scFeatures
This is the released version of scFeatures; for the devel version, see scFeatures.
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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, 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, pheatmap, limma, ggplot2, plotly, igraph, data.table, enrichplot, DOSE, rmarkdown |
| 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | scFeatures_1.12.0.zip |
| macOS Binary (big-sur-x86_64) | scFeatures_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | scFeatures_1.12.0.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 |