scCompoundDE
This is the development version of scCompoundDE; to use it, please install the devel version of Bioconductor.
Compositional and Transcriptional Decomposition of Pseudo-Bulk Differential Expression
Bioconductor version: Development (3.24)
scCompoundDE decomposes pseudo-bulk differential expression (DE) signals into two orthogonal components: transcriptional changes (cell-intrinsic expression shifts) and compositional changes (shifts in the relative abundance of cell subtypes). Standard pseudo-bulk DE tools confound these two sources of signal, producing spurious DE calls when subtype proportions differ between conditions. scCompoundDE fits per-subtype limma-voom models, estimates subtype proportion shifts, and uses a z-score-normalized decomposition to assign each gene a TC_ratio score — the fraction of its DE signal attributable to transcription versus composition. Genes are then classified as transcriptional (real biology), compositional (artifact), or mixed (requires caution). All functions operate natively on SingleCellExperiment objects and return a CDEResult S4 object that extends the standard DE output with full decomposition statistics.
Author: Subhadip Jana [aut, cre]
Maintainer: Subhadip Jana <subhadipjana1409 at gmail.com>
citation("scCompoundDE")):
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("scCompoundDE")
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("scCompoundDE")| Decomposing pseudo-bulk DE with scCompoundDE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Transcriptomics, WorkflowStep |
| Version | 0.99.1 |
| 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/scCompoundDE |
| Bug Reports | https://github.com/SubhadipJana1409/scCompoundDE/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 | scCompoundDE_0.99.1.tar.gz |
| Windows Binary (x86_64) | scCompoundDE_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | scCompoundDE_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | scCompoundDE_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scCompoundDE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scCompoundDE |
| Bioc Package Browser | https://code.bioconductor.org/browse/scCompoundDE/ |
| Package Short Url | https://bioconductor.org/packages/scCompoundDE/ |
| Package Downloads Report | Download Stats |