tradeSeq
This is the development version of tradeSeq; for the stable release version, see tradeSeq.
trajectory-based differential expression analysis for sequencing data
Bioconductor version: Development (3.24)
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]
, Kelly Street [aut, ctb], Lieven Clement [aut, ctb], Sandrine Dudoit [ctb]
Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux at berkeley.edu>
citation("tradeSeq")):
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("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")| Differential expression across conditions | HTML | |
| Monocle + tradeSeq | HTML | R Script |
| More details on working with fitGAM | HTML | R Script |
| The tradeSeq workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, MultipleComparison, RNASeq, Regression, Sequencing, SingleCell, Software, TimeCourse, Transcriptomics, Visualization |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS |
| System Requirements | |
| URL | https://statomics.github.io/tradeSeq/index.html |
| Bug Reports | https://github.com/statOmics/tradeSeq/issues |
See More
| Suggests | knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats |
| Linking To | |
| Enhances | |
| Depends On Me | OSCA.advanced |
| Imports Me | |
| Suggests Me | blase |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tradeSeq_1.27.0.tar.gz |
| Windows Binary (x86_64) | tradeSeq_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | tradeSeq_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | tradeSeq_1.27.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tradeSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tradeSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/tradeSeq/ |
| Package Short Url | https://bioconductor.org/packages/tradeSeq/ |
| Package Downloads Report | Download Stats |