use vignette as README and add citation, closes #74

README.md

@@ -1,11 +1,69 @@
+
 # SingleCellMultiModal
 
-This is a project for downloading Single Cell Multi-Modal data and representing
-them as MultiAssayExperiment objects. It will eventually be submitted to
-Bioconductor as an ExperimentHub package.
+## Overview
+
+`SingleCellMultiModal` is an R package that provides a convenient and
+user-friendly representation of multi-modal data using
+`MultiAssayExperiment`. This package introduces a suite of single-cell
+multimodal landmark datasets for benchmarking and testing multimodal
+analysis methods via the `ExperimentHub` Bioconductor package. The scope
+of this package is to provide efficient access to a selection of
+curated, pre-integrated, publicly available landmark datasets for
+methods development and benchmarking.
+
+## Installation
+
+``` r
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("SingleCellMultiModal")
+```
+
+## Loading packages
+
+``` r
+library(SingleCellMultiModal)
+library(MultiAssayExperiment)
+```
+
+# Citing SingleCellMultiModal
+
+Your citations are crucial in keeping our software free and open source.
+To cite our package see the citation (@Eckenrode2023-yq) in the
+Reference section. You may also browse to the publication at the link
+[here](https://doi.org/10.1371/journal.pcbi.1011324).
+
+## Representation
+
+Users can obtain integrative representations of multiple modalities as a
+`MultiAssayExperiment`, a common core Bioconductor data structure relied
+on by dozens of multimodal data analysis packages.
+`MultiAssayExperiment` harmonizes data management of multiple
+experimental assays performed on an overlapping set of specimens.
+Although originally developed for patient data from multi-omics cancer
+studies, the `MultiAssayExperiment` framework naturally applies also to
+single cells. A schematic of the data structure can be seen below. In
+this context, “patients” are replaced by “cells”. We use
+`MultiAssayExperiment` because it provides a familiar user experience by
+extending `SummarizedExperiment` concepts and providing open ended
+compatibility with standard data classes present in Bioconductor such as
+the `SingleCellExperiment`.
+
+<img src="https://github.com/waldronlab/MultiAssayExperiment/blob/c3c59a094e5a08111ee98b9f69579db5634d9fd4/vignettes/MultiAssayExperiment.png?raw=true" width="100%" />
+
+# Contributions
+
+Want to contribute to the `SingleCellMultiModal` package? We welcome
+contributions from the community. Please refer to our [Contributing
+Guidelines](https://github.com/waldronlab/SingleCellMultiModal/wiki/Contributing-Guidelines)
+for more details.
 
-## Contributing
+## Further resources
 
-Want to contribute a dataset? See the [Contributing Guidelines][]
+For more information on the `MultiAssayExperiment` data structure,
+please refer to @Ramos2017-tk as well as the [MultiAssayExperiment
+vignette](https://bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/MultiAssayExperiment.html).
 
-[Contributing Guidelines]: https://github.com/waldronlab/SingleCellMultiModal/wiki/Contributing-Guidelines
+# References

inst/scripts/README.Rmd

@@ -0,0 +1,23 @@
+---
+output: github_document
+knit: (function(inputFile, encoding) {
+  rmarkdown::render(inputFile, encoding = encoding, output_dir = "../../") })
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  cache = TRUE,
+  out.width = "100%"
+)
+```
+
+```{r,echo=FALSE,eval=FALSE}
+## Generate the ./README.md (relative to base folder)
+rmarkdown::render(input = "inst/scripts/README.Rmd", output_dir = ".")
+```
+
+```{r, child="../../vignettes/SingleCellMultiModal.Rmd"}
+
+```

vignettes/SingleCellMultiModal.Rmd

@@ -12,7 +12,19 @@ Package: SingleCellMultiModal
 bibliography: ../inst/REFERENCES.bib
 ---
 
-# Installation
+# SingleCellMultiModal
+
+## Overview 
+
+`SingleCellMultiModal` is an R package that provides a convenient and
+user-friendly representation of multi-modal data using `MultiAssayExperiment`.
+This package introduces a suite of single-cell multimodal landmark datasets for
+benchmarking and testing multimodal analysis methods via the `ExperimentHub`
+Bioconductor package. The scope of this package is to provide efficient access
+to a selection of curated, pre-integrated, publicly available landmark datasets
+for methods development and benchmarking.
+
+## Installation
 
 ```{r,eval=FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE))
@@ -21,26 +33,19 @@ if (!requireNamespace("BiocManager", quietly = TRUE))
 BiocManager::install("SingleCellMultiModal")
 ```
 
-## Load packages
+## Loading packages
 
 ```{r,include=TRUE,results="hide",message=FALSE,warning=FALSE}
 library(SingleCellMultiModal)
 library(MultiAssayExperiment)
 ```
 
-# Introduction
-
-This package introduces a suite of single-cell multimodal landmark datasets for
-benchmarking and testing multimodal analysis methods via the `ExperimentHub`
-Bioconductor package. The scope of this package is to provide efficient access
-to a selection of curated, pre-integrated, publicly available landmark datasets
-for methods development and benchmarking.
-
 # Citing SingleCellMultiModal
 
 Your citations are crucial in keeping our software free and open source. To
 cite our package see the citation (@Eckenrode2023-yq) in the Reference
-section. You may also browse to the publication at the link [here][1].
+section. You may also browse to the publication at
+[PLoS Computational Biology][1].
 
 [1]: https://doi.org/10.1371/journal.pcbi.1011324
 
@@ -70,9 +75,20 @@ knitr::include_graphics(
 )
 ```
 
+# Contributions
+
+Want to contribute to the `SingleCellMultiModal` package? We welcome
+contributions from the community. Please refer to our
+[Contributing Guidelines][2] for more details.
+
+[2]: https://github.com/waldronlab/SingleCellMultiModal/wiki/Contributing-Guidelines
+
+
 ## Further resources
 
 For more information on the `MultiAssayExperiment` data structure, please refer
-to @Ramos2017-tk as well as the [MultiAssayExperiment vignette](https://bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/MultiAssayExperiment.html).
+to @Ramos2017-tk as well as the [MultiAssayExperiment vignette][3].
+
+[3]: https://bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/MultiAssayExperiment.html
 
 # References