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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 (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Overview of scFeatures with case studies HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, SingleCell, Software, Spatial, Transcriptomics
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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
System Requirements
Bug Reports https://github.com/SydneyBioX/scFeatures/issues
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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_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64)
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/
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