A tool for representing genomic potential and transcriptomic expression into KEGG pathways
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Updated
Jul 28, 2024 - Python
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
KEGG-Chem is a Python program designed to retrieve KEGG compounds and associated data using an input of KEGG orthologues or modules, and can also retrieve SMILES, SDF files, and more from PubChem.
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.
Gene Set Clustering based on Functional annotation
"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.
A Python script for efficiently retrieving and organizing module-related data from the KEGG database, including entries, symbols, pathway IDs, and names.
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.
Library for KEGG pathway enrichment analysis
Computational protemics analysis of cancer cell-lines at the level of single-cells
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
PETAL (ParallEl paThways AnaLyzer): a Python tool for deep biological pathway analysis
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.
Application of KEGG pathway for DRF
An HTML parser for "KEGG Mapper – Reconstruct Result" pages
A standalone interactive application for detecting biological significance on a set of genes
A .NET wrapper for the Kyoto Encyclopedia of Genes and Genomes (KEGG) API.
GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF
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