recipe bioconductor-orthos

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

Homepage:

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

1.0.1-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-basilisk:

>=1.14.0,<1.15.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-orthosdata:

>=1.0.0,<1.1.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-colorspace:

depends r-cowplot:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-ggsci:

depends r-keras:

depends r-plyr:

depends r-reticulate:

depends r-rlang:

depends r-tensorflow:

depends r-tidyr:

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-orthos

and update with::

   mamba update bioconductor-orthos

To create a new environment, run:

mamba create --name myenvname bioconductor-orthos

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-orthos:<tag>

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

Download stats

Link to this page

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