Biocview "Metabolomics"

Accelerated similarity searching of small molecules

A flexible and comprehensive software for processing omics data.

Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

All the usefull tools for MS data processing and analysis

All the usefull tools from Xiaotao Shen

ALS for the Automatic Chemical Exploration of mixtures

Analysis of single and multiple phenomic data sets

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

A package to run mixture models for truncated metabolomics data with normal or lognormal distributions

a tool set for pathway based data integration and visualization

Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Automated Optimization of XCMS Data Processing parameters

Automated parameter selection for untargeted metabolomics data processing

Automated Report Generation For Metabolomics Analyses

Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Automated spectraL Processing System for NMR

Automatic Statistical Identification in Complex Spectra

Bioconductor Tools for Human Mitochondrial Variant Analysis

Biological Network Analysis

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Cheminformatics Toolkit for R

Classification and Feature Selection for 'Omics' Datasets

Clustering of MS2 Spectra for Metabolite Identification

Code for using BridgeDb identifier mapping framework from within R

Code to convert quantities, using the QUDT ontology

Collection of annotation related methods for mass spectrometry data

Collection of utility functions to work with .gda files in R

common_mz

Compositional omics model based visual integration

Composition Analyses for Metabolomics Data

Comprehensitive tools for metabolomics data processing and data analysis

Comprehensitive tools for metabolomics data processing and data analysis.

Comprehensitive tools for raw metabolomics data processing

Conducts pathway test of metabolomics data using a weighted permutation test

Constraint based modeling in R using metabolic reconstruction databases

Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

Convert mass spectrometry raw data to othter format data

Core Utils for Mass Spectrometry Data

Core Utils for Metabolomics Data

Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

cosmiq - COmbining Single Masses Into Quantities

COSMOS (Causal Oriented Search of Multi-Omic Space)

Covariate Assisted Large-scale Multiple testing

Creating and using (Chemical) Compound Annotation Databases

Creating and Using (Chemical) Compound Annotation Databases

Cross-target analysis of small molecule bioactivity

Data cleaning for LC-MS based metabolomics data

Data extraction pipeline for large-scale GC-MS metabolomics datasets

Data management and analysis of ion trees from ion-trap mass spectrometry

Data processing & analysis tools for Metabolomics and other omics

Decomposition of Isotopic Patterns

Differential Abundant Analysis for Metabolomics and Proteomics Data

Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Diffusion scores on biological networks

Direct Access to Orbitrap Data and Beyond

Drug-Target Interactions

dycone - analyze the dynamic landscape of metabolome data

Dynamic Programming Based Alignment of MS2 Chromatograms

Effective mobility scale transformation of CE-MS(/MS) data

Ensemble of Gene Set Enrichment Analyses

Evaluation of normalization methods and calculation of differential expression analysis statistics

Extensions to the xcms package

Fast identification of Cl or Br containing compounds in LC-MS

Functionality for Mass Spectrometry Features

GC-SIM-MS data processing and alaysis tool

getWorklist

Graphical User Interface for IsoCorrectoR

GRAPH Interaction from pathway Topological Environment

High throughput prioritized acquisition and processing of tandem mass spectra

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Improving metabolome characterization using molecular formula databases

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Infrastructure for Chromatographic Mass Spectrometry Data

Infrastructure for Ion Mobility enabled mass spectrometry

Infrastructure for Mass Spectrometry Experiments

Integrated Differential Expression and Differential Network Analysis (INDEED)

Integrating Multi-Omic Network Data With Summay-Level GWAS Data

Integrating Spectra with Python's matchms

Integrative analysis of the microbiome and metabolome

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

Interface to the 'Metabolights' REST API

Interpretation and enrichment for metabolomics data

LC-MS and GC-MS Data Analysis

LC/MS and GC/MS Data Analysis

LC/MS Metabolomics Data Processing Utilities

Linear Models for Microarray Data

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Lipid reaction prediction based on WormJam

MassQL support for Spectra

Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files

Mass spectrometry data backend

Mass spectrometry Data Backend for Bruker TimsTOF Files

Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass Spectrometry Data Backend for MassBank record Files

Mass Spectrometry Data Backend for NIST msp Files

Mass spectrometry data backends for The Human Metabolome Database

Mass Spectrometry Metabolomics Feature Clustering and Interpretation

Maximum rank reproducibility

Mechanism-Aware Imputation

Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.

