recipe bioconductor-tradeseq

trajectory-based differential expression analysis for sequencing data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/tradeSeq.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-tradeseq/meta.yaml

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.

package bioconductor-tradeseq

Versions:

1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-slingshot >=2.6.0,<2.7.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-trajectoryutils >=1.6.0,<1.7.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-igraph

• r-magrittr

• r-mass

• r-matrix

• r-matrixstats

• r-mgcv

• r-pbapply

• r-princurve

• r-rcolorbrewer

• r-tibble

• r-viridis

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-tradeseq

and update with:

conda update bioconductor-tradeseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-tradeseq:<tag>

(see bioconductor-tradeseq/tags for valid values for <tag>)

Download stats

Link to this page

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