SiFINeT: Single Cell Feature Identification with Network Topology

Cluster-independent method based on topology structure of gene co-expression network for identifying feature gene sets, extracting cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Without prior cell clustering, SifiNet circumvents potential inaccuracies in clustering that may influence subsequent analyses. This method is introduced in Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li, Cliburn Chan, Jichun Xie "SifiNet: a robust and accurate method to identify feature gene sets and annotate cells" (2024) <doi:10.1093/nar/gkae307>.

Version:	1.13
Depends:	R (≥ 3.6.0), methods, utils, stats
Imports:	Rcpp (≥ 1.0.9), quantreg (≥ 5.94), igraph (≥ 1.3.5), Matrix (≥ 1.5-1), ggraph (≥ 2.0.6), ggplot2 (≥ 3.3.6)
LinkingTo:	Rcpp, RcppArmadillo
Suggests:	rmarkdown (≥ 2.20), knitr (≥ 1.42)
Published:	2025-01-16
DOI:	10.32614/CRAN.package.SiFINeT
Author:	Qi Gao [aut, cre]
Maintainer:	Qi Gao <gqi at med.umich.edu>
License:	GPL-3
NeedsCompilation:	yes
Citation:	SiFINeT citation info
Materials:	README NEWS
CRAN checks:	SiFINeT results

Documentation:

Reference manual:	SiFINeT.pdf
Vignettes:	An introduction to the SifiNet package (source, R code)

Downloads:

Package source:	SiFINeT_1.13.tar.gz
Windows binaries:	r-devel: SiFINeT_1.13.zip, r-release: not available, r-oldrel: SiFINeT_1.13.zip
macOS binaries:	r-release (arm64): SiFINeT_1.13.tgz, r-oldrel (arm64): SiFINeT_1.13.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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