recipe bioconductor-tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/tigre.html

License:

AGPL-3

Recipe:

/bioconductor-tigre/meta.yaml

Links:

biotools: tigre

The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.

package bioconductor-tigre

versions:

1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1, 

1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0

depends bioconductor-annotate:

>=1.80.0,<1.81.0

depends bioconductor-annotate:

>=1.80.0,<1.81.0a0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationdbi:

>=1.64.1,<1.65.0a0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0a0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-gplots:

depends r-rsqlite:

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-tigre

and update with::

   mamba update bioconductor-tigre

To create a new environment, run:

mamba create --name myenvname bioconductor-tigre

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-tigre:<tag>

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

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