scFastDE
This is the development version of scFastDE; to use it, please install the devel version of Bioconductor.
Fast Donor-Weighted Pseudo-Bulk Differential Expression for scRNA-seq
Bioconductor version: Development (3.24)
scFastDE provides fast, donor-weighted pseudo-bulk differential expression analysis for multi-donor single-cell RNA-seq experiments. Unlike existing tools that loop over genes serially, scFastDE uses vectorised sparse matrix operations across all genes simultaneously, achieving 10-50x speed gains on large datasets. Donors are weighted by the square root of their cell count, giving principled influence to well-represented donors without discarding donors with few cells. Paired experimental designs (same donors in multiple conditions) are automatically detected; pseudo-bulk is then aggregated per donor-condition pair and a blocking model accounts for inter-donor variation. A sparse pseudo-bulk guard automatically handles cell types where some donors fall below a minimum cell threshold. All functions operate natively on SingleCellExperiment objects.
Author: Subhadip Jana [aut, cre]
Maintainer: Subhadip Jana <subhadipjana1409 at gmail.com>
citation("scFastDE")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scFastDE")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scFastDE")| Fast donor-weighted DE for multi-donor scRNA-seq with scFastDE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, CellBasedAssays, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software, StatisticalMethod, Transcriptomics, WorkflowStep |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | SingleCellExperiment, SummarizedExperiment, S4Vectors, BiocParallel, Matrix, limma, methods, stats, ggplot2, rlang, utils |
| System Requirements | |
| URL | https://github.com/SubhadipJana1409/scFastDE |
| Bug Reports | https://github.com/SubhadipJana1409/scFastDE/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scuttle, withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scFastDE_0.99.3.tar.gz |
| Windows Binary (x86_64) | scFastDE_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | scFastDE_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | scFastDE_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scFastDE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scFastDE |
| Bioc Package Browser | https://code.bioconductor.org/browse/scFastDE/ |
| Package Short Url | https://bioconductor.org/packages/scFastDE/ |
| Package Downloads Report | Download Stats |