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bioconductor.org "Metabolomics" keyword

View the packages on the bioconductor.org package registry that are tagged with the "Metabolomics" keyword.

Top 2.5% on bioconductor.org
mzR 2.42.0
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
5 versions - Latest release: 3 months ago - 23 dependent packages - 1.04 million downloads total - 42 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.64.1
Linear Models for Microarray and Omics Data
14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
MsBackendMassbank 1.16.1
Mass Spectrometry Data Backend for MassBank record Files
7 versions - Latest release: 1 day ago - 24.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
ptairMS 1.16.0
Pre-processing PTR-TOF-MS Data
5 versions - Latest release: 3 months ago - 6.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
MsBackendMsp 1.12.0
Mass Spectrometry Data Backend for NIST msp Files
5 versions - Latest release: 2 months ago - 14.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
eiR 1.48.0
Accelerated similarity searching of small molecules
5 versions - Latest release: 3 months ago - 20.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.6.3
LC-MS and GC-MS Data Analysis
11 versions - Latest release: 30 days ago - 15 dependent packages - 901 thousand downloads total - 185 stars on GitHub - 1 maintainer
MsQuality 1.8.0
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
7 versions - Latest release: 3 months ago - 5.42 thousand downloads total - 7 stars on GitHub - 1 maintainer
rawDiag 1.4.0
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
4 versions - Latest release: 3 months ago - 3.28 thousand downloads total - 36 stars on GitHub - 1 maintainer
LimROTS 1.0.3
LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for...
3 versions - Latest release: 3 days ago - 1.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
PepsNMR 1.26.0
Pre-process 1H-NMR FID signals
5 versions - Latest release: 3 months ago - 1 dependent package - 15.8 thousand downloads total - 9 stars on GitHub - 1 maintainer
yamss 1.34.1
Tools for high-throughput metabolomics
5 versions - Latest release: 2 months ago - 17 thousand downloads total - 3 stars on GitHub - 1 maintainer
MetaboDynamics 1.0.2
Bayesian analysis of longitudinal metabolomics data
2 versions - Latest release: about 1 month ago - 1.59 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
ChemmineR 3.60.0
Cheminformatics Toolkit for R
5 versions - Latest release: 2 months ago - 8 dependent packages - 503 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.18.2
Spectra Infrastructure for Mass Spectrometry Data
9 versions - Latest release: about 1 month ago - 15 dependent packages - 93.5 thousand downloads total - 41 stars on GitHub - 1 maintainer
bioassayR 1.46.0
Cross-target analysis of small molecule bioactivity
5 versions - Latest release: 2 months ago - 30.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
BiGGR 1.44.0
Constraint based modeling in R using metabolic reconstruction databases
5 versions - Latest release: 2 months ago - 31.6 thousand downloads total - 2 maintainers
MsBackendMgf 1.16.0
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
5 versions - Latest release: 2 months ago - 3 dependent packages - 33.5 thousand downloads total - 5 stars on GitHub - 2 maintainers
RFLOMICS 1.0.1
Interactive web application for Omics-data analysis
2 versions - Latest release: about 2 months ago - 981 downloads total - 0 stars on GitHub - 1 maintainer
drugTargetInteractions 1.16.0
Drug-Target Interactions
5 versions - Latest release: 2 months ago - 7.24 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaboCoreUtils 1.16.1
Core Utils for Metabolomics Data
6 versions - Latest release: about 1 month ago - 5 dependent packages - 75.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
FELLA 1.28.0
Interpretation and enrichment for metabolomics data
5 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 1 maintainer
peakPantheR 1.22.0
Peak Picking and Annotation of High Resolution Experiments
6 versions - Latest release: 3 months ago - 9.43 thousand downloads total - 12 stars on GitHub - 1 maintainer
limpca 1.4.0
An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family ...
