Package Recipe 'bioconductor-intercellar'

recipe bioconductor-intercellar

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/InterCellar.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-intercellar/meta.yaml

InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions.

package bioconductor-intercellar¶

Versions:

2.16.0-0, 2.12.0-0, 2.8.0-0, 2.6.0-0, 2.4.0-0, 2.0.0-0, 1.0.0-0

Depends:

on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-colorspace
on r-colourpicker
on r-config
on r-data.table
on r-dendextend
on r-dplyr
on r-dt
on r-factoextra
on r-fmsb
on r-fs
on r-ggplot2
on r-golem
on r-htmltools
on r-htmlwidgets
on r-igraph
on r-plotly
on r-plyr
on r-readxl
on r-rlang
on r-scales
on r-shiny
on r-shinyalert
on r-shinycssloaders
on r-shinydashboard
on r-shinyfeedback
on r-shinyfiles
on r-signal
on r-tibble
on r-tidyr
on r-umap
on r-visnetwork
on r-wordcloud2

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-intercellar

to add into an existing workspace instead, run:

pixi add bioconductor-intercellar

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-intercellar

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-intercellar

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-intercellar:<tag>

(see bioconductor-intercellar/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-intercellar/README.html)