Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "Metabolomics" keyword

yamss 1.30.0
Tools for high-throughput metabolomics
3 versions - Latest release: about 1 month ago - 11.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
structToolbox 1.16.0
Data processing & analysis tools for Metabolomics and other omics
3 versions - Latest release: about 1 month ago - 1 dependent package - 6.45 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 2.5% on bioconductor.org
mzR 2.38.0
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
3 versions - Latest release: about 1 month ago - 23 dependent packages - 958 thousand downloads total - 40 stars on GitHub - 1 maintainer
AlpsNMR 4.6.0
Automated spectraL Processing System for NMR
3 versions - Latest release: 26 days ago - 5.05 thousand downloads total - 13 stars on GitHub - 1 maintainer
MsBackendMassbank 1.12.0
Mass Spectrometry Data Backend for MassBank record Files
4 versions - Latest release: about 1 month ago - 20.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
rawDiag 0.99.34
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
2 versions - Latest release: about 1 month ago - 67 downloads total - 36 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.2.1
LC-MS and GC-MS Data Analysis
6 versions - Latest release: 19 days ago - 15 dependent packages - 853 thousand downloads total - 157 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
CompoundDb 1.6.0
Creating and Using (Chemical) Compound Annotation Databases
3 versions - Latest release: 7 months ago - 3 dependent packages - 16.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
MsBackendSql 1.2.0
SQL-based Mass Spectrometry Data Backend
3 versions - Latest release: 7 months ago - 1.62 thousand downloads total - 4 stars on GitHub - 1 maintainer
limpca 1.0.0
An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family ...
1 version - Latest release: about 1 month ago - 192 downloads total - 0 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
ChemmineR 3.54.0
Cheminformatics Toolkit for R
3 versions - Latest release: 7 months ago - 8 dependent packages - 482 thousand downloads total - 13 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.48.0
GRAPH Interaction from pathway Topological Environment
3 versions - Latest release: 6 months ago - 11 dependent packages - 233 thousand downloads total - 5 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis
3 versions - Latest release: 6 months ago - 8.68 thousand downloads total - 7 stars on GitHub - 1 maintainer
PepsNMR 1.20.0
Pre-process 1H-NMR FID signals
3 versions - Latest release: 6 months ago - 1 dependent package - 9.18 thousand downloads total - 10 stars on GitHub - 1 maintainer
CluMSID 1.18.0
Clustering of MS2 Spectra for Metabolite Identification
3 versions - Latest release: 6 months ago - 6.85 thousand downloads total - 9 stars on GitHub - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing
3 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
3 versions - Latest release: 6 months ago - 1 dependent package - 7.56 thousand downloads total - 11 stars on GitHub - 1 maintainer
drugTargetInteractions 1.10.1
Drug-Target Interactions
3 versions - Latest release: 7 months ago - 3.41 thousand downloads total - 1 stars on GitHub - 1 maintainer
bioassayR 1.40.0
Cross-target analysis of small molecule bioactivity
3 versions - Latest release: 6 months ago - 24.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
metaMS 1.38.0
MS-based metabolomics annotation pipeline
3 versions - Latest release: 6 months ago - 1 dependent package - 22.4 thousand downloads total - 14 stars on GitHub - 1 maintainer
OmicsLonDA 1.18.0 removed
Omics Longitudinal Differential Analysis
2 versions - Latest release: 6 months ago - 5.95 thousand downloads total - 5 stars on GitHub - 1 maintainer
peakPantheR 1.16.1
Peak Picking and Annotation of High Resolution Experiments
4 versions - Latest release: 3 months ago - 5.72 thousand downloads total - 12 stars on GitHub - 1 maintainer
metabolomicsWorkbenchR 1.12.0
Metabolomics Workbench in R
3 versions - Latest release: 7 months ago - 1 dependent package - 4.37 thousand downloads total - 1 maintainer
MsQuality 1.2.1
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
4 versions - Latest release: 2 months ago - 1.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 26 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
MetNet 1.20.0
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
3 versions - Latest release: 7 months ago - 6.9 thousand downloads total - 1 maintainer
MsBackendMgf 1.10.0
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
3 versions - Latest release: 7 months ago - 3 dependent packages - 22 thousand downloads total - 4 stars on GitHub - 2 maintainers
vsclust 1.4.0
Feature-based variance-sensitive quantitative clustering
3 versions - Latest release: 7 months ago - 1.7 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.14.1
Core Utils for Mass Spectrometry Data
4 versions - Latest release: 6 months ago - 19 dependent packages - 157 thousand downloads total - 16 stars on GitHub - 1 maintainer
cliqueMS 1.16.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
3 versions - Latest release: 7 months ago - 7.77 thousand downloads total - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.14.0
Spectra Infrastructure for Mass Spectrometry Data
4 versions - Latest release: 25 days ago - 15 dependent packages - 47.5 thousand downloads total - 31 stars on GitHub - 1 maintainer
metabomxtr 1.36.0
A package to run mixture models for truncated metabolomics data with normal or lognormal distribu...
