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One key exploratory analysis step in single-cell genomics data analysis is the prediction of features with different activity levels. For example, we want to predict differentially expressed genes (DEGs) in single-cell RNA-seq data, spatial DEGs in spatial transcriptomics data, or differentially accessible regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially active features in single cell omics datasets without relying on the clustering of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler divergence to find features (e.g., genes, genomic regions, etc) that are active in subsets of cells that are non-randomly positioned inside an input space (such as 1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For the theoretical background of 'singleCellHaystack' we refer to our original paper Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3> and our update Vandenbon and Diez (Scientific Reports, 2023) <doi:10.1038/s41598-023-38965-2>.
Version: | 1.0.2 |
Imports: | methods, Matrix, splines, ggplot2, reshape2 |
Suggests: | knitr, rmarkdown, testthat, SummarizedExperiment, SingleCellExperiment, SeuratObject, cowplot, wrswoR, sparseMatrixStats, ComplexHeatmap, patchwork |
Published: | 2024-01-11 |
DOI: | 10.32614/CRAN.package.singleCellHaystack |
Author: | Alexis Vandenbon |
Maintainer: | Alexis Vandenbon <alexis.vandenbon at gmail.com> |
BugReports: | https://github.com/alexisvdb/singleCellHaystack/issues |
License: | MIT + file LICENSE |
URL: | https://alexisvdb.github.io/singleCellHaystack/, https://github.com/alexisvdb/singleCellHaystack |
NeedsCompilation: | no |
Citation: | singleCellHaystack citation info |
Materials: | NEWS |
In views: | Omics |
CRAN checks: | singleCellHaystack results |
Reference manual: | singleCellHaystack.pdf |
Vignettes: |
Application on toy example |
Package source: | singleCellHaystack_1.0.2.tar.gz |
Windows binaries: | r-devel: singleCellHaystack_1.0.2.zip, r-release: singleCellHaystack_1.0.2.zip, r-oldrel: singleCellHaystack_1.0.2.zip |
macOS binaries: | r-release (arm64): singleCellHaystack_1.0.2.tgz, r-oldrel (arm64): singleCellHaystack_1.0.2.tgz, r-release (x86_64): singleCellHaystack_1.0.2.tgz, r-oldrel (x86_64): singleCellHaystack_1.0.2.tgz |
Old sources: | singleCellHaystack archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.