3 versions - Latest release: 2 months ago - 3.24 thousand downloads total - 2 stars on GitHub - 1 maintainer
NormalyzerDE 1.26.0
Evaluation of normalization methods and calculation of differential expression analysis statistics
5 versions - Latest release: 3 months ago - 18.6 thousand downloads total - 24 stars on GitHub - 1 maintainer
rawrr 1.16.0
Direct Access to Orbitrap Data and Beyond
7 versions - Latest release: 3 months ago - 1 dependent package - 16.1 thousand downloads total - 58 stars on GitHub - 1 maintainer
MsDataHub 1.8.0
Mass Spectrometry Data on ExperimentHub
5 versions - Latest release: 2 months ago - 2 dependent packages - 5.51 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
Rdisop 1.68.0
Decomposition of Isotopic Patterns
5 versions - Latest release: 3 months ago - 2 dependent packages - 123 thousand downloads total - 4 stars on GitHub - 1 maintainer
funOmics 1.2.0
Aggregating Omics Data into Higher-Level Functional Representations
2 versions - Latest release: 3 months ago - 2.34 thousand downloads total - 6 stars on GitHub - 1 maintainer
MsBackendSql 1.8.0
SQL-based Mass Spectrometry Data Backend
5 versions - Latest release: 2 months ago - 5.11 thousand downloads total - 4 stars on GitHub - 1 maintainer
MsFeatures 1.16.0
Functionality for Mass Spectrometry Features
5 versions - Latest release: 2 months ago - 2 dependent packages - 81.4 thousand downloads total - 7 stars on GitHub - 1 maintainer
netboost 2.16.0
Network Analysis Supported by Boosting
5 versions - Latest release: 3 months ago - 8.54 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
metaMS 1.44.0
MS-based metabolomics annotation pipeline
5 versions - Latest release: 3 months ago - 1 dependent package - 28.3 thousand downloads total - 15 stars on GitHub - 1 maintainer
squallms 1.2.0
Speedy quality assurance via lasso labeling for LC-MS data
2 versions - Latest release: 3 months ago - 2.01 thousand downloads total - 3 stars on GitHub - 1 maintainer
hdxmsqc 1.4.0
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
4 versions - Latest release: 3 months ago - 2.27 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
ChemmineOB 1.46.0
R interface to a subset of OpenBabel functionalities
5 versions - Latest release: 3 months ago - 2 dependent packages - 231 thousand downloads total - 11 stars on GitHub - 1 maintainer
diffuStats 1.28.0
Diffusion scores on biological networks
5 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 1 maintainer
MAI 1.14.0
Mechanism-Aware Imputation
5 versions - Latest release: 3 months ago - 6.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
vsclust 1.10.0
Feature-based variance-sensitive quantitative clustering
5 versions - Latest release: 3 months ago - 5.01 thousand downloads total - 1 maintainer
MsExperiment 1.10.1
Infrastructure for Mass Spectrometry Experiments
6 versions - Latest release: 19 days ago - 2 dependent packages - 42.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
IsoCorrectoRGUI 1.24.0
Graphical User Interface for IsoCorrectoR
5 versions - Latest release: 3 months ago - 1 dependent package - 8.86 thousand downloads total - 1 maintainer
metabomxtr 1.42.0
A package to run mixture models for truncated metabolomics data with normal or lognormal distribu...
5 versions - Latest release: 3 months ago - 19.4 thousand downloads total - 1 maintainer
Top 8.5% on bioconductor.org
RMassBank 3.18.0
Workflow to process tandem MS files and build MassBank records
5 versions - Latest release: 3 months ago - 35.8 thousand downloads total - 1 maintainer
cosmosR 1.16.0
COSMOS (Causal Oriented Search of Multi-Omic Space)
5 versions - Latest release: 3 months ago - 8.53 thousand downloads total - 61 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment
5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
ncGTW 1.22.0
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misali...
5 versions - Latest release: 3 months ago - 9.51 thousand downloads total - 1 maintainer
IsoCorrectoR 1.26.0
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isoto...
5 versions - Latest release: 3 months ago - 1 dependent package - 11.8 thousand downloads total - 1 maintainer
SpectraQL 1.2.1
MassQL support for Spectra
3 versions - Latest release: about 1 month ago - 1.67 thousand downloads total - 9 stars on GitHub - 1 maintainer
MsBackendMetaboLights 1.2.0
Retrieve Mass Spectrometry Data from MetaboLights
2 versions - Latest release: 3 months ago - 1.68 thousand downloads total - 2 stars on GitHub - 1 maintainer
MetaboAnnotation 1.12.0
Utilities for Annotation of Metabolomics Data
8 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 16 stars on GitHub - 1 maintainer
BridgeDbR 2.18.0
Code for using BridgeDb identifier mapping framework from within R
5 versions - Latest release: 3 months ago - 22.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
mixOmics 6.32.0
Omics Data Integration Project
5 versions - Latest release: 3 months ago - 9 dependent packages - 275 thousand downloads total - 1 maintainer
MetCirc 1.38.0
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
5 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
metabCombiner 1.18.0
Method for Combining LC-MS Metabolomics Feature Measurements
5 versions - Latest release: 3 months ago - 8.17 thousand downloads total - 6 stars on GitHub - 1 maintainer
phenomis 1.10.0
Postprocessing and univariate analysis of omics data
7 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
sparsenetgls 1.26.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...
