dominoSignal
Cell Communication Analysis for Single Cell RNA Sequencing
Bioconductor version: 3.24 · Package version: 1.7.0
dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dominoSignal")Details
| Maintainer | Kavita Krishnan <kkrishnan@som.umaryland.edu> |
| Author | Christopher Cherry [aut] (ORCID: <https://orcid.org/0000-0002-5481-0055>), Jacob T Mitchell [aut] (ORCID: <https://orcid.org/0000-0002-5370-9692>), Sushma Nagaraj [aut] (ORCID: <https://orcid.org/0000-0001-5166-1309>), Kavita Krishnan [aut, cre] (ORCID: <https://orcid.org/0000-0003-1345-0249>), Dmitrijs Lvovs [aut], Elana Fertig [ctb] (ORCID: <https://orcid.org/0000-0003-3204-342X>), Jennifer Elisseeff [ctb] (ORCID: <https://orcid.org/0000-0002-5066-1996>) |
| License | GPL-3 | file LICENSE |
| URL | https://FertigLab.github.io/dominoSignal/ |
| Bug Reports | https://github.com/FertigLab/dominoSignal/issues |
| Downloads rank | 347 |
| Source branch | devel |
| biocViews | Network, SingleCell, Software, SystemsBiology, Transcriptomics |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | dominoSignal_1.7.0.tar.gz |
| Windows binary (x86_64) | dominoSignal_1.7.0.zip |
| macOS binary (arm64) | dominoSignal_1.7.0.tgz |
| macOS binary (x86_64) | dominoSignal_1.7.0.tgz |