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update package name in DESCRIPTION and README
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| Package: domino2 | ||
| Package: dominoSignal | ||
| Title: Cell Communication Analysis for Single Cell RNA Sequencing | ||
| Version: 0.99.1 | ||
| Version: 0.99.2 | ||
| Authors@R: c( | ||
| person("Christopher", "Cherry", role = c("aut"), email = "[email protected]", comment = c(ORCID = "0000-0002-5481-0055")), | ||
| person("Jacob T", "Mitchell", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0002-5370-9692")), | ||
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@@ -11,8 +11,8 @@ Authors@R: c( | |
| person("Jennifer", "Elisseeff", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-5066-1996")) | ||
| ) | ||
| Description: | ||
| Domino2 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. | ||
| BugReports: https://github.com/FertigLab/domino2/issues | ||
| 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. | ||
| BugReports: https://github.com/FertigLab/dominoSignal/issues | ||
| Depends: | ||
| R(>= 4.2.0), | ||
| Imports: | ||
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| License: GPL-3 | file LICENSE | ||
| Encoding: UTF-8 | ||
| LazyData: false | ||
| RoxygenNote: 7.2.3 | ||
| RoxygenNote: 7.3.1 | ||
| biocViews: | ||
| SystemsBiology, | ||
| SingleCell, | ||
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| rmarkdown, | ||
| Seurat, | ||
| testthat, | ||
| formatR | ||
| formatR, | ||
| BiocFileCache, | ||
| SingleCellExperiment | ||
| VignetteBuilder: knitr | ||
| Language: en-US | ||
| Roxygen: list(markdown = TRUE) | ||
| URL: https://fertiglab.github.io/domino2/ | ||
| URL: https://fertiglab.github.io/dominoSignal/ | ||
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| [](https://github.com/FertigLab/domino2/actions?workflow=r-build-check) | ||
| [](https://github.com/FertigLab/dominoSignal/actions?workflow=r-build-check) | ||
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| ## Introducing domino2: Improved Inference of Cell Signaling from Single Cell RNA Sequencing Data <a href="https://fertiglab.github.io/domino2/"><img src="man/figures/logo.svg" align="right" height="138" alt="domino2 repository" /></a> | ||
| ## Introducing dominoSignal: Improved Inference of Cell Signaling from Single Cell RNA Sequencing Data <a href="https://fertiglab.github.io/dominoSignal/"><img src="man/figures/logo.svg" align="right" height="138" alt="dominoSignal logo" /></a> | ||
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| Domino2 is an updated version of the original [domino](https://github.com/Elisseeff-Lab/domino) R package published in Nature Biomedical Engineering in [Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics](https://doi.org/10.1038/s41551-021-00770-5). Domino2 is a tool for analysis of intra- and intercellular signaling in single cell RNA sequencing data based on transcription factor activation and receptor and ligand linkages. | ||
| dominoSignal is an updated version of the original [domino](https://github.com/Elisseeff-Lab/domino) R package published in Nature Biomedical Engineering in [Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics](https://doi.org/10.1038/s41551-021-00770-5). dominoSignal is a tool for analysis of intra- and intercellular signaling in single cell RNA sequencing data based on transcription factor activation and receptor and ligand linkages between clusters. | ||
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| ### Installation | ||
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| Domino2 is undergoing active development where aspects of how data is used, analyzed, and interpreted is subject to change as new features and fixes are implemented. **v0.2.2** of Domino2 serves as the first stable development version during these active updates for reproducible usage. | ||
| dominoSignal is undergoing active development where aspects of how data is used, analyzed, and interpreted is subject to change as new features and fixes are implemented. **v0.99.1** of dominoSignal serves as the first stable development version during these active updates for reproducible usage. | ||
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| The most current version of Domino2 for reproducible usage is on the [FertigLab GitHub](https://github.com/FertigLab). Domino2 is the continuation of Domino software hosted on the [Elisseeff-Lab GitHub](https://github.com/Elisseeff-Lab/domino). The most current stable branch of Domino2 can be installed using the remotes package. | ||
