InterCellar

DOI: 10.18129/B9.bioc.InterCellar    

This is the development version of InterCellar; for the stable release version, see InterCellar.

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

Bioconductor version: Development (3.14)

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, the user can define interaction-pairs modules and link them to significant functional terms from Pathways or Gene Ontology.

Author: Marta Interlandi [cre, aut]

Maintainer: Marta Interlandi <marta.interlandi01 at gmail.com>

Citation (from within R, enter citation("InterCellar")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("InterCellar")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("InterCellar")

 

HTML R Script InterCellar User Guide
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GO, SingleCell, Software, Transcriptomics, Visualization
Version 1.1.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb
LinkingTo
Suggests testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, igraph
SystemRequirements
Enhances
URL https://github.com/martaint/InterCellar
BugReports https://github.com/martaint/InterCellar/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package InterCellar_1.1.0.tar.gz
Windows Binary InterCellar_1.1.0.zip
macOS 10.13 (High Sierra) InterCellar_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InterCellar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InterCellar
Package Short Url https://bioconductor.org/packages/InterCellar/
Package Downloads Report Download Stats

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