InterCellar

DOI: 10.18129/B9.bioc.InterCellar    

This package is for version 3.13 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: 3.13

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>

Installation

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

if (!requireNamespace("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")

 

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

Details

biocViews	GO, SingleCell, Software, Transcriptomics, Visualization
Version	1.0.0
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_1.0.0.tar.gz
Windows Binary	InterCellar_1.0.0.zip
macOS 10.13 (High Sierra)	InterCellar_1.0.0.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