Software |
| Version | 2.34.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (13.5 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 |
| Linking To | |
| Suggests | BiocStyle, BiocGenerics |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
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| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/segmentSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/segmentSeq |
| Package Short Url | https://bioconductor.org/packages/segmentSeq/ |
| Package Downloads Report | Download Stats |