kegg

There are 2 repositories under kegg topic.

YuLab-SMU / clusterProfiler
:bar_chart: A universal enrichment tool for interpreting omics data
enrichment-analysis go gsea kegg rstats visualization
Language:R 1072
jmzeng1314 / GEO
geo go kegg limma
Language:R 817
cokelaer / bioservices
Access to Biological Web Services from Python.
biomodels chebi chembl eutils kegg muscle python quickgo unichem uniprot wikipathways
Language:Python 292
ggkegg
noriakis / ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
ggplot2 ggraph kegg pathway r tidygraph visualization
Language:R 225
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.
chemoinformatics gc-ms gcxgc kegg lc-ms lipidomics maldi mass-spectrometry metabolomics metadna ms-dial ms-imaging mzkit r-sharp raman-spectroscopy single-cell single-cell-metabolism visualbasic
Language:Visual Basic .NET 57
Pex2892 / PETAL
PETAL (ParallEl paThways AnaLyzer): a Python tool for deep biological pathway analysis
python3 python kegg-pathway kegg parallel biological biological-data-analysis unict
Language:Python 35
Matteopaluh / KEMET
KEGG Module Evaluation Tool
gap-filling gem genome-scale-metabolic-model kegg kegg-modules metabolic-models metabolic-reconstruction
Language:Python 29
yamada-lab / functree-ng
An interactive radial tree for functional hierarchies and omics data visualization
hierarchy-viewer tree-visualization ontology-visualization kegg metagenomics
Language:HTML 23
decodebiology / geneSCF_inactive
GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF
gene-set-clustering enrichment-analysis gene-annotation gene-ontology kegg kegg-pathway kegg-gene pathways pathway-analysis reactome functional-analysis real-time-processing real-time-analytics
Language:Perl 20
mentatpsi / KEGG-Crawler
A parallel API crawler for the retrieval of Kyoto Encyclopedia of Genes and Genomes metabolic and genomics data.
kegg kegg-reaction keggrest python metabolites pathway reactions genetics
Language:Python 20
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.
kegg kegg-pathway sbml gml kgml-files graphml biopax kegg-pathway-database conversion visualization
Language:Java 19
nasqar / ClusterProfShinyGSEA
A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries
geneset-enrichment geneset-enrichment-analysis gsea web-application shiny-apps r kegg kegg-pathway visualization bioinformatics
Language:R 18
OSS-Lab / MetQy
Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
r-package kegg metabolism data-mining
Language:R 18
Drug-Similarity-and-Link-Prediction-using-Graph-Embeddings-on-Medical-Knowledge-Graph
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.
ampligraph neural-network graphs knowledge-graph graph-neural-networks machine-learning biomedical graph-convolutional-networks kegg link-prediction
Language:Jupyter Notebook 17
guokai8 / bioAnno
Build Annotation package by using information from KEGG, NCBI, Ensembl
annotations package kegg gene ontology
Language:R 15
harryhaller001 / keggtools
Library for KEGG pathway enrichment analysis
enrichment-analysis kegg kegg-pathway python
Language:Python 14
bio2bel / kegg
A Bio2BEL package for integrating pathway-related information from KEGG in BEL
pathways systems-biology networks-biology proteins biological-expression-language kegg
Language:Python 13
nasqar / ClusterProfShinyORA
A web-based application to perform Over-Representation Analysis (ORA) using clusterProfiler and shiny R libraries
over-representation-analysis geneset-enrichment web-application shiny-apps shiny r kegg kegg-pathway bioinformatics visualization
Language:R 13
AllEnricher
zd105 / AllEnricher
A comprehensive gene set function enrichment tool for multiple species.
disease do enrichment-analysis go kegg non-model-species
Language:Shell 13
guokai8 / richR
Function Enrichment analysis and Network construction
enrichment-analysis kegg gsea enrichment plot
Language:R 11
SilasK / ipath3
Python wrapper for ipath3
ipath kegg metabolites pandas-dataframe python3 wrapper
Language:Jupyter Notebook 10
neurotransmissionevolution
dalmolingroup / neurotransmissionevolution
Research compendium for Viscardi et al, 2020.
research-compendium bioinformatics r evolution kegg stringdb expression-atlas orthology neurotransmission network-analysis igraph
Language:TeX 4
Gabriele-Conti / KEGGSearch
Comprehensive KEGG Data Retrieval Using Multiple Sources
bioinformatics genetic genetic-analysis kegg kegg-modules kegg-pathway microbiome microbiome-analysis microbiota r
Language:R 4
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.
chebi hmdb kegg kegg-compounds kegg-pathway metabolomics metabolomics-database smpdb
Language:C# 4
shamitashetty / RNA-sequencing-analysis-in-R
Analysis of RNA-seq data using DESeq2
r rna-seq-analysis rnaseq deseq2 kegg
Language:R 4
SMRUCC / GCModeller.Core
GCModeller Individual Components: GCModeller base core assembly library on common biological database read and write I/O
gcmodeller scibasic ncbi kegg uniprot genbank bioinformatics
Language:Visual Basic .NET 4
suqingdong / kegg_viewer
Generate Highlighted SVG/PNG for KEGG Pathway
kegg pathway
Language:Python 4
BioDeep / KEGG.molDraw
Drawing chemical compound structures and glycan structures with capabilities to search against the KEGG databases
vb-net kegg bioinformatics gdi microsoft-visualbasic
Language:Visual Basic .NET 3
lucaz88 / genome_comparison_code
Companion repository to the article: "Comparative whole-genome approach to identify bacterial traits for microbial interactions"
genome-annotation kegg r
Language:R 3
PEHGP / kaas
KEGG Automatic Annotation Server Localization
kegg
Language:Python 3
Shaumik-Ashraf / BiosystemsProject
A command-line interface and biochemical pathway finder based on KEGG
kegg bioengineering bioinformatics biosystems depth-first-search mit-licensed
Language:Python 3
cannin / sbgn2sif
Converting SBGN-encoded pathways to the SIF file format
sif sbgn sbgnml biological-networks sbgn-to-sif pathways reactome kegg sbgn2sif
Language:Python 2
ceabiodb / biodbKegg
A biodb extension package for KEGG databases.
kegg kegg-databases biodb
Language:R 2
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...
bam-files clusterprofiler deseq2 deseq2-analysis differentially-expressed-genes gene-set-enrichment-analysis geneontology gsea kegg ora r reactome reactome-pathway rna-seq rna-seq-analysis rna-seq-pipeline script wikipathways diseaseontology over-rapresentation-analysis
Language:Jupyter Notebook 2
JulieMarieCharmillon / kegg_parser
An HTML parser for "KEGG Mapper – Reconstruct Result" pages
kegg kegg-pathway parser python beautifulsoup4 csv-files kegg-modules
Language:Python 2
noriakis / q2-pathway
The unified functional prediction and comparative analysis for 16S rRNA gene sequencing data
16s inference kegg qiime2 qiime2-plugin
Language:Python 2

