InterCellar
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.24 of Bioconductor. This package has been removed from Bioconductor. For the last 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: Development (3.24)
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("InterCellar")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 2.19.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_2.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | InterCellar_2.19.0.tgz |
| macOS Binary (sonoma-arm64) | InterCellar_2.19.0.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 |