recipe bioconductor-standr

Spatial transcriptome analyses of Nanostring's DSP data in R

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-standr/meta.yaml

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

package bioconductor-standr

versions:

1.6.0-0,  1.4.2-0,  1.2.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-ruvseq:

>=1.36.0,<1.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-spatialexperiment:

>=1.12.0,<1.13.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggalluvial:

depends r-ggplot2:

depends r-mclustcomp:

depends r-patchwork:

depends r-readr:

depends r-rlang:

depends r-ruv:

depends r-tibble:

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-standr

and update with::

   mamba update bioconductor-standr

To create a new environment, run:

mamba create --name myenvname bioconductor-standr

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-standr:<tag>

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

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Link to this page

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