3 versions - Latest release: 7 months ago - 15 thousand downloads total - 1 maintainer
PanViz 1.4.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data
3 versions - Latest release: 7 months ago - 1.66 thousand downloads total - 3 stars on GitHub - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting
3 versions - Latest release: 7 months ago - 4.72 thousand downloads total - 1 maintainer
adductomicsR 1.18.0
Processing of adductomic mass spectral datasets
3 versions - Latest release: 7 months ago - 6.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
cosmiq 1.36.0
cosmiq - COmbining Single Masses Into Quantities
3 versions - Latest release: 7 months ago - 15.9 thousand downloads total - 1 maintainer
IsoCorrectoR 1.20.0
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isoto...
3 versions - Latest release: 7 months ago - 1 dependent package - 7.23 thousand downloads total - 1 maintainer
IsoCorrectoRGUI 1.18.0
Graphical User Interface for IsoCorrectoR
3 versions - Latest release: 7 months ago - 1 dependent package - 5.43 thousand downloads total - 1 maintainer
sparsenetgls 1.20.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...
3 versions - Latest release: 7 months ago - 5.7 thousand downloads total - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data
3 versions - Latest release: 7 months ago - 1.98 thousand downloads total - 1 maintainer
combi 1.14.0
Compositional omics model based visual integration
3 versions - Latest release: 7 months ago - 4.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
SIMAT 1.34.0
GC-SIM-MS data processing and alaysis tool
3 versions - Latest release: 7 months ago - 13.2 thousand downloads total - 1 maintainer
marr 1.12.0
Maximum rank reproducibility
3 versions - Latest release: 7 months ago - 3.29 thousand downloads total - 2 stars on GitHub - 1 maintainer
diffuStats 1.22.0
Diffusion scores on biological networks
3 versions - Latest release: 7 months ago - 9.33 thousand downloads total - 1 maintainer
Macarron 1.6.0
Prioritization of potentially bioactive metabolic features from epidemiological and environmental...
3 versions - Latest release: 7 months ago - 1.93 thousand downloads total - 1 maintainer
MsFeatures 1.10.0
Functionality for Mass Spectrometry Features
3 versions - Latest release: 7 months ago - 2 dependent packages - 52.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
MsDataHub 1.2.0
Mass Spectrometry Data on ExperimentHub
3 versions - Latest release: 7 months ago - 2 dependent packages - 1.52 thousand downloads total - 1 stars on GitHub - 1 maintainer
MWASTools 1.26.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies
3 versions - Latest release: 7 months ago - 1 dependent package - 13.6 thousand downloads total - 2 maintainers
MetaPhOR 1.4.0
Metabolic Pathway Analysis of RNA
3 versions - Latest release: 7 months ago - 1.67 thousand downloads total - 1 maintainer
MatrixQCvis 1.10.0
Shiny-based interactive data-quality exploration for omics data
3 versions - Latest release: 7 months ago - 4.12 thousand downloads total - 1 maintainer
INDEED 2.16.0
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis...
3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 4 stars on GitHub - 2 maintainers
BridgeDbR 2.12.0
Code for using BridgeDb identifier mapping framework from within R
3 versions - Latest release: 7 months ago - 18 thousand downloads total - 4 stars on GitHub - 1 maintainer
BiGGR 1.38.0
Constraint based modeling in R using metabolic reconstruction databases
3 versions - Latest release: 7 months ago - 25.6 thousand downloads total - 2 maintainers
Top 9.4% on bioconductor.org
IPO 1.28.0
Automated Optimization of XCMS Data Processing parameters
3 versions - Latest release: 7 months ago - 18.9 thousand downloads total - 34 stars on GitHub - 1 maintainer
MetCirc 1.32.0
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
3 versions - Latest release: 7 months ago - 10.7 thousand downloads total - 1 maintainer
ASICS 2.18.1
Automatic Statistical Identification in Complex Spectra
4 versions - Latest release: 2 months ago - 10.9 thousand downloads total - 1 maintainer
Metab 1.36.0 removed
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
2 versions - Latest release: 7 months ago - 14.9 thousand downloads total - 1 maintainer
MAI 1.8.0
Mechanism-Aware Imputation
3 versions - Latest release: 7 months ago - 2.68 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.5% on bioconductor.org
RMassBank 3.12.0
Workflow to process tandem MS files and build MassBank records
3 versions - Latest release: 7 months ago - 29.5 thousand downloads total - 1 maintainer
DIAlignR 2.10.0
Dynamic Programming Based Alignment of MS2 Chromatograms
3 versions - Latest release: 7 months ago - 4.83 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
fmcsR 1.44.0
Mismatch Tolerant Maximum Common Substructure Searching
3 versions - Latest release: 7 months ago - 1 dependent package - 51.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses
4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
hmdbQuery 1.22.0
utilities for exploration of human metabolome database
3 versions - Latest release: 7 months ago - 9.07 thousand downloads total - 1 maintainer
mbOmic 1.6.0 removed
Integrative analysis of the microbiome and metabolome
2 versions - Latest release: 7 months ago - 896 downloads total - 0 stars on GitHub - 1 maintainer
SDAMS 1.22.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...
