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.
Package details |
|
---|---|
Author | Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>), 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] (<https://orcid.org/0000-0002-8081-6725>) |
Maintainer | Daniel Osorio <dcosorioh@tamu.edu> |
License | GPL (>= 2) |
Version | 1.0.1 |
URL | https://github.com/cailab-tamu/scTenifoldKnk |
Package repository | View on CRAN |
Installation |
Install the latest version of this package by entering the following in R:
|
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.