Package Recipe 'bioconductor-orthos'

recipe bioconductor-orthos

`orthos` is an R package for variance decomposition using conditional variational auto-encoders

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/orthos.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-orthos/meta.yaml

`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.

package bioconductor-orthos¶

Versions:

1.8.0-0, 1.4.0-0, 1.0.1-0

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-basilisk >=1.22.0,<1.23.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-hdf5array >=1.38.0,<1.39.0
on bioconductor-orthosdata >=1.8.0,<1.9.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-colorspace
on r-cowplot
on r-dplyr
on r-ggplot2 >=3.4.0
on r-ggpubr
on r-ggrepel
on r-ggsci
on r-keras >=2.16.0
on r-plyr
on r-reticulate
on r-rlang
on r-tensorflow
on r-tidyr

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-orthos

to add into an existing workspace instead, run:

pixi add bioconductor-orthos

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-orthos

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-orthos

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-orthos:<tag>

(see bioconductor-orthos/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-orthos/README.html)