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 (3.21)
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] (ORCID:
Maintainer: Marta Interlandi <marta.interlandi01 at gmail.com>
citation("InterCellar")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GO, SingleCell, Software, Transcriptomics, Visualization |
| Version | 2.13.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_2.13.0.tar.gz |
| Windows Binary (x86_64) | InterCellar_2.13.0.zip |
| macOS Binary (x86_64) | InterCellar_2.13.0.tgz |
| macOS Binary (arm64) | |
| 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 |