InterCellar

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see InterCellar.

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

Bioconductor version: 3.15

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 "4.2") and enter:


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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GO, SingleCell, Software, Transcriptomics, Visualization
Version	2.2.0
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

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_2.2.0.tar.gz
Windows Binary	InterCellar_2.2.0.zip
macOS Binary (x86_64)	InterCellar_2.2.0.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
Old Source Packages for BioC 3.15	Source Archive