recipe bioconductor-pwomics

Pathway-based data integration of omics data

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-pwomics/meta.yaml

Links:

biotools: pwomics, doi: 10.1093/bioinformatics/btv323

pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and phosphoproteins. A separate downstream analysis of phosphoproteomic data including pathway identification, transcription factor identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream transcription factors and potential proteomic regulators. The cross-platform comparative analysis allows for comprehensive analysis of single time point experiments and time-series experiments by providing static and dynamic analysis tools for data integration. In addition, it provides functions to identify individual signaling axes based on data integration.

package bioconductor-pwomics

versions:

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0, 

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0,  1.12.0-0,  1.10.1-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-rbiopaxparser:

>=2.42.0,<2.43.0

depends bioconductor-stringdb:

>=2.14.0,<2.15.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-gplots:

depends r-igraph:

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-pwomics

and update with::

   mamba update bioconductor-pwomics

To create a new environment, run:

mamba create --name myenvname bioconductor-pwomics

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-pwomics:<tag>

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

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