recipe bioconductor-tradeseq

trajectory-based differential expression analysis for sequencing data

Homepage:

https://bioconductor.org/packages/3.18/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:

1.16.0-0,  1.14.0-0,  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:

>=2.62.0,<2.63.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-slingshot:

>=2.10.0,<2.11.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-trajectoryutils:

>=1.10.0,<1.11.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-igraph:

depends r-magrittr:

depends r-mass:

depends r-matrix:

depends r-matrixstats:

depends r-mgcv:

depends r-pbapply:

depends r-princurve:

depends r-rcolorbrewer:

depends r-tibble:

depends r-viridis:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-tradeseq

and update with::

   mamba update bioconductor-tradeseq

To create a new environment, run:

mamba create --name myenvname bioconductor-tradeseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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