scFeatures

This is the development version of scFeatures; for the stable release version, see scFeatures.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews	CellBasedAssays, SingleCell, Software, Spatial, Transcriptomics
Version	1.1.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, Seurat, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, SpatialExperiment, SummarizedExperiment, rmarkdown, methods, stats, DT, cli, SingleCellSignalR, MatrixGenerics
Linking To
Suggests	knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler
System Requirements
Enhances
URL
Bug Reports	https://github.com/SydneyBioX/scFeatures/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scFeatures_1.1.0.tar.gz
Windows Binary	scFeatures_1.1.0.zip
macOS Binary (x86_64)	scFeatures_1.1.0.tgz
macOS Binary (arm64)
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