tradeSeq

DOI: 10.18129/B9.bioc.tradeSeq    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see tradeSeq.

trajectory-based differential expression analysis for sequencing data

Bioconductor version: 3.10

tradeSeq provides a flexible method for finding genes that are differentially expressed along one or multiple trajectories, using a variety of tests suited to answer questions of interest, e.g. the discovery of genes that whose expression is associated with pseudotime, or who are differentially expressed (in a specific region) along the trajectory. It fits a 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] , Kelly Street [ctb], Lieven Clement [ctb], Sandrine Dudoit [ctb]

Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux at berkeley.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	'Vignette for **tradeSeq**
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, TimeCourse, Transcriptomics, Visualization
Version	1.0.1
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, clusterExperiment, BiocParallel, pbapply, ggplot2, princurve, methods, S4Vectors
LinkingTo
Suggests	knitr, rmarkdown, cowplot, dplyr, tidyr, testthat
SystemRequirements
Enhances
URL	https://statomics.github.io/tradeSeq/index.html
BugReports	https://github.com/statOmics/tradeSeq/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	tradeSeq_1.0.1.tar.gz
Windows Binary	tradeSeq_1.0.1.zip
Mac OS X 10.11 (El Capitan)	tradeSeq_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tradeSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tradeSeq
Package Short Url	https://bioconductor.org/packages/tradeSeq/
Package Downloads Report	Download Stats