YuLab-SMU/clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

Language: R - Size: 15.1 MB - Last synced: about 20 hours ago - Pushed: 1 day ago - Stars: 947 - Forks: 245

noriakis/q2-pathway

QIIME 2 plugin for visualizing and analyzing pathway information based on gene family abundances

Language: Python - Size: 158 KB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

guokai8/richR

Function Enrichment analysis and Network construction

Language: R - Size: 3.09 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 6 - Forks: 4

cokelaer/bioservices

Access to Biological Web Services from Python.

Language: Python - Size: 5.46 MB - Last synced: 7 days ago - Pushed: 10 days ago - Stars: 271 - Forks: 61

BioDeep/KEGG.molDraw

Drawing chemical compound structures and glycan structures with capabilities to search against the KEGG databases

Language: Visual Basic .NET - Size: 8.71 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 3 - Forks: 3

yutayamate/functree-cli

Command line interface for FuncTree (Deprecated, Experimental)

Language: JavaScript - Size: 1.79 MB - Last synced: 28 days ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

noriakis/ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

Language: R - Size: 14.7 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 191 - Forks: 16

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.

Language: Visual Basic .NET - Size: 487 MB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 44 - Forks: 14

mentatpsi/KEGG-Crawler

A parallel API crawler for the retrieval of Kyoto Encyclopedia of Genes and Genomes metabolic and genomics data.

Language: Python - Size: 25.2 MB - Last synced: 30 days ago - Pushed: 10 months ago - Stars: 20 - Forks: 4

Matteopaluh/KEMET

KEGG Module Evaluation Tool

Language: Python - Size: 178 MB - Last synced: 9 days ago - Pushed: 6 months ago - Stars: 22 - Forks: 5

SMRUCC/GCModeller-CAD-blueprint

Auto generated bio-CAD blueprint by Machine Learning

Language: Visual Basic - Size: 47.5 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

gaenssle/VicinityAnalyzer

Check the neighbouring genes in KEGG genomes for KEGG Orthology (KO), domains and keywords

Language: Python - Size: 61.5 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

gaenssle/DomainAnalyzer

Analyze domains regarding their taxonomic distribution, motifs with other domains and export their fasta sequence

Language: Python - Size: 198 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

suqingdong/kegg_viewer

Generate Highlighted SVG/PNG for KEGG Pathway

Language: Python - Size: 199 KB - Last synced: 3 months ago - Pushed: almost 4 years ago - Stars: 4 - Forks: 1

Lachiemckbioinfo/KEGGChem

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.

Language: Python - Size: 266 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

harryhaller001/keggtools

Library for KEGG pathway enrichment analysis

Language: Python - Size: 13.1 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 12 - Forks: 2

bio2bel/kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

Language: Python - Size: 297 KB - Last synced: 2 days ago - Pushed: over 2 years ago - Stars: 13 - Forks: 4

yamada-lab/functree-ng

An interactive radial tree for functional hierarchies and omics data visualization

Language: HTML - Size: 10.9 MB - Last synced: 28 days ago - Pushed: over 1 year ago - Stars: 22 - Forks: 6

vsmicrogenomics/KEGG_Modules_Fetcher

A Python script for efficiently retrieving and organizing module-related data from the KEGG database, including entries, symbols, pathway IDs, and names.

Language: Python - Size: 0 Bytes - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

ceabiodb/biodbKegg 📦

A biodb extension package for KEGG databases.

Language: R - Size: 330 KB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

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.

Language: C# - Size: 126 MB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

jmzeng1314/GEO

Language: R - Size: 376 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 695 - Forks: 528

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.

Language: Java - Size: 63.7 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 14 - Forks: 10

SilasK/ipath3

Python wrapper for ipath3

Language: Jupyter Notebook - Size: 337 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 10 - Forks: 1

OSS-Lab/MetQy

Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)

Language: R - Size: 277 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 17 - Forks: 9

guokai8/bioAnno

Build Annotation package by using information from KEGG, NCBI, Ensembl

Language: R - Size: 1.18 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1

etheleon/pymegan

Python package and wrapper around MEGAN6 CE's blast2lca

Language: Perl - Size: 57.6 MB - Last synced: 7 months ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 2

JulieMarieCharmillon/kegg_parser

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

Language: Python - Size: 6.84 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1

zd105/AllEnricher

A comprehensive gene set function enrichment tool for multiple species.

