A tool for representing genomic potential and transcriptomic expression into KEGG pathways

A standalone interactive application for detecting biological significance on a set of genes

PETAL (ParallEl paThways AnaLyzer): a Python tool for deep biological pathway analysis

Gene Set Clustering based on Functional annotation

GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF

A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.

A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Library for KEGG pathway enrichment analysis

A web-based application to perform Over-Representation Analysis (ORA) using clusterProfiler and shiny R libraries

Overrepresentation analysis for KEGG and PID pathways using community detection

Computational protemics analysis of cancer cell-lines at the level of single-cells

metabolomicsDB is a collection of three open-source command-line tools and an API. The tools create a meta-database of HMDB and ChEBI, while the API allows others to read the meta-database and use it on their own projects.

An HTML parser for "KEGG Mapper – Reconstruct Result" pages

"Pathway_Feature_Identification.py" is a script for analyzing microbial genomic data, identifying antimicrobial resistance-associated pathways using KEGG data, and applying logistic regression for feature selection.

DESeq2 Analysis and visualization of specific genes, notably Pasilla. Script aims to identify and filter differentially expressed genes and neatly store the results. The project also includes Gene Ontology (GO) and Kegg pathway analyses, providing insights into the biological processes affected by the Pasilla gene depletion.

Repository for the presentation of work developed by the student Duarte Velho for the UC Project, of the Master in Bioinformatics of the University of Minho, academic year 23-24.

SPECifIC - Sub-Pathway ExtraCtor and enrICher

A .NET wrapper for the Kyoto Encyclopedia of Genes and Genomes (KEGG) API.