Seqtometry
This is the development version of Seqtometry; to use it, please install the devel version of Bioconductor.
Signature scoring for single cell analysis
Bioconductor version: Development (3.23)
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.
Author: Robert Kousnetsov [aut, cre], Daniel Hawiger [cph, fnd]
Maintainer: Robert Kousnetsov <robert.kousnetsov at health.slu.edu>
citation("Seqtometry")):
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("Seqtometry")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GeneExpression, GeneSetEnrichment, SingleCell, Software |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BiocSingular, checkmate, data.table, future.apply, Matrix, MatrixGenerics, purrr, Rcpp, RcppHNSW, RSpectra, zeallot |
| System Requirements | |
| URL | https://github.com/HawigerLab/Seqtometry |
| Bug Reports | https://github.com/HawigerLab/Seqtometry/issues |
See More
| Suggests | box, dplyr, future, ggplot2, harmony, knitr, MASS, patchwork, rmarkdown, scater, scuttle, SingleCellExperiment, sparseMatrixStats, stringr, TENxPBMCData, testthat (>= 3.0.0), tibble |
| Linking To | Rcpp, RcppArmadillo |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/Seqtometry |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Seqtometry |
| Package Short Url | https://bioconductor.org/packages/Seqtometry/ |
| Package Downloads Report | Download Stats |