wSIR
Weighted Sliced Inverse Regression (wSIR) for supervised dimension reduction of spatial transcriptomics and single cell gene expression data
Bioconductor version: 3.24 · Package version: 0.99.9
Weighted Sliced Inverse Regression (wSIR) is a supervised dimension reduction algorithm for spatial transcriptomics gene expression data. For a provided gene expression matrix and dataframe of each cell's spatial coordinates, wSIR creates a low-dimensional representation of the gene expression data that preserves the ability to predict spatial coordinates that was present in the gene expression data. Furthermore, wSIR provides interpretable loadings which allow for projection of new single-cell gene expression data into a low-dimensional space which preserves the spatial information present in the gene expression data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("wSIR")Details
| Maintainer | Max Woollard <mwoo5086@uni.sydney.edu.au> |
| Author | Max Woollard [aut, cre] (ORCID: <https://orcid.org/0009-0000-6319-6926>), Pratibha Panwar [ctb] (ORCID: <https://orcid.org/0000-0002-7437-7084>), Linh Nghiem [aut] (ORCID: <https://orcid.org/0000-0003-2874-9067>), Shila Ghazanfar [aut] (ORCID: <https://orcid.org/0000-0001-7861-6997>) |
| License | MIT + file LICENSE |
| URL | https://sydneybiox.github.io/wSIR, https://github.com/SydneyBioX/wSIR |
| Bug Reports | https://github.com/sydneybiox/wSIR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellBasedAssays, DimensionReduction, GeneExpression, Regression, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/wSIR/ |
Citation
From within R, enter citation("wSIR"):
Max Woollard, Linh Nghiem, Shila Ghazanfar. wSIR: Weighted Sliced Inverse Regression (wSIR) for supervised dimension reduction of spatial transcriptomics and single cell gene expression data. doi:10.18129/B9.bioc.wSIR, R package version 0.99.9, https://bioconductor.org/packages/wSIR.
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 | wSIR_0.99.9.tar.gz |
| Windows binary (x86_64) | wSIR_0.99.9.zip |
| macOS binary (arm64) | wSIR_0.99.9.tgz |
| macOS binary (x86_64) | wSIR_0.99.9.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: magrittr (>= 2.0), ggplot2 (>= 3.5.1), umap (>= 0.2.10), vctrs (>= 0.6), stringr (>= 1.5.1), distances (>= 0.1.11), Rcpp (>= 1.0.11), doBy (>= 4.6.0), BiocParallel (>= 1.38.0), rlang, methods, BiocGenerics (>= 0.50.0), SummarizedExperiment (>= 1.34.0), SingleCellExperiment (>= 1.26.0), SpatialExperiment (>= 1.14.0)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, BiocStyle, class, testthat (>= 3.0.0)