Package: scTenifoldKnk
Type: Package
Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
        Networks
Version: 1.1
Authors@R: c(person(given = "Daniel", family = "Osorio", email = "dcosorioh@gmail.com", role = c("aut","cre"), 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 = "Yongjian", family = "Yang", 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 J.", 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.
URL: https://github.com/cailab-tamu/scTenifoldKnk
BugReports: https://github.com/cailab-tamu/scTenifoldKnk/issues
License: GPL (>=2)
Encoding: UTF-8
RoxygenNote: 7.3.3
biocViews:
Imports: Matrix, methods, stats, MASS, scTenifoldNet (>= 1.4), cli,
        enrichR, igraph, reshape2, grDevices
Suggests: testthat (>= 2.1.0)
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev libssl-dev perl
Repository: https://cailab-tamu.r-universe.dev
Date/Publication: 2026-07-10 21:16:13 UTC
RemoteUrl: https://github.com/cailab-tamu/sctenifoldknk
RemoteRef: HEAD
RemoteSha: d635a5855295b4ee75909438b09b2ea27ce3437c
NeedsCompilation: no
Packaged: 2026-07-10 21:52:06 UTC; root
Author: Daniel Osorio [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4424-8422>),
  Yan Zhong [aut, ctb],
  Guanxun Li [aut, ctb],
  Qian Xu [aut, ctb],
  Yongjian Yang [aut, ctb],
  Yanan Tian [aut, ctb],
  Robert Chapkin [aut, ctb],
  Jianhua Huang [aut, ctb],
  James J. Cai [aut, ctb, ths] (ORCID:
    <https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@gmail.com>