wSIR
This is the development version of wSIR; to use it, please install the devel version of Bioconductor.
Weighted Sliced Inverse Regression (wSIR) for supervised dimension reduction of spatial transcriptomics and single cell gene expression data
Bioconductor version: Development (3.24)
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.
Author: Max Woollard [aut, cre]
, Pratibha Panwar [ctb]
, Linh Nghiem [aut]
, Shila Ghazanfar [aut]
Maintainer: Max Woollard <mwoo5086 at uni.sydney.edu.au>
citation("wSIR")):
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("wSIR")
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("wSIR")| wSIR supervised dimension reduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, DimensionReduction, GeneExpression, Regression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| 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) |
| System Requirements | |
| URL | https://sydneybiox.github.io/wSIR https://github.com/SydneyBioX/wSIR |
| Bug Reports | https://github.com/sydneybiox/wSIR/issues |
See More
| Suggests | knitr, BiocStyle, class, testthat (>= 3.0.0) |
| 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 | wSIR_0.99.9.tar.gz |
| Windows Binary (x86_64) | wSIR_0.99.9.zip |
| macOS Binary (big-sur-x86_64) | wSIR_0.99.9.tgz |
| macOS Binary (sonoma-arm64) | wSIR_0.99.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/wSIR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/wSIR |
| Bioc Package Browser | https://code.bioconductor.org/browse/wSIR/ |
| Package Short Url | https://bioconductor.org/packages/wSIR/ |
| Package Downloads Report | Download Stats |