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# DeconvoBuddies <img src="man/figures/logo.png" align="right" height="138"/>
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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
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("DeconvoBuddies")
```
And the development version from [GitHub](https://github.com/) with:
``` r
BiocManager::install("LieberInstitute/DeconvoBuddies")
```
## Application of 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 with fetch_deconvo_data
sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#> 2025-02-27 10:37:58.767148 loading file /Users/louise.huuki/Library/Caches/org.R-project.R/R/BiocFileCache/fd1c5d42efb7_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
## explore the single cell experiment object
sce_DLPFC_example
#> class: SingleCellExperiment
#> dim: 557 10000
#> metadata(3): Samples cell_type_colors cell_type_colors_broad
#> assays(1): logcounts
#> rownames(557): GABRD PRDM16 ... AFF2 MAMLD1
#> rowData names(7): source type ... gene_type binomial_deviance
#> colnames(10000): 8_AGTGACTGTAGTTACC-1 17_GCAGCCAGTGAGTCAG-1 ...
#> 12_GGACGTCTCTGACAGT-1 1_GGTTAACTCTCTCTAA-1
#> colData names(32): Sample Barcode ... cellType_layer layer_annotation
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
```
### 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.
<img src="man/figures/README-plot_gene_expression-1.png" width="100%" />
### Plot Deconvoltion Cell Type Proportions
Create composition bar plots of predicted cell type proportions.
<img src="man/figures/README-demo_plot_composition_bar-1.png" width="100%" />
## 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
print(citation("DeconvoBuddies"), bibtex = TRUE)
#> To cite package 'DeconvoBuddies' in publications use:
#>
#> Huuki-Myers LA, Maynard KR, Hicks SC, Zandi P, Kleinman JE, Hyde TM,
#> Goes FS, Collado-Torres L (2025). _DeconvoBuddies: a R/Bioconductor
#> package with deconvolution helper functions_.
#> doi:10.18129/B9.bioc.DeconvoBuddies
#> <https://doi.org/10.18129/B9.bioc.DeconvoBuddies>,
#> https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R
#> package version 0.99.37,
#> <http://www.bioconductor.org/packages/DeconvoBuddies>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {DeconvoBuddies: a R/Bioconductor package with deconvolution helper functions},
#> author = {Louise A. Huuki-Myers and Kristen R. Maynard and Stephanie C. Hicks and Peter Zandi and Joel E. Kleinman and Tom M. Hyde and Fernando S. Goes and Leonardo Collado-Torres},
#> year = {2025},
#> url = {http://www.bioconductor.org/packages/DeconvoBuddies},
#> note = {https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R package version 0.99.37},
#> doi = {10.18129/B9.bioc.DeconvoBuddies},
#> }
#>
#> Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ,
#> Gonzalez-Padilla D, Maden SK, Kleinman JE, Hyde TM, Hicks SC, Maynard
#> KR, Collado-Torres L (2025). "Benchmark of cellular deconvolution
#> methods using a multi-assay dataset from postmortem human prefrontal
#> cortex." _Genome Biol_. doi:10.1186/s13059-025-03552-3
#> <https://doi.org/10.1186/s13059-025-03552-3>,
#> <https://doi.org/10.1186/s13059-025-03552-3>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex},
#> author = {Louise A. Huuki-Myers and Kelsey D. Montgomery and Sang Ho Kwon and Sophia Cinquemani and Nicholas J. Eagles and Daianna Gonzalez-Padilla and Sean K. Maden and Joel E. Kleinman and Thomas M. Hyde and Stephanie C. Hicks and Kristen R. Maynard and Leonardo Collado-Torres},
#> year = {2025},
#> journal = {Genome Biol},
#> doi = {10.1186/s13059-025-03552-3},
#> url = {https://doi.org/10.1186/s13059-025-03552-3},
#> }
```
**DeconvoBuddies** is related to
[*lute*](https://doi.org/10.1186/s12864-025-11508-x), with both
manuscripts published with a bi-directional link between them.
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 *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*, and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/3.20/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://.github.io/DeconvoBuddies) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.20/biocthis)*.
This package is submitted to
[Bioconductor](https://github.com/Bioconductor/Contributions/issues/3503)
