Seqtometry
Signature scoring for single cell analysis
Bioconductor version: 3.23 · Package version: 1.0.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package provides functions used in Seqtometry (Kousnetsov et al. 2024), a method for analyzing single cell (scRNA-seq or scATAC-seq) data via signature (gene set) enrichment scores. The Seqtometry scores may be useful for annotating or characterizing cells, either in a flow cytometry like workflow (where scores are standalone features used for progressive partitoning as described in the Seqtometry publication) or in a cluster-based workflow (as features of clusters). The exported impute function (a port of Python's MAGIC-impute, van Dijk et al. 2018), may also be useful for single cell analysis on its own.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Seqtometry")Details
| Maintainer | Robert Kousnetsov <robert.kousnetsov@health.slu.edu> |
| Author | Robert Kousnetsov [aut, cre], Daniel Hawiger [cph, fnd] |
| License | MIT + file LICENSE |
| URL | https://github.com/HawigerLab/Seqtometry |
| Bug Reports | https://github.com/HawigerLab/Seqtometry/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/Seqtometry/ |
Citation
From within R, enter citation("Seqtometry"):
Robert Kousnetsov. Seqtometry: Signature scoring for single cell analysis. doi:10.18129/B9.bioc.Seqtometry, R package version 1.0.1, https://bioconductor.org/packages/Seqtometry.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Seqtometry_1.0.1.tar.gz |
| Windows binary (x86_64) | Seqtometry_1.0.1.zip |
| macOS binary (arm64) | Seqtometry_1.0.1.tgz |
| macOS binary (x86_64) | Seqtometry_1.0.1.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocSingular, checkmate, data.table, DelayedMatrixStats, future.apply, Matrix, MatrixGenerics, purrr, Rcpp, RcppHNSW, RSpectra, sparseMatrixStats, zeallot
LinkingTo: Rcpp, RcppArmadillo
Suggests: BiocStyle, box, dplyr, future, ggplot2, harmony, knitr, MASS, patchwork, rmarkdown, scater, scuttle, SingleCellExperiment, stringr, TENxPBMCData, testthat (>= 3.0.0), tibble