recipe bioconductor-ctrap

Identification of candidate causal perturbations from differential gene expression data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-ctrap/meta.yaml

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

package bioconductor-ctrap

versions:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.3-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-binr:

depends r-cowplot:

depends r-data.table:

depends r-dplyr:

depends r-dt:

depends r-fastmatch:

depends r-ggplot2:

depends r-ggrepel:

depends r-highcharter:

depends r-htmltools:

depends r-httr:

depends r-pbapply:

depends r-purrr:

depends r-qs:

depends r-r.utils:

depends r-readxl:

depends r-reshape2:

depends r-rlang:

depends r-scales:

depends r-shiny:

>=1.7.0

depends r-shinycssloaders:

depends r-tibble:

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-ctrap

and update with::

   mamba update bioconductor-ctrap

To create a new environment, run:

mamba create --name myenvname bioconductor-ctrap

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-ctrap:<tag>

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

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