STAGEs: A web-based tool that integrates data visualization and pathway enrichment analysis for gene expression studies Article Open access 02 May 2023 GOAT: efficient and robust identification of gene set enrichment Article Open access 19 June 2024 reString: an open-source Python software to...
Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID....
d, Along the inferred single-cell trajectories, pathway-enrichment analysis is performed, and transient effects of drug activity are identified at the pathway level. Full size image Performance evaluation of the imputation of single-cell data In this Article we used two drug-induced single-cell ...
Enrichment analysis was conducted with the clusterProfiler package, using a minimum set size of 10 and a maximum of 500 proteins per GO term for over-representation consideration. GO term definitions can be found at https://www.ebi.ac.uk/QuickGO/. Pathway associations The GO over-representation...
Pathway enrichment Proteins selected by the MOFA model were searched for in the UniProt database [35], and their entry number was then subsequently used within the Reactome database [36]. A separate over-representation analysis was performed for each LF. This analysis used hypergeometric distributio...
对于通路分析结果的可视化而言,最常用的展现方式就是在通路中高亮显示富集到的基因。kegg 提供了在Color Pathway在线服务,可以方便的完成这一任务。 网址如下: http://www.kegg.jp/kegg/tool/map_pathway3.html 这个工具使用比较简单,分为4步: 在Select KEGG pathway map输入框中输入想要标记的pathway ID ; ...
-pathway, molecule-disease, molecule-drug, molecule-organ; 2) inter-association analysis between pathway, disease, drug and organ; and 3) enrichment analysis and inter-association analysis: 3a) self-validation and 3b) identification of previously undiscovered components by the enrichment analysis....
python version 2.7 (numpy, scipy, matplotlib) R version 3.4.0 (LSD, data.table, ggplot2) Performing PEGASAS analysis After installing PEGASAS and its dependencies, the user can follow the two steps below to perform the analysis and to generate plots for correlation and Gene Ontology (GO) anal...
Python genescf/GeneSCF Star21 Code Issues Pull requests Gene Set Clustering based on Functional annotation genereal-timecancerup-to-dategene-set-enrichmentkegg-pathwayenrichment-analysisgeneontologygseagene-set-clusteringreactome-pathwayfunctional-enrichment-analysisgene-set-analysisenrichment-testingdownload-pat...
Alternative splicing analysis In order to detect alternatively spliced exons (ASEs), we used DEXSeq version 1.16.10 to determine differential exon usage in the wing hinge RNA-Seq data [81]. First, the python script dexseq_prepare_annotation.py pro- vided by DEXSeq was used to process the ...