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scTenifoldKnk: In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networks

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.

Version: 1.0.1
Imports: pbapply, RSpectra, Matrix, methods, stats, utils, MASS, scTenifoldNet
Suggests: testthat (≥ 2.1.0)
Published: 2021-01-22
DOI: 10.32614/CRAN.package.scTenifoldKnk
Author: Daniel Osorio ORCID iD [aut, cre], 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 ORCID iD [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh at tamu.edu>
BugReports: https://github.com/cailab-tamu/scTenifoldKnk/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/cailab-tamu/scTenifoldKnk
NeedsCompilation: no
Materials: README
In views: Omics
CRAN checks: scTenifoldKnk results

Documentation:

Reference manual: scTenifoldKnk.pdf

Downloads:

Package source: scTenifoldKnk_1.0.1.tar.gz
Windows binaries: r-devel: scTenifoldKnk_1.0.1.zip, r-release: scTenifoldKnk_1.0.1.zip, r-oldrel: scTenifoldKnk_1.0.1.zip
macOS binaries: r-release (arm64): scTenifoldKnk_1.0.1.tgz, r-oldrel (arm64): scTenifoldKnk_1.0.1.tgz, r-release (x86_64): scTenifoldKnk_1.0.1.tgz, r-oldrel (x86_64): scTenifoldKnk_1.0.1.tgz
Old sources: scTenifoldKnk archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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