Package Recipe 'bioconductor-shinydsp'

recipe bioconductor-shinydsp

A Shiny App For Visualizing Nanostring GeoMx DSP Data

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/shinyDSP.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-shinydsp/meta.yaml

This package is a Shiny app for interactively analyzing and visualizing Nanostring GeoMX Whole Transcriptome Atlas data. Users have the option of exploring a sample data to explore this app's functionality. Regions of interest (ROIs) can be filtered based on any user-provided metadata. Upon taking two or more groups of interest, all pairwise and ANOVA-like testing are automatically performed. Available ouputs include PCA, Volcano plots, tables and heatmaps. Aesthetics of each output are highly customizable.

package bioconductor-shinydsp¶

Versions:

1.2.0-0

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-standr >=1.14.0,<1.15.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-bsicons
on r-bslib
on r-circlize
on r-cowplot
on r-dplyr
on r-dt
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-htmltools
on r-magrittr
on r-pals
on r-readr
on r-scales
on r-shiny
on r-shinycssloaders
on r-shinyjs
on r-shinyvalidate
on r-shinywidgets
on r-stringr
on r-tibble
on r-tidyr
on r-withr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-shinydsp

to add into an existing workspace instead, run:

pixi add bioconductor-shinydsp

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-shinydsp

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-shinydsp

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-shinydsp:<tag>

(see bioconductor-shinydsp/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-shinydsp/README.html)