5 versions - Latest release: 3 months ago - 9.08 thousand downloads total - 1 maintainer
MatrixQCvis 1.16.0
Shiny-based interactive data-quality exploration for omics data
5 versions - Latest release: 3 months ago - 8.85 thousand downloads total - 1 maintainer
autonomics 1.16.0
Unified Statistical Modeling of Omics Data
8 versions - Latest release: 3 months ago - 7.36 thousand downloads total - 3 stars on GitHub - 1 maintainer
msPurity 1.34.0
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabol...
6 versions - Latest release: 3 months ago - 16.7 thousand downloads total - 16 stars on GitHub - 1 maintainer
MsBackendRawFileReader 1.14.0
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
5 versions - Latest release: 3 months ago - 6.28 thousand downloads total - 6 stars on GitHub - 1 maintainer
fobitools 1.16.0
Tools for Manipulating the FOBI Ontology
5 versions - Latest release: 3 months ago - 6.81 thousand downloads total - 1 stars on GitHub - 1 maintainer
DIAlignR 2.16.0
Dynamic Programming Based Alignment of MS2 Chromatograms
5 versions - Latest release: 3 months ago - 6.81 thousand downloads total - 6 stars on GitHub - 1 maintainer
MSPrep 1.18.0
Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data
5 versions - Latest release: 3 months ago - 8.89 thousand downloads total - 10 stars on GitHub - 1 maintainer
metabolomicsWorkbenchR 1.18.0
Metabolomics Workbench in R
6 versions - Latest release: 3 months ago - 1 dependent package - 8.53 thousand downloads total - 1 maintainer
SIMAT 1.40.0
GC-SIM-MS data processing and alaysis tool
5 versions - Latest release: 3 months ago - 17.5 thousand downloads total - 1 maintainer
pairkat 1.14.0
PaIRKAT
5 versions - Latest release: 3 months ago - 6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MetNet 1.26.1
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
6 versions - Latest release: about 2 months ago - 11 thousand downloads total - 1 maintainer
adductomicsR 1.24.0
Processing of adductomic mass spectral datasets
5 versions - Latest release: 3 months ago - 12.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
combi 1.20.0
Compositional omics model based visual integration
5 versions - Latest release: 3 months ago - 8.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses
6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
timeOmics 1.20.0
Time-Course Multi-Omics data integration
5 versions - Latest release: 3 months ago - 1 dependent package - 9.42 thousand downloads total - 21 stars on GitHub - 1 maintainer
SDAMS 1.28.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...
5 versions - Latest release: 3 months ago - 11.7 thousand downloads total - 1 maintainer
rgoslin 1.12.0
Lipid Shorthand Name Parsing and Normalization
5 versions - Latest release: 3 months ago - 7.28 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.48.0
a tool set for pathway based data integration and visualization
5 versions - Latest release: 3 months ago - 9 dependent packages - 594 thousand downloads total - 41 stars on GitHub - 1 maintainer
structToolbox 1.20.0
Data processing & analysis tools for Metabolomics and other omics
7 versions - Latest release: 3 months ago - 1 dependent package - 11.3 thousand downloads total - 10 stars on GitHub - 1 maintainer
AlpsNMR 4.10.0
Automated spectraL Processing System for NMR
5 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
statTarget 1.38.0
Statistical Analysis of Molecular Profiles
5 versions - Latest release: 3 months ago - 26.7 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
IPO 1.34.0
Automated Optimization of XCMS Data Processing parameters
5 versions - Latest release: 3 months ago - 24.2 thousand downloads total - 34 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
fmcsR 1.50.0
Mismatch Tolerant Maximum Common Substructure Searching
5 versions - Latest release: 3 months ago - 1 dependent package - 59.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
pmp 1.20.0
Peak Matrix Processing and signal batch correction for metabolomics datasets
6 versions - Latest release: 3 months ago - 2 dependent packages - 12.6 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.20.0
Core Utils for Mass Spectrometry Data
7 versions - Latest release: 3 months ago - 19 dependent packages - 227 thousand downloads total - 17 stars on GitHub - 1 maintainer
MAIT 1.42.0
Statistical Analysis of Metabolomic Data
5 versions - Latest release: 3 months ago - 25.1 thousand downloads total - 1 maintainer
INDEED 2.22.0
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis...
