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tradeSeq
This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see tradeSeq.
trajectory-based differential expression analysis for sequencing data
Bioconductor version: 3.21
tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
Author: Koen Van den Berge [aut], Hector Roux de Bezieux [aut, cre] ORCID iD ORCID: 0000-0002-1489-8339 , Kelly Street [aut, ctb], Lieven Clement [aut, ctb], Sandrine Dudoit [ctb]
Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux at berkeley.edu>
citation("tradeSeq")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tradeSeq")
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("tradeSeq")
Details
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Follow Installation instructions to use this package in your R session.