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.
Get the latest stable R
release from
CRAN. 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")
DeconvoBuddies contains paired snRNA-seq, bulk RNA-seq, and cell type proportion data from the human DLPFC.
## Access data with fetch_deconvo_data
sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#> 2024-08-07 12:39:29.443059 loading file /Users/louise.huuki/Library/Caches/org.R-project.R/R/BiocFileCache/58f79a421ca_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):
DeconvBuddies 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.
#> No summary function supplied, defaulting to `mean_se()`
#> No summary function supplied, defaulting to `mean_se()`
Create composition bar plots of predicted cell type proportions.
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.
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 (2024). _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 0.99.0,
#> <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 = {2024},
#> url = {http://www.bioconductor.org/packages/DeconvoBuddies},
#> note = {https://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R package version 0.99.0},
#> 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.
Please note that the DeconvoBuddies project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
For more details, check the dev
directory.
This package was developed using biocthis.
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