Package Recipe 'bioconductor-tigre'

recipe bioconductor-tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Homepage:: https://bioconductor.org/packages/3.20/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:

1.64.0-0, 1.60.0-0, 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,

1.64.0-0, 1.60.0-0, 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:

on bioconductor-annotate >=1.88.0,<1.89.0
on bioconductor-annotate >=1.88.0,<1.89.0a0
on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0a0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biobase >=2.70.0,<2.71.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-dbi
on r-gplots
on r-rsqlite

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-tigre

to add into an existing workspace instead, run:

pixi add bioconductor-tigre

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-tigre

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-tigre

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tigre/README.html)