recipe bioconductor-isee

Interactive SummarizedExperiment Explorer

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-isee/meta.yaml

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

package bioconductor-isee

versions:

2.14.0-0,  2.12.0-0,  2.10.0-0,  2.6.0-0,  2.4.0-0,  2.2.4-0,  2.2.0-0,  2.0.0-0,  1.6.0-0, 

2.14.0-0,  2.12.0-0,  2.10.0-0,  2.6.0-0,  2.4.0-0,  2.2.4-0,  2.2.0-0,  2.0.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-colourpicker:

depends r-dt:

depends r-ggplot2:

depends r-ggrepel:

depends r-igraph:

depends r-mgcv:

depends r-rintrojs:

depends r-shiny:

depends r-shinyace:

depends r-shinydashboard:

depends r-shinyjs:

depends r-shinywidgets:

depends r-vipor:

depends r-viridislite:

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-isee

and update with::

   mamba update bioconductor-isee

To create a new environment, run:

mamba create --name myenvname bioconductor-isee

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-isee:<tag>

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

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