diff --git a/README.md b/README.md new file mode 100644 index 0000000..843e761 --- /dev/null +++ b/README.md @@ -0,0 +1,186 @@ + + + +# DeconvoBuddies + + + +[![Codecov test +coverage](https://codecov.io/gh/lahuuki/DeconvoBuddies/branch/main/graph/badge.svg)](https://codecov.io/gh/lahuuki/DeconvoBuddies?branch=main) +[![check-bioc](https://github.com/LieberInstitute/DeconvoBuddies/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/DeconvoBuddies/actions/workflows/check-bioc.yml) +[![Lifecycle: +stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) +[![Bioc release +status](http://www.bioconductor.org/shields/build/release/bioc/DeconvoBuddies.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/DeconvoBuddies) +[![Bioc devel +status](http://www.bioconductor.org/shields/build/devel/bioc/DeconvoBuddies.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/DeconvoBuddies) +[![Bioc downloads +rank](https://bioconductor.org/shields/downloads/release/DeconvoBuddies.svg)](http://bioconductor.org/packages/stats/bioc/DeconvoBuddies/) +[![Bioc +support](https://bioconductor.org/shields/posts/DeconvoBuddies.svg)](https://support.bioconductor.org/tag/DeconvoBuddies) +[![Bioc +history](https://bioconductor.org/shields/years-in-bioc/DeconvoBuddies.svg)](https://bioconductor.org/packages/release/bioc/html/DeconvoBuddies.html#since) +[![Bioc last +commit](https://bioconductor.org/shields/lastcommit/devel/bioc/DeconvoBuddies.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/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 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. + + + +### 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 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://github.com/LieberInstitute/DeconvoBuddies/DeconvoBuddies - R +#> package version 0.99.10, +#> . +#> +#> 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 +#> , +#> . +#> +#> 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)