Metabolite identification based on MS1 and MS2 spectra

Metabolite Set Enrichment Analysis (MSEA)

Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Metabolomics Workbench in R

MetDNA

Method for Combining LC-MS Metabolomics Feature Measurements

Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

MetNormalizer

Miscellaneous Functions for Metabolomics Analyses

Mismatch Tolerant Maximum Common Substructure Searching

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolite Profiles

MRS Data Preprocessing and Normalisation

ms2Plot

MS-based metabolomics annotation pipeline

MsQuality - Quality metric calculation from Spectra and MsExperiment objects

MWASTools: an integrated pipeline to perform metabolome-wide association studies

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data

Network Analysis Supported by Boosting

Omics Data Integration Project

Omics Longitudinal Differential Analysis

Optimized LC-MS Spectra Processing

Overlay omics data onto SBGN pathway diagram

Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

PaIRKAT

parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

Pathway analysis for metabolomics data

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

PeakABro

Peak Matrix Processing and signal batch correction for metabolomics datasets

Peak Picking and Annotation of High Resolution Experiments

Phenotype-driven module identification

Pipelines for Bi-Clustering Using Matrix Factorization

Play with databases about mass spectrometry

Predict metabolic pathway activity based on metabolomics data

Pre-process 1H-NMR FID signals

Preprocessing of FIA-HRMS data

Preprocessing of spectra data from high resolution mass spectrometry

Pre-processing PTR-TOF-MS Data

Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Processing of adductomic mass spectral datasets

Proteomics Label Free Quantification

Quality assessment of LC-MS based metabolomics data

Quantitative features for mass spectrometry data

Quantitative Metabolomics Data Processing Tools

RAMClust: a novel feature clustering method enables spectral-matching based annotation for metabolomics data

Rank Product method for identifying differentially expressed genes with application in meta-analysis

R interface to a subset of OpenBabel functionalities

rWikiPathways - R client library for the WikiPathways API

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Shiny-based interactive data-quality exploration for omics data

Signal batch correction for (LC)-MS data

Signature discovery from omics data

Spectra Infrastructure for Mass Spectrometry Data

Spectral Processing for High Resolution Flow Infusion Mass Spectrometry

Spectrum Infrastructure for Mass Spectrometry Data

SQL-based Mass Spectrometry Data Backend

Statistical analysis for LC-MS-based metabolomics data

Statistical analysis of hydrogen deuterium exchange mass spectrometry

Statistical Analysis of Metabolomic Data

Statistical Analysis of Molecular Profiles

Strucutral and Functional Enrichment Analyses

Targeted Metabolic and Stable Isotope Tracer.

Time-Course Multi-Omics data integration

Tools for high-throughput metabolomics

Tools for Manipulating the FOBI Ontology

Tools for Metabolomics Data

Translate metabolites ID

Unified Input and Output for Processing of Metabolomic Profiling Experiments

Unified Statistical Modeling of Omics Data

Untargeted LC-MS data annotation

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

Utilities for Annotation of Metabolomics Data

utilities for exploration of human metabolome database

Utility Functions from the Eurac Research Computational Metabolomics Team

Visualising and Exploring Spectra Data

Viz tool for xcms peak picking parameter optimisation

W4M Cluster Peak Pics

Web API Framework for Mass Spectrometry Data Transfer

What the package does (short line)

Workflow Project Templates for Metabolomics Analyses

Workflow to process tandem MS files and build MassBank records

Biocview "Metabolomics"

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