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+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# 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")
+#> 2025-01-29 13:19:21.30937 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 0.99.10,
+#>   <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 0.99.10},
+#>     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 (2024). "Benchmark of cellular deconvolution
+#>   methods using a multi-assay reference dataset from postmortem human
+#>   prefrontal cortex." _bioRxiv_. doi:10.1101/2024.02.09.579665
+#>   <https://doi.org/10.1101/2024.02.09.579665>,
+#>   <https://doi.org/10.1101/2024.02.09.579665>.
+#> 
+#> A BibTeX entry for LaTeX users is
+#> 
+#>   @Article{,
+#>     title = {Benchmark of cellular deconvolution methods using a multi-assay reference 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 = {2024},
+#>     journal = {bioRxiv},
+#>     doi = {10.1101/2024.02.09.579665},
+#>     url = {https://doi.org/10.1101/2024.02.09.579665},
+#>   }
+```
+
+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)