3 versions - Latest release: 7 months ago - 7.52 thousand downloads total - 1 maintainer
LOBSTAHS 1.28.0
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
3 versions - Latest release: 7 months ago - 10.7 thousand downloads total - 3 maintainers
MAIT 1.36.0
Statistical Analysis of Metabolomic Data
3 versions - Latest release: 7 months ago - 20.1 thousand downloads total - 1 maintainer
biosigner 1.30.0
Signature discovery from omics data
3 versions - Latest release: 7 months ago - 2 dependent packages - 14.2 thousand downloads total - 1 maintainer
pairkat 1.8.0
PaIRKAT
3 versions - Latest release: 7 months ago - 2.16 thousand downloads total - 0 stars on GitHub - 1 maintainer
pmp 1.14.1
Peak Matrix Processing and signal batch correction for metabolomics datasets
4 versions - Latest release: 2 months ago - 2 dependent packages - 7.79 thousand downloads total - 1 maintainer
ncGTW 1.16.0
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misali...
3 versions - Latest release: 7 months ago - 4.88 thousand downloads total - 1 maintainer
FELLA 1.22.0
Interpretation and enrichment for metabolomics data
3 versions - Latest release: 7 months ago - 13.6 thousand downloads total - 1 maintainer
MobilityTransformR 1.6.0
Effective mobility scale transformation of CE-MS(/MS) data
3 versions - Latest release: 7 months ago - 1.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
statTarget 1.32.0
Statistical Analysis of Molecular Profiles
3 versions - Latest release: 7 months ago - 22 thousand downloads total - 1 maintainer
MSPrep 1.12.0
Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data
3 versions - Latest release: 7 months ago - 4.49 thousand downloads total - 8 stars on GitHub - 1 maintainer
metapone 1.8.0
Conducts pathway test of metabolomics data using a weighted permutation test
3 versions - Latest release: 7 months ago - 2.69 thousand downloads total - 1 maintainer
NormalyzerDE 1.20.0
Evaluation of normalization methods and calculation of differential expression analysis statistics
3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 18 stars on GitHub - 1 maintainer
metabCombiner 1.14.0
Method for Combining LC-MS Metabolomics Feature Measurements
3 versions - Latest release: 16 days ago - 3.49 thousand downloads total - 6 stars on GitHub - 1 maintainer
cosmosR 1.12.0
COSMOS (Causal Oriented Search of Multi-Omic Space)
3 versions - Latest release: 18 days ago - 3.88 thousand downloads total - 52 stars on GitHub - 1 maintainer
rgoslin 1.8.0
Lipid Shorthand Name Parsing and Normalization
3 versions - Latest release: 18 days ago - 2.54 thousand downloads total - 5 stars on GitHub - 1 maintainer
MsExperiment 1.6.0
Infrastructure for Mass Spectrometry Experiments
3 versions - Latest release: 18 days ago - 2 dependent packages - 14.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
MetaboAnnotation 1.8.0
Utilities for Annotation of Metabolomics Data
4 versions - Latest release: 25 days ago - 9.58 thousand downloads total - 11 stars on GitHub - 1 maintainer
MetaboCoreUtils 1.12.0
Core Utils for Metabolomics Data
3 versions - Latest release: 18 days ago - 5 dependent packages - 33.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
MsBackendRawFileReader 1.10.0
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
3 versions - Latest release: 18 days ago - 2.52 thousand downloads total - 4 stars on GitHub - 1 maintainer
qmtools 1.8.0
Quantitative Metabolomics Data Processing Tools
3 versions - Latest release: 18 days ago - 2.05 thousand downloads total - 1 stars on GitHub - 1 maintainer
SBGNview 1.18.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
3 versions - Latest release: 19 days ago - 7.83 thousand downloads total - 23 stars on GitHub - 1 maintainer
rWikiPathways 1.24.0
rWikiPathways - R client library for the WikiPathways API
