Package: scTenifoldKnk
Type: Package
Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
        Networks
Version: 2.1.0
Author: Zaoqu Liu [ctb, cre], Daniel Osorio [aut], Yan Zhong [aut,
        ctb], Guanxun Li [aut, ctb], Qian Xu [aut, ctb], Andrew
        Hillhouse [aut, ctb], Jingshu Chen [aut, ctb], Laurie Davidson
        [aut, ctb], Yanan Tian [aut, ctb], Robert Chapkin [aut, ctb],
        Jianhua Huang [aut, ctb], James Cai [aut, ctb, ths]
Maintainer: Zaoqu Liu <liuzaoqu@163.com>
Authors@R: c(person(given = "Zaoqu", family = "Liu", email = "liuzaoqu@163.com", role = c("ctb", "cre"), comment = c(ORCID = '0000-0002-0452-742X')),
              person(given = "Daniel", family = "Osorio", email = "dcosorioh@tamu.edu", role = c("aut"), comment = c(ORCID = '0000-0003-4424-8422')),
              person(given = "Yan", family = "Zhong", role = c("aut","ctb")),
              person(given = "Guanxun", family = "Li", role = c("aut","ctb")),
              person(given = "Qian", family = "Xu", role = c("aut","ctb")),
              person(given = "Andrew", family = "Hillhouse", role = c("aut","ctb")),
              person(given = "Jingshu", family = "Chen", role = c("aut","ctb")),
              person(given = "Laurie", family = "Davidson", role = c("aut","ctb")),
              person(given = "Yanan", family = "Tian", role = c("aut","ctb")),
              person(given = "Robert", family = "Chapkin", role = c("aut","ctb")),
              person(given = "Jianhua", family = "Huang", role = c("aut","ctb")),
              person(given = "James", family = "Cai", role = c("aut", "ctb", "ths"), comment = c(ORCID = '0000-0002-8081-6725'))
              )
Description: A workflow based on 'scTenifoldNet' to perform in-silico
        knockout experiments using single-cell RNA sequencing
        (scRNA-seq) data from wild-type (WT) control samples as input.
        First, the package constructs a single-cell gene regulatory
        network (scGRN) and knocks out a target gene from the adjacency
        matrix of the WT scGRN by setting the gene's outdegree edges to
        zero. Then, it compares the knocked out scGRN with the WT scGRN
        to identify differentially regulated genes, called
        virtual-knockout perturbed genes, which are used to assess the
        impact of the gene knockout and reveal the gene's function in
        the analyzed cells. This version includes C++ acceleration with
        Eigen library, cross-platform compatibility (macOS, Linux,
        Windows), and Seurat v4/v5 support.
URL: https://zaoqu-liu.github.io/scTenifoldKnk/,
        https://github.com/Zaoqu-Liu/scTenifoldKnk
BugReports: https://github.com/Zaoqu-Liu/scTenifoldKnk/issues
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 7.3.3
Imports: Matrix, RSpectra, MASS, stats, parallel, methods, Rcpp,
        RcppEigen, utils
LinkingTo: Rcpp, RcppEigen
Suggests: testthat (>= 2.1.0), SeuratObject, knitr, rmarkdown
VignetteBuilder: knitr
SystemRequirements: GNU make
NeedsCompilation: yes
Config/pak/sysreqs: make
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-23 08:35:24 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/scTenifoldKnk
RemoteRef: HEAD
RemoteSha: 08118337f6fc22cca5a22c443ccb78ef920dfa3b
Packaged: 2026-07-22 07:41:02 UTC; root