Package: SiFINeT 1.13

Qi Gao

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>.

Authors:Qi Gao [aut, cre]

SiFINeT_1.13.tar.gz
SiFINeT_1.13.tar.gz(r-4.7-arm64)SiFINeT_1.13.tar.gz(r-4.7-x86_64)SiFINeT_1.13.tar.gz(r-4.6-arm64)SiFINeT_1.13.tar.gz(r-4.6-x86_64)
SiFINeT_1.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SiFINeT/json (API)

# Install 'SiFINeT' in R:

install.packages('SiFINeT', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblas cpp openmp

3.06 score 23 scripts 189 downloads 15 exports 54 dependencies

Last updated from:2981dc1586. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	212
linux-devel-x86_64	OK	196
source / vignettes	OK	249
linux-release-arm64	OK	229
linux-release-x86_64	OK	194
wasm-release	OK	147

Exports:assign_shared_feature cal_coexp cal_coexp_sp cal_connectivity create_network create_SiFINeT_object enrich_feature_set EstNull extract_subnetwork feature_coexp filter_lowexp find_unique_feature geneset_topology norm_FDR_SQAUC quantile_thres

Dependencies:base64enc cachem cli cpp11 dplyr farver fastmap generics ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable igraph isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixModels memoise pillar pkgconfig polyclip purrr quantreg R6 RColorBrewer Rcpp RcppArmadillo rlang S7 scales SparseM stringi stringr survival systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr

Introduction to SifiNet

Rendered fromSifiNet_tutorial.Rmdusingknitr::rmarkdown

Last update: 2025-01-16
Started: 2025-01-16

Help page	Topics
assign_shared_feature	assign_shared_feature
cal_coexp This function calculates the coexpression patterns between genes and returns the coexpression matrix.	cal_coexp
cal_coexp_sp This function calculates the coexpression patterns between genes in sparse matrix and returns the coexpression matrix.	cal_coexp_sp
cal_conn This function calculates the first 3 order connectivities for each gene and returns the list of vectors of connectivities.	cal_conn
cal_connectivity	cal_connectivity
create_network	create_network
create_SiFINeT_object	create_SiFINeT_object
enrich_feature_set	enrich_feature_set
EstNull This function is a Rcpp version of Wenguang Sun and Tony T. Cai's EstNull.func R function, estimating null distribution from data. Sun, W., & Cai, T. T. (2007). Oracle and Adaptive Compound Decision Rules for False Discovery Rate Control. Journal of the American Statistical Association, 102(479), 901–912.	EstNull
extract_subnetwork	extract_subnetwork
feature_coexp	feature_coexp
filter_lowexp	filter_lowexp
find_unique_feature	find_unique_feature
geneset_topology	geneset_topology
norm_FDR_SQAUC The function controls the false discovery rate (FDR) of coexpression patterns using SQAUC method Jichun Xie and Ruosha Li. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates". In: J R Stat Soc Series B Stat Methodol (2018). doi: 10.1111/rssb.12288.	norm_FDR_SQAUC
quantile_thres	quantile_thres
The SiFINeT Class	SiFINeT SiFINeT-class

Package: SiFINeT 1.13

SiFINeT: Single Cell Feature Identification with Network Topology

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)