sagenhaft
This is the development version of sagenhaft; for the stable release version, see sagenhaft.
Collection of functions for reading and comparing SAGE libraries
Bioconductor version: Development (3.24)
This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.
Author: Tim Beissbarth <tim.beissbarth at bioinf.med.uni-goettingen.de>, with contributions from Gordon Smyth <smyth at wehi.edu.au>
Maintainer: Tim Beissbarth <tim.beissbarth at bioinf.med.uni-goettingen.de>
citation("sagenhaft")):
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("sagenhaft")
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("sagenhaft")| SAGEnhaft | R Script | |
| Reference Manual |
Details
| biocViews | SAGE, Software |
| Version | 1.83.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10), SparseM (>= 0.73), methods |
| Imports | graphics, stats, utils |
| System Requirements | |
| URL | http://www.bioinf.med.uni-goettingen.de |
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 | sagenhaft_1.83.0.tar.gz |
| Windows Binary (x86_64) | sagenhaft_1.83.0.zip |
| macOS Binary (big-sur-x86_64) | sagenhaft_1.83.0.tgz |
| macOS Binary (sonoma-arm64) | sagenhaft_1.83.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sagenhaft |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sagenhaft |
| Bioc Package Browser | https://code.bioconductor.org/browse/sagenhaft/ |
| Package Short Url | https://bioconductor.org/packages/sagenhaft/ |
| Package Downloads Report | Download Stats |