(1) 确定 TO-GCN 的 PCC 截止值, (2) 使用初始 TF 种子生成 TO-GCN 级别的 TF 基因列表,以及 (3) 在每个 TO- GCN 级别生成一个基因列表。 地址:https://github.com/petitmingchang/TO-GCN_STAR-Protocol 注:这里的TF指转录因子。 准备基因表达数据 在进入管道之前,我们需要准备两个具有不同时间点的...
g++ Cutoff_STAR.cpp -o Cutoff g++ TO-GCN_STAR.cpp -o TO-GCN g++ GeneLevel_STAR.cpp -o GeneLevel (1) Cutoff: Determine the PCC cutoff for TO-GCN First of all, you need postive and negative cutoff values of Pearson’s Correlation Coefficients (PCCs) for constructing the GCN. Our metho...
最后一步是确定GCN中节点的时间顺序(级别)。时间顺序由广度优先搜索(BFS)算法指定,从您选择的一组种子节点开始(在seeds.txt中列出)。在大多数情况下,我们会选择一些在第一个时间点高表达,在接下来的时间点低表达的基因作为种子。在我们的研究中,我们选择了一个ID为Zm00001d041056的基因,并运行To-GCN程序来分配C...
As mentioned above, there are three steps for the pipeline. Therefore, we provided a program for each step: (1) Cutoff, (2) GCN, and (3) TO-GCN. You can directly run the program by downloading the corresponding binary codes for different system platforms, Linux, MacOSX, or Windows. You...
Github地址https://github.com/petitmingchang/TO-GCN (Fig 1) 该软件支持Mac、Windows、Linux,演示在Linux中进行。 直接git clone https://github.com/petitmingchang/TO-GCN.git 下载即可 下载后可以看到里面一共三个脚本(Fig 2):Cutoff.cpp-GCN.cpp-TO-GCN.cpp,依次运行即可。
https://www.pnas.org/content/116/8/3091#sec-1 github 用于构建时间序列共表达网络分析。适合于转录组数据挖掘。输入文件为全部的表达基因和关注的表达基因，就能得到共表达网络。
K. et al. Yeast life span extension by depletion of 60s ribosomal subunits is mediated by Gcn4. Cell 133, 292–302. https://doi.org/10.1016/j.cell.2008.02.037 (2008). Article CAS PubMed PubMed Central Google Scholar Browne, G. J. & Proud, C. G. Regulation of peptide-chain ...
The extraction of features and construction of WSI graph representations by TIAToolbox can be easily integrated with code for training a GCN. The modular nature of TIAToolbox allows for easy integration into a Jupyter notebook as part of the toolbox examples to successfully reproduce the SlideGra...
https://github.com/broadinstitute/inferCNV https://github.com/broadinstitute/infercnv Seurat v4.0.3 https://satijalab.org/seurat/ Harmony v0.1.0 Korsunsky et al., 2019 https://github.com/immunogenomics/harmony R v4.0.3 https://www.r-project.org/ Prism 7 GraphPad graphpad.com/scientific-...
比较转录组分析工具:TO-GCN https://www.pnas.org/content/116/8/3091#sec-1 github 用于构建时间序列共表达网络分析。适合于转录组数据挖掘。输入文件为全部的表达基因和关注的表达基因,就能得到共表达网络。