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

Bioconductor version: Release (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>

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


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

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


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 1.4.0
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, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT
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Suggests knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR,, clusterProfiler
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Follow Installation instructions to use this package in your R session.

Source Package scFeatures_1.4.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) scFeatures_1.4.0.tgz
macOS Binary (arm64) scFeatures_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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