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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 (3.19)

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.

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 "4.4") and enter:


if (!require("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")
InterCellar User Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GO, SingleCell, Software, Transcriptomics, Visualization
Version 2.9.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
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, igraph
System Requirements
URL https://github.com/martaint/InterCellar
Bug Reports https://github.com/martaint/InterCellar/issues
See More
Suggests testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package InterCellar_2.9.0.tar.gz
Windows Binary InterCellar_2.9.0.zip
macOS Binary (x86_64) InterCellar_2.9.0.tgz
macOS Binary (arm64) InterCellar_2.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InterCellar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InterCellar
Bioc Package Browser https://code.bioconductor.org/browse/InterCellar/
Package Short Url https://bioconductor.org/packages/InterCellar/
Package Downloads Report Download Stats