list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene-expression normalization, imputation, gene filtering, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein network interaction visualization, and pseudo-time cell ...
基因本体论富集分析(Gene Ontology Enrichment Analysis):这是最常用的富集分析类型,用于检验基因集合中基因本体论(GO)条目的富集情况。这可以帮助研究者了解基因集合中的基因在生物学过程、分子功能和细胞组成方面的共同特征。 通路富集分析(Pathway Enrichment Analysis):这种类型的富集分析主要关注基因在代谢途径和信号传导...
1,打开绘图页面 首先,使用浏览器(推荐chrome或者edge)打开KEGG Pathway二级分类汇总绘制页面。左侧为常见作图导航,中间为数据输入框和可选参数,右侧为描述和结果示例。也可以在搜索框中搜索pathway,找到绘图页面。 http://www.bioinformatics.com.cn/plot_basic_pathway_enrichment_second_class_summary_bar_plot_206 图...
GO Express: https://www.bioconductor.org/packages/release/bioc/html/GOexpress.html GO Extender: https://www.msu.edu/~jinchen/GOExtender/ DAL: http://iwera.ir/~ahmad/dal/ Negative GO enrichment: https://sites.google.com/site/guoxian85/neggoa Variant Set VSE: https://cran.r-project.or...
Part1aPEAR: an R package for enrichment network visualisation 桑树下的胖蚕宝 date: 2023.06.13 The interpretation of pathway enrichment analysis (PEA) results is frequently complicated by an overwhelming and redundant list of significantly affected pathways. Here, we present an R pack- age aPEAR ...
GO enrichment analysis revealed that age-upregulated genes were mainly associated with cytokine-mediated signaling pathway and apoptotic signaling pathway and that age-downregulated genes were mainly related to epithelial cell proliferation and ECM organization (Figure 2F). For example, IFI27, encoding ...
To determine the assembly importance score for the RF models, we performed gene set enrichment analysis (GSEA76, implemented using GSEApy77) on the gene list ranked according to the gene-level feature importance scores derived from the RF models. The absolute normalized enrichment scores generated ...
The role of dysregulation of mRNA alternative splicing (AS) in the development and progression of solid tumors remains to be defined. Here we describe the first comprehensive AS landscape in the spectrum of human prostate cancer (PCa) evolution. We find that the severity of splicing dysregulation...
Gene ontology (GO) enrichment analysis revealed that >50% of the differentially expressed proteins comprised GO slim terms belonging to metabolic processes (Figure S5C). Visualizing the enzyme expression levels by mapping them to a metabolic network graph using iPath3,60 highlighted changes in ...
Abstract: A curated list of resources for learning bioinformatics. Some of this repo resources were collected by BioInstaller project. You can use BioInstaller to directly download the source code or database files, or fetch the meta information by BioInstaller::get.meta()$item. Purpose: Provide...