5 versions - Latest release: 3 months ago - 8.74 thousand downloads total - 4 stars on GitHub - 2 maintainers
hmdbQuery 1.28.0
utilities for exploration of human metabolome database
5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 1 maintainer
cosmiq 1.42.0
cosmiq - COmbining Single Masses Into Quantities
5 versions - Latest release: 3 months ago - 21.1 thousand downloads total - 1 maintainer
MWASTools 1.32.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies
5 versions - Latest release: 3 months ago - 1 dependent package - 18.9 thousand downloads total - 2 maintainers
metapone 1.14.0
Conducts pathway test of metabolomics data using a weighted permutation test
5 versions - Latest release: 3 months ago - 6.14 thousand downloads total - 1 maintainer
ASICS 2.24.0
Automatic Statistical Identification in Complex Spectra
7 versions - Latest release: 3 months ago - 18.3 thousand downloads total - 1 maintainer
qmtools 1.12.0
Quantitative Metabolomics Data Processing Tools
5 versions - Latest release: 3 months ago - 5.72 thousand downloads total - 2 stars on GitHub - 1 maintainer
CluMSID 1.24.0
Clustering of MS2 Spectra for Metabolite Identification
5 versions - Latest release: 2 months ago - 10.4 thousand downloads total - 10 stars on GitHub - 1 maintainer
SBGNview 1.22.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 26 stars on GitHub - 1 maintainer
MetMashR 1.2.0
Metabolite Mashing with R
2 versions - Latest release: 3 months ago - 1.21 thousand downloads total - 2 stars on GitHub - 1 maintainer
QFeatures 1.18.0
Quantitative features for mass spectrometry data
7 versions - Latest release: 3 months ago - 6 dependent packages - 89.8 thousand downloads total - 27 stars on GitHub - 1 maintainer
LOBSTAHS 1.33.0
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
5 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 3 maintainers
cliqueMS 1.22.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
6 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
CAMERA 1.64.0
Collection of annotation related methods for mass spectrometry data
5 versions - Latest release: 3 months ago - 8 dependent packages - 120 thousand downloads total - 1 maintainer
biosigner 1.36.0
Signature discovery from omics data
5 versions - Latest release: 3 months ago - 2 dependent packages - 20.2 thousand downloads total - 1 maintainer
Top 3.1% on bioconductor.org
RankProd 3.34.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis
5 versions - Latest release: 3 months ago - 4 dependent packages - 114 thousand downloads total - 1 maintainer
Macarron 1.12.2
Prioritization of potentially bioactive metabolic features from epidemiological and environmental...
7 versions - Latest release: 29 days ago - 5.81 thousand downloads total - 1 maintainer
marr 1.18.0
Maximum rank reproducibility
5 versions - Latest release: 3 months ago - 6.83 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software 115 MassSpectrometry 64 Proteomics 53 ImmunoOncology 30 Infrastructure 23 DataImport 22 Visualization 22 Preprocessing 17 DifferentialExpression 17 mass-spectrometry 16 metabolomics 16 Transcriptomics 15 Pathways 15 GraphAndNetwork 14 Network 14 GeneExpression 14 Regression 14 Clustering 13 Cheminformatics 13 Microarray 13 Sequencing 12 QualityControl 12 RNASeq 11 MultipleComparison 11 Lipidomics 11 KEGG 10 BiomedicalInformatics 9 GeneSetEnrichment 9 SystemsBiology 9 Classification 9 Normalization 8 r 8 Genetics 7 proteomics 7 DimensionReduction 7 BatchEffect 6 PrincipalComponent 6 StatisticalMethod 6 bioconductor 6 MicrotitrePlateAssay 6 CellBasedAssays 6 TimeCourse 5 ShinyApps 5 rstats 5 CellBiology 5 Pharmacogenetics 5 Pharmacogenomics 5 Bayesian 5 Transcription 4 GO 4 GeneSignaling 4 Epigenetics 4 Annotation 4 FeatureExtraction 4 PeakDetection 4 GenePrediction 3 ExperimentalDesign 3 bioconductor-package 3 Metagenomics 3 bioinformatics 3 Microbiome 3 r-package 3 GeneTarget 3 ThirdPartyClient 3 GUI 3 GenomeWideAssociation 3 Alignment 3 mRNAMicroarray 3 OneChannel 3 FunctionalGenomics 3 FunctionalPrediction 3 Survival 3 TwoChannel 3 rpackage 3 Coverage 2 ProprietaryPlatforms 2 pathways 2 annotation 2 DifferentialSplicing 2 feature-detection 2 ExonArray 2 AlternativeSplicing 2 WorkflowStep 2 machine-learning 2 MicroRNAArray 2 CopyNumberVariation 2 dims 2 fast 2 multiplatform 2 SNP 2 NetworkEnrichment 2 ResearchField 2 Bioinformatics 2 lc-ms 2 NetworkInference 2 metabolomics-data 2 Reactome 2 text-mining 1 databases 1 ontology 1