diff --git a/DESCRIPTION b/DESCRIPTION
index fd00b62f..74f3dd61 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
-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 = "ccherry.6574@gmail.com", comment = c(ORCID = "0000-0002-5481-0055")),
person("Jacob T", "Mitchell", role = c("aut", "cre"), email = "jmitch81@jhmi.edu", comment = c(ORCID = "0000-0002-5370-9692")),
@@ -11,8 +11,8 @@ Authors@R: c(
person("Jennifer", "Elisseeff", role = "ctb", email = "jhe@jhu.edu", 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:
@@ -31,7 +31,7 @@ Imports:
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: false
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
biocViews:
SystemsBiology,
SingleCell,
@@ -43,8 +43,10 @@ Suggests:
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/
diff --git a/README.md b/README.md
index 11c90986..684583e9 100644
--- a/README.md
+++ b/README.md
@@ -1,33 +1,33 @@
-[](https://github.com/FertigLab/domino2/actions?workflow=r-build-check)
+[](https://github.com/FertigLab/dominoSignal/actions?workflow=r-build-check)
-## Introducing domino2: Improved Inference of Cell Signaling from Single Cell RNA Sequencing Data
+## Introducing dominoSignal: Improved Inference of Cell Signaling from Single Cell RNA Sequencing Data
-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.
### Installation
-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.
-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.
```r
if(!require(remotes)){
install.packages('remotes')
}
-remotes::install_github('FertigLab/domino2')
+remotes::install_github('FertigLab/dominoSignal')
```
### Usage Overview
-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:
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
-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).
### Citation
@@ -35,7 +35,7 @@ If you use our package in your analysis, please cite us:
> 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).
diff --git a/man/figures/logo.svg b/man/figures/logo.svg
index 5339e89f..b1251f97 100644
--- a/man/figures/logo.svg
+++ b/man/figures/logo.svg
@@ -1 +1 @@
-
\ No newline at end of file
+
\ No newline at end of file
