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README.Rmd
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---
output: github_document
editor_options:
markdown:
wrap: 72
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# DeconvoBuddies <img src="man/figures/logo.png" align="right" height="138"/>
<!-- badges: start -->
[](https://codecov.io/gh/lahuuki/DeconvoBuddies?branch=main)
[](https://github.com/LieberInstitute/DeconvoBuddies/actions/workflows/check-bioc.yml)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/DeconvoBuddies)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/DeconvoBuddies)
[](http://bioconductor.org/packages/stats/bioc/DeconvoBuddies/)
[](https://support.bioconductor.org/tag/DeconvoBuddies)
[](https://bioconductor.org/packages/release/bioc/html/DeconvoBuddies.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/DeconvoBuddies/)
<!-- badges: end -->
The goal of `DeconvoBuddies` is to provide helper functions for the
deconvolution process, as well as a paired dataset designed to test the
performance of deconvolution arguments. The dataset is from Human DLPFC,
and contains bulk RNA-seq, single nucleus RNA-seq, and estimated cell
type proportions from RNAScope/IF.
## Installation instructions
Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install `DeconvoBuddies` using
from [Bioconductor](http://bioconductor.org/) the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("DeconvoBuddies")
```
And the development version from [GitHub](https://github.com/) with:
```{r 'install_dev', eval = FALSE}
BiocManager::install("LieberInstitute/DeconvoBuddies")
```
## Application of DeconvoBuddies
```{r 'load_packages', warning = FALSE, echo=FALSE}
suppressMessages({
library("DeconvoBuddies")
})
```
### Access Datasets
`DeconvoBuddies` contains paired snRNA-seq, bulk RNA-seq, and cell type proportion
data from the human DLPFC from [this study](https://github.com/LieberInstitute/Human_DLPFC_Deconvolution).
```{r `access data}
## Access data with fetch_deconvo_data
sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
## explore the single cell experiment object
sce_DLPFC_example
```
### Find Marker Genes and Visualize Expression
`DeconvoBuddies` has tools for finding marker genes ideal for deconvolution,
and plotting functions to quickly visualize the expression of selected genes in a
snRNA-seq data.
```{r plot_gene_expression, echo=FALSE, warning=FALSE}
plot_gene_express(
sce = sce_DLPFC_example,
category = "cellType_broad_hc",
genes = c("GAD2", "CD22")
)
```
### Plot Deconvoltion Cell Type Proportions
Create composition bar plots of predicted cell type proportions.
```{r demo_plot_composition_bar, echo=FALSE}
set.seed(123)
## load example data
data("est_prop")
## pivot data to long format and join with test estimated proportion data
est_prop_long <- est_prop |>
tibble::rownames_to_column("RNum") |>
tidyr::pivot_longer(!RNum, names_to = "cell_type", values_to = "prop")
## composition bar plot
plot_composition_bar(
est_prop_long |>
dplyr::filter(RNum %in% sample(rownames(est_prop), 10)),
x_col = "RNum"
)
```
## Citation
Below is the citation output from using `citation('DeconvoBuddies')` in
R. Please run this yourself to check for any updates on how to cite
**DeconvoBuddies**.
```{r 'citation', eval = requireNamespace('DeconvoBuddies')}
print(citation("DeconvoBuddies"), bibtex = TRUE)
```
Please note that the `DeconvoBuddies` was only made possible thanks to
many other R and bioinformatics software authors, which are cited either
in the vignettes and/or the paper(s) describing this package.
## Code of Conduct
Please note that the DeconvoBuddies project is released with a
[Contributor Code of
Conduct](http://bioconductor.org/about/code-of-conduct/). By
contributing to this project, you agree to abide by its terms.
## Development tools
- Continuous code testing is possible thanks to [GitHub
actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
through `r BiocStyle::CRANpkg('usethis')`,
`r BiocStyle::CRANpkg('remotes')`, and
`r BiocStyle::CRANpkg('rcmdcheck')` customized to use
[Bioconductor's docker
containers](https://www.bioconductor.org/help/docker/) and
`r BiocStyle::Biocpkg('BiocCheck')`.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
- The [documentation website](http://.github.io/DeconvoBuddies) is
automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
- The code is styled automatically thanks to
`r BiocStyle::CRANpkg('styler')`.
- The documentation is formatted thanks to
`r BiocStyle::CRANpkg('devtools')` and
`r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
This package is submitted to [Bioconductor](https://github.com/Bioconductor/Contributions/issues/3503)