Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: metabolites

Repositories

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: R - Size: 81.4 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 36 - Forks: 16

gu-yaowen/MTPredictor

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

Language: Python - Size: 5.15 MB - Last synced: 3 days ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

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: R - Size: 21.9 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 8 - Forks: 8

lucinamay/biosynfoni

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

Language: Python - Size: 11.1 MB - Last synced: about 12 hours ago - Pushed: 1 day ago - Stars: 8 - Forks: 1

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

eMetaboHUB/Forum-DiseasesChem

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

Language: Python - Size: 30.8 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 14 - Forks: 6

NCBI-Hackathons/MR_BACOn

Mendelian Randomization with Biomarker Associations for Causality with Outcomes

Language: R - Size: 29 MB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 22 - Forks: 9

YonghuiDong/MSbox

Tools for Metabolomics and mass Spectrometry users

Language: R - Size: 7.97 MB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

computational-metabolomics/beamspy-galaxy

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

Language: Python - Size: 1.1 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 2 - Forks: 2

glasgowcompbio/pyBatman

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

Language: Jupyter Notebook - Size: 10.1 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 1 - Forks: 2

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: HTML - Size: 5.86 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

YuLab-SMU/MMINP

Microbe-Metabolite INteractions-based metabolic profiles Predictor

Language: R - Size: 11.8 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1

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

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: MATLAB - Size: 6.84 KB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

kevinVervier/CarboLogR

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

Language: R - Size: 1.03 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

Wishartlab-openscience/Biotransformer

A computational tool for the prediction and identification of metabolites.

Language: Java - Size: 69.2 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 1

jp-cranfield/mSOM

mSOM (metaboliteSOM)

Language: Jupyter Notebook - Size: 9 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

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: R - Size: 47.7 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 3 - Forks: 1