recipe bioconductor-spatiallibd

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data






Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators.

package bioconductor-spatiallibd

(downloads) docker_bioconductor-spatiallibd



depends bioconductor-annotationhub:


depends bioconductor-biocfilecache:


depends bioconductor-biocgenerics:


depends bioconductor-data-packages:


depends bioconductor-edger:


depends bioconductor-experimenthub:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-limma:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-scater:


depends bioconductor-scuttle:


depends bioconductor-singlecellexperiment:


depends bioconductor-spatialexperiment:


depends bioconductor-summarizedexperiment:


depends curl:

depends r-base:


depends r-benchmarkme:

depends r-cowplot:

depends r-dt:

depends r-fields:

depends r-ggplot2:

depends r-golem:

depends r-jsonlite:

depends r-magick:

depends r-matrix:

depends r-paletteer:

depends r-plotly:

depends r-png:

depends r-rcolorbrewer:

depends r-sessioninfo:

depends r-shiny:

depends r-shinywidgets:

depends r-statmod:

depends r-tibble:

depends r-viridislite:



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-spatiallibd

and update with::

   mamba update bioconductor-spatiallibd

To create a new environment, run:

mamba create --name myenvname bioconductor-spatiallibd

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<tag>

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

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