kegg

YuLab-SMU / clusterProfiler

jmzeng1314 / GEO

cokelaer / bioservices

noriakis / ggkegg

xieguigang / mzkit

Pex2892 / PETAL

Matteopaluh / KEMET

yamada-lab / functree-ng

decodebiology / geneSCF_inactive

mentatpsi / KEGG-Crawler

draeger-lab / KEGGtranslator

nasqar / ClusterProfShinyGSEA

OSS-Lab / MetQy

prakhargurawa / Drug-Similarity-and-Link-Prediction-using-Graph-Embeddings-on-Medical-Knowledge-Graph

guokai8 / bioAnno

harryhaller001 / keggtools

bio2bel / kegg

nasqar / ClusterProfShinyORA

zd105 / AllEnricher

guokai8 / richR

SilasK / ipath3

dalmolingroup / neurotransmissionevolution

Gabriele-Conti / KEGGSearch

klevdiamanti / metabolomicsDB

shamitashetty / RNA-sequencing-analysis-in-R

SMRUCC / GCModeller.Core

suqingdong / kegg_viewer

BioDeep / KEGG.molDraw

lucaz88 / genome_comparison_code

PEHGP / kaas

Shaumik-Ashraf / BiosystemsProject

cannin / sbgn2sif

ceabiodb / biodbKegg

francescopatane96 / RNA-seq_Pipeline

JulieMarieCharmillon / kegg_parser

noriakis / q2-pathway