scFeatures
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
Bioconductor version: Release (3.20)
scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.
Author: Yue Cao [aut, cre], Yingxin Lin [aut], Ellis Patrick [aut], Pengyi Yang [aut], Jean Yee Hwa Yang [aut]
Maintainer: Yue Cao <yue.cao at sydney.edu.au>
citation("scFeatures")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scFeatures")
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("scFeatures")| Overview of scFeatures with case studies | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT |
| System Requirements | |
| URL | https://sydneybiox.github.io/scFeatures/ https://github.com/SydneyBioX/scFeatures/ |
| Bug Reports | https://github.com/SydneyBioX/scFeatures/issues |
See More
| Suggests | knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler |
| 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 | scFeatures_1.6.0.tar.gz |
| Windows Binary (x86_64) | scFeatures_1.6.0.zip (64-bit only) |
| macOS Binary (x86_64) | scFeatures_1.6.0.tgz |
| macOS Binary (arm64) | scFeatures_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scFeatures |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scFeatures |
| Bioc Package Browser | https://code.bioconductor.org/browse/scFeatures/ |
| Package Short Url | https://bioconductor.org/packages/scFeatures/ |
| Package Downloads Report | Download Stats |