Language: Shell - Size: 55 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 12 - Forks: 4

tonibois/KeggDrugVirtualScreening

A software for analysis and fast virtual screen of KEGG_DRUG molecular database of accepted drugs classificated by ATC codes

Language: HTML - Size: 26.6 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 3

nasqar/ClusterProfShinyGSEA

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

Language: R - Size: 1.96 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 15 - Forks: 8

Pex2892/PETAL

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

Language: Python - Size: 47.6 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 35 - Forks: 7

arnaudporet/kgml2sif

Converting KGML encoded KEGG pathways to the SIF file format

Language: Python - Size: 2.96 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 2

RabbltMan/SimplePlotForGSEA

极简的、带有UI界面的GSEA图表生成脚本。

Language: Python - Size: 7.81 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

noriakis/ckegg

Command line tool to examine KEGG PATHWAY

Language: C - Size: 20.5 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

decodebiology/geneSCF_inactive

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

Language: Perl - Size: 53.8 MB - Last synced: 5 months ago - Pushed: over 3 years ago - Stars: 20 - Forks: 8

lucaz88/genome_comparison_code

Companion repository to the article: "Comparative whole-genome approach to identify bacterial traits for microbial interactions"

Language: R - Size: 16.3 MB - Last synced: 11 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

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...

Language: Jupyter Notebook - Size: 31.3 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

nasqar/ClusterProfShinyORA

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

Language: R - Size: 2.37 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 10 - Forks: 6

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.

Language: Jupyter Notebook - Size: 8.83 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 12 - Forks: 3

Shaumik-Ashraf/BiosystemsProject

A command-line interface and biochemical pathway finder based on KEGG

Language: Python - Size: 1.65 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 3 - Forks: 1

ctSkennerton/kegg_hmm_models

Create HMMs from KEGG orthologs

Language: Makefile - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 1

hunglin59638/leo

Leo is a web-based toolkit for Laboratory of Animal Proteomics in the department of Animal Science, National Chung Hsing University

Language: R - Size: 83 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

suqingdong/django_rest_kegg

Application of KEGG pathway for DRF

Language: Python - Size: 21.5 KB - Last synced: 3 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

xieguigang/GCModeller.Core Fork of SMRUCC/GCModeller.Core

GCModeller base core assembly library on common biological database read and write I/O

Language: Visual Basic .NET - Size: 22.6 MB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

Rabadash8820/DotKEGG

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

Language: C# - Size: 229 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

PEHGP/kaas

KEGG Automatic Annotation Server Localization

Language: Python - Size: 18.6 KB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 0

SMRUCC/GCModeller.Core

GCModeller Individual Components: GCModeller base core assembly library on common biological database read and write I/O

Language: Visual Basic .NET - Size: 22.5 MB - Last synced: 18 days ago - Pushed: almost 4 years ago - Stars: 4 - Forks: 2

dalmolingroup/neurotransmissionevolution

Research compendium for Viscardi et al, 2020.

Language: TeX - Size: 191 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

PSSUN/bioscript

bioinformatics scripts

Language: Python - Size: 26.4 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

cannin/sbgn2sif Fork of arnaudporet/sbgn2sif

Converting SBGN-encoded pathways to the SIF file format

Language: Python - Size: 187 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 2 - Forks: 1

BioDeep/KEGG-metabolite-network

KEGG metabolite network canvas based on the d3.js

Language: JavaScript - Size: 26.7 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

gualapuromoises/pathwaysKEGG

Extract pathways from KEGG database using EC entries.

Language: R - Size: 1.48 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

alexandrabenamar/metabolic-pathways

A SWING interface for KEGG metabolic pathways: visualization of metabolical networks

Language: Java - Size: 56.6 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0