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 [aut, cre], Diego Diez [aut] 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 Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=singleCellHaystack to link to this page.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4