metabolites

There are 27 repositories under metabolites topic.

  • pmartR/pmartR

    The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.

    Language:R37127016

  • NCBI-Hackathons/MR_BACOn

    Mendelian Randomization with Biomarker Associations for Causality with Outcomes

    Language:R2312109

  • mentatpsi/KEGG-Crawler

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

    Language:Python20314

  • eMetaboHUB/Forum-DiseasesChem

    A Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.

    Language:Python15496

  • YuLab-SMU/MMINP

    Microbe-Metabolite INteractions-based metabolic profiles Predictor

    Language:R13404

  • SilasK/ipath3

    Python wrapper for ipath3

    Language:Jupyter Notebook10311

  • ipb-halle/MetFamily

    Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.

    Language:R911547

  • lucinamay/biosynfoni

    a *biosynformatic* fingerprint to explore natural product distance and diversity

    Language:Python82171

  • DanieleBizzarri/MiMIR

    This package contains a Rshiny webtool developed to allow the calculation of the metabolic predictors developed by the groups of MOLEPI and LCBC (LUMC), from raw Nightingale Health 1H-NMR metabolomics data.

    Language:R7101

  • Wishartlab-openscience/Biotransformer

    A computational tool for the prediction and identification of metabolites.

    Language:Java6002

  • bridgedb/BridgeDbR

    Bioconductor R package for BridgeDb

    Language:R49243

  • dgets/lasttime

    Keep track of date/dosage of medication administration history

    Language:Python421220

  • computational-metabolomics/metfrag-galaxy

    Metfrag for Galaxy

    Language:HTML3593

  • computational-metabolomics/beamspy-galaxy

    Galaxy tools for BEAMSpy: Birmingham mEtabolite Annotation for Mass SpectroMetry (Python Package)

    Language:Python2302

  • gu-yaowen/MTPredictor

    A Drug Metabolite & Toxicity Property Predictor Based on Graph Neural Network

    Language:Python2100

  • JPSieg/JPSiegMetaboMetaloRNA

    Raw data and code for "The Metabolome Weakens RNA Helix Stability and Increases RNA Chemical Stability"

    Language:Python2100

  • aarthi31/MetQuest-OLD

    Enumeration of biosynthetic pathways from metabolic networks

    Language:Python1202

  • glasgowcompbio/pyBatman

    A pipeline to infer metabolite concentrations from 1D NMR data using BATMAN (Bayesian AuTomated Metabolite Analyser for NMR)

    Language:Jupyter Notebook1212
  • MNXref

    MetaNetX/MNXref

    MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks

    1300

  • midas-wyss/tovaglieri_metabolites

    Language:HTML1200

  • YonghuiDong/MSbox

    Tools for Metabolomics and mass Spectrometry users

    Language:R1210

  • Asplund-Samuelsson/lipsmap

    Interaction proteomics analysis

    Language:R0160

  • CreMoProduction/mevis

    compare peak area of annotated metabolites using criteria and make comparing plots for all of them as well as volcano plot

    Language:R0120

  • jp-cranfield/mSOM

    mSOM (metaboliteSOM)

    Language:Jupyter Notebook0100

  • kevinVervier/CarboLogR

    This repository provides a GUI app for phenotype assays analysis from raw data to chemoinformatics.

    Language:R0100

  • mlempp/Metabolite_TF_interaction_Ecoli

    Cellular metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. Methods to detect these regulatory interactions are mostly based on in vitro binding assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that are potential effectors of transcription factors in E. coli. By switching the culture conditions between starvation and growth for 20 hours, we induced strong metabolite concentration changes and accompanying gene expression changes, which were measured by LC-MS/MS and RNA sequencing. From the transcriptome data we calculated the activity of 209 transcriptional regulators with Network Component Analysis, and then tested which metabolites correlated with these activities. This approach captured, for instance, the in vivo Hill-kinetics of CRP regulation by cyclic-AMP, a canonical example of allosteric transcription factor regulation in E. coli. By testing correlations between all pairs of transcription factors and metabolites, we predicted putative effectors of 71 transcription factors, and validated five of them in vitro. These results show that the combination of transcriptomics and metabolomics can generate hypotheses about metabolism-transcription interactions that are relevant in vivo and drive transitions between physiological states.

    Language:MATLAB0210

  • TegestGaetti/PRA3006-Visualising-the-chemical-structure-of-metabolite-in-biological-pathways

    This repository contains an HTML file presenting a webpage with a table of metabolites of a pathway collected from WikiPathways.

    Language:HTML0300