# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "scTenifoldKnk" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'scTenifoldKnk: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
  Networks'
version: 2.1.0
doi: 10.32614/CRAN.package.scTenifoldKnk
abstract: 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.
authors:
- family-names: Liu
  given-names: Zaoqu
  email: liuzaoqu@163.com
  orcid: https://orcid.org/0000-0002-0452-742X
- family-names: Osorio
  given-names: Daniel
  email: dcosorioh@tamu.edu
  orcid: https://orcid.org/0000-0003-4424-8422
- family-names: Zhong
  given-names: Yan
- family-names: Li
  given-names: Guanxun
- family-names: Xu
  given-names: Qian
- family-names: Hillhouse
  given-names: Andrew
- family-names: Chen
  given-names: Jingshu
- family-names: Davidson
  given-names: Laurie
- family-names: Tian
  given-names: Yanan
- family-names: Chapkin
  given-names: Robert
- family-names: Huang
  given-names: Jianhua
- family-names: Cai
  given-names: James
  orcid: https://orcid.org/0000-0002-8081-6725
repository: https://zaoqu-liu.r-universe.dev
repository-code: https://github.com/Zaoqu-Liu/scTenifoldKnk
commit: 08118337f6fc22cca5a22c443ccb78ef920dfa3b
url: https://zaoqu-liu.github.io/scTenifoldKnk/
date-released: '2026-01-23'
contact:
- family-names: Liu
  given-names: Zaoqu
  email: liuzaoqu@163.com
  orcid: https://orcid.org/0000-0002-0452-742X