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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |
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) | |
| macOS Binary (big-sur-x86_64) | |
| 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 |