| dominoSignal is the continuation of Domino software hosted on the [Elisseeff-Lab GitHub](https://github.com/Elisseeff-Lab/domino). The most up to date stable version is on the [FertigLab GitHub](https://github.com/FertigLab). This version of dominoSignal can be installed using the remotes package. | ||
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| ```r | ||
| if(!require(remotes)){ | ||
| install.packages('remotes') | ||
| } | ||
| remotes::install_github('FertigLab/domino2') | ||
| remotes::install_github('FertigLab/dominoSignal') | ||
| ``` | ||
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| ### Usage Overview | ||
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| Here is an overview of how domino2 might be used in analysis of a single cell RNA sequencing data set: | ||
| Here is an overview of how dominoSignal might be used in analysis of a single cell RNA sequencing data set: | ||
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| 1. Transcription factor activation scores are calculated (we recommend using [pySCENIC](https://pyscenic.readthedocs.io/en/latest/), but other methods can be used as well) | ||
| 2. A ligand-receptor database is used to map linkages between ligands and receptors (we recommend using [CellphoneDB](https://www.cellphonedb.org/), but other methods can be used as well). | ||
| 2. A ligand-receptor database is used to map linkages between ligands and receptors (we recommend using [CellPhoneDB](https://www.cellphonedb.org/), but other methods can be used as well). | ||
| 3. A domino object is created using counts, z-scored counts, clustering information, and the data from steps 1 and 2. | ||
| 4. Parameters such as the maximum number of transcription factors and receptors or the minimum correlation threshold (among others) are used to make a cell communication network | ||
| 5. Communication networks can be extracted from within the domino object or visualized using a variety of plotting functions | ||
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| Please see [our website](https://fertiglab.github.io/domino2/) for an example analysis that includes all of these steps in detail, from downloading and running [pySCENIC](https://pyscenic.readthedocs.io/en/latest/) to building and visualizing domino results. Other articles include [further details on plotting functions](https://fertiglab.github.io/domino2/articles/plotting_vignette.html) and [the structure of the domino object](https://fertiglab.github.io/domino2/articles/domino_object_vignette.html). | ||
| Please see [our website](https://fertiglab.github.io/dominoSignal/) for tutorials on all of these steps, from downloading and running [pySCENIC](https://pyscenic.readthedocs.io/en/latest/) in the [SCENIC tutorial](https://fertiglab.github.io/dominoSignal/articles/tf_scenic_vignette.html) to building and visualizing domino results on the [Getting Started page](https://fertiglab.github.io/dominoSignal/articles/dominoSignal). Other articles include [further details on plotting functions](https://fertiglab.github.io/dominoSignal/articles/plotting_vignette.html) and [the structure of the domino object](https://fertiglab.github.io/dominoSignal/articles/domino_object_vignette.html). | ||
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| ### Citation | ||
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| If you use our package in your analysis, please cite us: | ||
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| > Cherry C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, Garmire LX, Elisseeff JH. Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics. Nat Biomed Eng. 2021 Oct;5(10):1228-1238. doi: 10.1038/s41551-021-00770-5. Epub 2021 Aug 2. PMID: 34341534; PMCID: PMC9894531. | ||
| > Cherry C, Mitchell J, Nagaraj S, Krishnan K, Lvovs D, Fertig E, Elisseeff J (2023). domino2: Cell Communication Analysis for Single Cell RNA Sequencing. R package version 0.2.2. | ||
| > Cherry C, Mitchell J, Nagaraj S, Krishnan K, Lvovs D, Fertig E, Elisseeff J (2024). dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing. R package version 0.99.1. | ||
| ### Contact Us | ||
| If you find any bugs or have questions, please let us know [here](https://github.com/FertigLab/domino_development/issues). | ||
| If you find any bugs or have questions, please let us know [here](https://github.com/FertigLab/dominoSignal/issues). |
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