recipe bioconductor-top

TOP Constructs Transferable Model Across Gene Expression Platforms

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-top/meta.yaml

TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

package bioconductor-top

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-classifyr:

>=3.6.0,<3.7.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-caret:

depends r-directpa:

depends r-doparallel:

depends r-dplyr:

depends r-ggnewscale:

depends r-ggplot2:

depends r-ggraph:

depends r-ggrepel:

depends r-ggthemes:

depends r-glmnet:

depends r-hmisc:

depends r-igraph:

depends r-latex2exp:

depends r-magrittr:

depends r-plotly:

depends r-proc:

depends r-purrr:

depends r-reshape2:

depends r-statmod:

depends r-stringr:

depends r-survival:

depends r-tibble:

depends r-tidygraph:

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-top

and update with::

   mamba update bioconductor-top

To create a new environment, run:

mamba create --name myenvname bioconductor-top

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-top:<tag>

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

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Link to this page

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