3 versions - Latest release: 19 days ago - 5 dependent packages - 56.6 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
mixOmics 6.28.0
Omics Data Integration Project
3 versions - Latest release: 24 days ago - 9 dependent packages - 214 thousand downloads total - 1 maintainer
QFeatures 1.14.1
Quantitative features for mass spectrometry data
4 versions - Latest release: 21 days ago - 6 dependent packages - 35.5 thousand downloads total - 20 stars on GitHub - 1 maintainer
fobitools 1.12.0
Tools for Manipulating the FOBI Ontology
3 versions - Latest release: 27 days ago - 2.91 thousand downloads total - 1 stars on GitHub - 1 maintainer
ptairMS 1.12.0
Pre-processing PTR-TOF-MS Data
3 versions - Latest release: 23 days ago - 2.85 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
CAMERA 1.60.0
Collection of annotation related methods for mass spectrometry data
3 versions - Latest release: 24 days ago - 8 dependent packages - 108 thousand downloads total - 1 maintainer
Top 4.1% on bioconductor.org
Rdisop 1.64.0
Decomposition of Isotopic Patterns
3 versions - Latest release: 24 days ago - 2 dependent packages - 72.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
timeOmics 1.16.0
Time-Course Multi-Omics data integration
3 versions - Latest release: 24 days ago - 1 dependent package - 5.04 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 3.1% on bioconductor.org
RankProd 3.30.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis
3 versions - Latest release: 24 days ago - 4 dependent packages - 106 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
ropls 1.36.0
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
3 versions - Latest release: 24 days ago - 9 dependent packages - 83.4 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
ChemmineOB 1.42.0
R interface to a subset of OpenBabel functionalities
3 versions - Latest release: 24 days ago - 2 dependent packages - 217 thousand downloads total - 9 stars on GitHub - 1 maintainer
msPurity 1.30.0
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabol...
3 versions - Latest release: 25 days ago - 12.4 thousand downloads total - 15 stars on GitHub - 1 maintainer
Related Keywords
Software 106 MassSpectrometry 61 Proteomics 47 ImmunoOncology 29 Infrastructure 21 Visualization 20 DataImport 20 DifferentialExpression 15 Preprocessing 15 Network 14 GraphAndNetwork 14 metabolomics 14 mass-spectrometry 14 Pathways 13 Regression 13 GeneExpression 13 Transcriptomics 13 Sequencing 12 Cheminformatics 12 Microarray 12 Clustering 12 RNASeq 10 QualityControl 10 MultipleComparison 10 Lipidomics 10 SystemsBiology 9 GeneSetEnrichment 9 BiomedicalInformatics 9 Normalization 8 Classification 8 KEGG 7 r 7 Genetics 7 proteomics 7 DimensionReduction 7 bioconductor 6 StatisticalMethod 6 Pharmacogenomics 5 Pharmacogenetics 5 MicrotitrePlateAssay 5 CellBasedAssays 5 BatchEffect 5 PrincipalComponent 5 rstats 5 Transcription 4 Epigenetics 4 PeakDetection 4 TimeCourse 4 CellBiology 4 Bayesian 4 GeneSignaling 4 Annotation 4 TwoChannel 3 bioinformatics 3 ThirdPartyClient 3 Survival 3 bioconductor-package 3 Microbiome 3 ShinyApps 3 Alignment 3 GUI 3 rpackage 3 GenomeWideAssociation 3 GeneTarget 3 GenePrediction 3 FeatureExtraction 3 FunctionalGenomics 3 r-package 3 OneChannel 3 Metagenomics 3 Coverage 2 ResearchField 2 GO 2 NetworkEnrichment 2 Reactome 2 Bioinformatics 2 SNP 2 pathways 2 CopyNumberVariation 2 NetworkInference 2 fast 2 multiplatform 2 feature-detection 2 machine-learning 2 AlternativeSplicing 2 DifferentialSplicing 2 ExonArray 2 MicroRNAArray 2 ProprietaryPlatforms 2 mRNAMicroarray 2 lc-ms 2 dims 2 annotation 2 ExperimentalDesign 2 data-access 1 mass-spectromtry 1 transcriptomics 1 phosphoproteomics 1 biological-intrerpretation 1 network-modelling 1