Search Results for "kegg"
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Showing 27 open source projects for "kegg"
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clusterProfiler
A universal enrichment tool for interpreting omics data
...It supports both over-representation analysis and gene set enrichment analysis, letting you work with unranked gene lists or ranked statistics from differential pipelines. The package connects to multiple knowledge bases—such as Gene Ontology, KEGG, Reactome, Disease Ontology, MeSH and others—through a consistent interface so you can query different biological lenses without rewriting code. It is designed for breadth, covering coding and non-coding features and thousands of organisms by leveraging continuously updated annotations. Results are returned in tidy, manipulation-friendly structures and pair naturally with rich visualization functions (via companion tooling) to summarize pathways, terms, and gene–set relationships. -
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EC2KEGG
Comparative analysis of enzyme lists
This is a perl-based package to perform comparative analysis of metabolic pathways between two organisms. The package takes as an input a reference organism and a list of enzymes (EC numbers). Then, it finds shared and unique enzymes and generates links to KEGG Pathways maps to highlight the overlaps. Statistical enrichment analysis is also provided. -
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This project moved to GitHub in 2021 and is available at: https://cbrinkrolf.github.io/VANESA/ This tool is a platform-independent software to create individual pathways and to examine biological networks of distributed, heterogeneous data sources, e.g. KEGG, BRENDA. VANESA also offers Petri net modeling of extended hybrid Petri nets which can be also simulated using the OpenModelica framework.
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xMSannotator
R package for network based annotation of metabolomics data
xMSannotator uses a multi-criteria scoring scheme and provides an interface to perform annotation of high-resolution mass spectral data using KEGG, HMDB, T3DB, LipidMaps, and selected data sources in ChemSpider. -
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xMSanalyzer
An R package for metabolomics data extraction and quality assessment
xMSanalyzer comprises of utilities that can be classified into four main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat -
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KPGminer
Retrieve gene sets for KEGG pathways that suits GSEA analyses
Retrieve gene sets for KEGG pathways that suits GSEA analyses -
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XTalkiiS
Find data-driven crosstalks among inter-/intra-species signalling path
This tool can automatically load all the organism-specific pathways from KEGG and then detect cross-talks among selected pathways based on user-specified gene-gene relationship information (see example file) in an inter-/intra species manner. -
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Ben(Zai)Ten is a graphical modeling environment for computational and systems biology. It supports the community exchange standards: SBML, SBRML, SED-ML as well as ontologies: MIRIAM, SBO, ChEBI, KEGG, GO
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BPGA
A tool for ultra-fast pan-genome analysis of microbes.
BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc. -
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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rnea
Regulatory Network Enrichment Analysis
Given a differential expression file RNEA extracts lists of prioritized TFs, miRNAs, KEGG pathways and categories and GO terms and at the same time it combines them at an HTML file. Most importantly a regulatory subnetwork is extracted showing how the activated regulators interact with their target genes and between each other. In this way, given a genome-wide expression experiment, RNEA prioritizes important regulatory and functional components. -
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modDFS
Find whether a KEGG module is complete in a proteome
Given module definitions and reaction information based on a KEGG database, modDFS does a depth first search to find whether a set of KOs are sufficient for completion of a module. For cases where only 1 absent KO would've been enough for module completion, that module is reported to be complete(only lenient). For cyclic modules, completion is defined as having all the module reaction steps present. -
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KO2EC
Flexible tool for converting KEGG Ontology (KO) to EC Numbers
KO2EC is able to convert KEGG Orthology (KO) terms into EC numbers in case of the terms indicate enzymes. It uses the vocabulary definitions from KEGG, which is useful in converting the output from KAAS into EC numbers. -
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Scripts (written in Java) to process miRNA/gene expression data (TCGA) into pathway modification diagrams (KEGG), assisting researchers in identifying miRNA/gene differential-expression "hotspots" in (cancer) pathways.
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MAPT (Mapping and Analysis of Pathways through Time) is a tool for mining information from annotated KEGG pathways which have been colored using PAICE. MAPT is a user-friendly tool for both time-series and single-timepoint dataset analysis, with features such as clustering, visualization and annotation-upload.
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Scripts (written in Java) that generate modified pathway diagrams (from KEGG Pathway Database @genome.jp) showing pathway element alterations (up-regulation, mutation, etc.) in ovarian & prostate cancer, glioblastoma & sarcoma (data from cbioportal).
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BioPathXplore is a Bioinformatics Pathway eXploration tool for the visualization and exploration of biological pathways through the integration of KEGG pathways and high throughput data, using Petri nets.
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PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
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Blast2KEGG provides an approach mapping predicted genes to pathways by their annotations, then draw on KEGG maps. It performs fuzzy matching from enzyme name to EC number. There are annotation editor and genome broswer integrated in this application.
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Hoea is a python module for hierarchical ontology enrichment analysis, which facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.
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A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.
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The SNP ratio test can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses. See link below for more.
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SBMLforge is a tool that enables the user to convert and merge KEGG metabolic and signaling pathways (KGML format) to create a single SBML pathway model.
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This project use the open source Protege knowledge base tool to create knowledge base version of the main public database of genomic data available on the internet (GO, Kegg, Entrez) to draw biological pathway.
