StabMap
Stabilised mosaic single cell data integration using unshared features
Bioconductor version: Release (3.20)
StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.
Author: Shila Ghazanfar [aut, cre, ctb], Aiden Jin [ctb], Nicholas Robertson [ctb]
Maintainer: Shila Ghazanfar <shazanfar at gmail.com>
citation("StabMap")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("StabMap")
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("StabMap")| Mosaic single cell data integration | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| License | GPL-2 |
| Depends | R (>= 4.4.0) |
| Imports | igraph, slam, BiocNeighbors, Matrix, MASS, abind, SummarizedExperiment, methods, MatrixGenerics, BiocGenerics, BiocSingular, BiocParallel |
| System Requirements | |
| URL | https://sydneybiox.github.io/StabMap https://sydneybiox.github.io/StabMap/ |
| Bug Reports | https://github.com/sydneybiox/StabMap/issues |
See More
| Suggests | scran, scater, knitr, UpSetR, gridExtra, SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0), purrr, sparseMatrixStats |
| 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 | StabMap_1.0.0.tar.gz |
| Windows Binary (x86_64) | StabMap_1.0.0.zip |
| macOS Binary (x86_64) | StabMap_1.0.0.tgz |
| macOS Binary (arm64) | StabMap_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/StabMap |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/StabMap |
| Bioc Package Browser | https://code.bioconductor.org/browse/StabMap/ |
| Package Short Url | https://bioconductor.org/packages/StabMap/ |
| Package Downloads Report | Download Stats |