GitHub - LieberInstitute/DeconvoBuddies: Helper Functions for LIBD Deconvolution (original) (raw)

DeconvoBuddies

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 fromCRAN. Then install DeconvoBuddies using from Bioconductor the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") }

BiocManager::install("DeconvoBuddies")

And the development version from GitHub with:

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.

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.

Plot Deconvoltion Cell Type Proportions

Create composition bar plots of predicted cell type proportions.

Citation

Below is the citation output from using citation('DeconvoBuddies') in R. Please run this yourself to check for any updates on how to citeDeconvoBuddies.

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 tolute, 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 aContributor 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 actionsthrough usethis,remotes, and_rcmdcheck_ customized to use Bioconductor’s docker containers and_BiocCheck_.
• Code coverage assessment is possible thanks tocodecov and_covr_.
• The documentation website is automatically updated thanks to_pkgdown_.
• The code is styled automatically thanks to_styler_.
• The documentation is formatted thanks to_devtools_ and_roxygen2_.

For more details, check the dev directory.

This package was developed using_biocthis_.

This package is submitted toBioconductor