scFeatures

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see scFeatures.

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

Bioconductor version: 3.21

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 (from within R, enter citation("scFeatures")):

Installation

To install this package, start R (version "4.5") 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 PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, SingleCell, Software, Spatial, Transcriptomics

Version 1.8.0

In Bioconductor since BioC 3.17 (R-4.3) (2.5 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

Suggests knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scFeatures_1.8.0.tar.gz

Windows Binary (x86_64) scFeatures_1.8.0.zip

macOS Binary (x86_64) scFeatures_1.8.0.tgz

macOS Binary (arm64) scFeatures_1.8.0.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/

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