kegg
There are 56 repositories under kegg topic.
YuLab-SMU/clusterProfiler
:bar_chart: A universal enrichment tool for interpreting omics data
cokelaer/bioservices
Access to Biological Web Services from Python.
noriakis/ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
xieguigang/mzkit
Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.
Pex2892/PETAL
PETAL (ParallEl paThways AnaLyzer): a Python tool for deep biological pathway analysis
Matteopaluh/KEMET
KEGG Module Evaluation Tool
yamada-lab/functree-ng
An interactive radial tree for functional hierarchies and omics data visualization
decodebiology/geneSCF_inactive
GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF
mentatpsi/KEGG-Crawler
A parallel API crawler for the retrieval of Kyoto Encyclopedia of Genes and Genomes metabolic and genomics data.
OSS-Lab/MetQy
Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
draeger-lab/KEGGtranslator
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.
nasqar/ClusterProfShinyGSEA
A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries
prakhargurawa/Drug-Similarity-and-Link-Prediction-using-Graph-Embeddings-on-Medical-Knowledge-Graph
Utilizing graphical neural networks and embeddings on a medical database KEGG to perform link predictions and drug similarity systems.
bio2bel/kegg
A Bio2BEL package for integrating pathway-related information from KEGG in BEL
zd105/AllEnricher
A comprehensive gene set function enrichment tool for multiple species.
guokai8/bioAnno
Build Annotation package by using information from KEGG, NCBI, Ensembl
harryhaller001/keggtools
Library for KEGG pathway enrichment analysis
nasqar/ClusterProfShinyORA
A web-based application to perform Over-Representation Analysis (ORA) using clusterProfiler and shiny R libraries
SilasK/ipath3
Python wrapper for ipath3
guokai8/richR
Function Enrichment analysis and Network construction
dalmolingroup/neurotransmissionevolution
Research compendium for Viscardi et al, 2020.
klevdiamanti/metabolomicsDB
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.
SMRUCC/GCModeller.Core
GCModeller Individual Components: GCModeller base core assembly library on common biological database read and write I/O
suqingdong/kegg_viewer
Generate Highlighted SVG/PNG for KEGG Pathway
BioDeep/KEGG.molDraw
Drawing chemical compound structures and glycan structures with capabilities to search against the KEGG databases
shamitashetty/RNA-sequencing-analysis-in-R
Analysis of RNA-seq data using DESeq2
Shaumik-Ashraf/BiosystemsProject
A command-line interface and biochemical pathway finder based on KEGG
arnaudporet/kgml2sif
Converting KGML encoded KEGG pathways to the SIF file format
cannin/sbgn2sif
Converting SBGN-encoded pathways to the SIF file format
ceabiodb/biodbKegg
A biodb extension package for KEGG databases.
ctSkennerton/kegg_hmm_models
Create HMMs from KEGG orthologs
francescopatane96/RNA-seq_Pipeline
Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...
JulieMarieCharmillon/kegg_parser
An HTML parser for "KEGG Mapper – Reconstruct Result" pages
lucaz88/genome_comparison_code
Companion repository to the article: "Comparative whole-genome approach to identify bacterial traits for microbial interactions"
tonibois/KeggDrugVirtualScreening
A software for analysis and fast virtual screen of KEGG_DRUG molecular database of accepted drugs classificated by ATC codes