DeconRNASeq
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DeconRNASeq.
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
Bioconductor version: Release (3.23)
DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.
Author: Ting Gong <tinggong at gmail.com> Joseph D. Szustakowski <joseph.szustakowski at novartis.com>
Maintainer: Ting Gong <tinggong at gmail.com>
citation("DeconRNASeq")):
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")
BiocManager::install("DeconRNASeq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DifferentialExpression, Software |
| Version | 1.53.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 years) |
| License | GPL-2 |
| Depends | R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid |
| Imports | |
| System Requirements | |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | DeconRNASeq_1.53.1.zip |
| macOS Binary (big-sur-x86_64) | DeconRNASeq_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | DeconRNASeq_1.53.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DeconRNASeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DeconRNASeq |
| Package Short Url | https://bioconductor.org/packages/DeconRNASeq/ |
| Package Downloads Report | Download Stats |