knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
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")
suppressMessages({ library("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") ## explore the single cell experiment object sce_DLPFC_example
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.
plot_gene_express( sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22") )
Create composition bar plots of predicted cell type proportions.
set.seed(123) ## 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" )
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)
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.
r BiocStyle::CRANpkg('usethis')
,
r BiocStyle::CRANpkg('remotes')
, and
r BiocStyle::CRANpkg('rcmdcheck')
customized to use
Bioconductor's docker
containers and
r BiocStyle::Biocpkg('BiocCheck')
.r BiocStyle::CRANpkg('covr')
.r BiocStyle::CRANpkg('pkgdown')
.r BiocStyle::CRANpkg('styler')
.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')
.
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