ROSeq
This is the released version of ROSeq; for the devel version, see ROSeq.
Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data
Bioconductor version: Release (3.23)
ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used.
Author: Krishan Gupta [aut, cre], Manan Lalit [aut], Aditya Biswas [aut], Abhik Ghosh [aut], Debarka Sengupta [aut]
Maintainer: Krishan Gupta <krishang at iiitd.ac.in>
citation("ROSeq")):
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("ROSeq")
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("ROSeq")| ROSeq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, SingleCell, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | pbmcapply, edgeR, limma |
| System Requirements | |
| URL | https://github.com/krishan57gupta/ROSeq |
| Bug Reports | https://github.com/krishan57gupta/ROSeq/issues |
See More
| Suggests | knitr, rmarkdown, testthat, RUnit, 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 | ROSeq_1.24.0.tar.gz |
| Windows Binary (x86_64) | ROSeq_1.24.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | ROSeq_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | ROSeq_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ROSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ROSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/ROSeq/ |
| Package Short Url | https://bioconductor.org/packages/ROSeq/ |
| Package Downloads Report | Download Stats |