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

MetNet 1.20.0
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
3 versions - Latest release: 6 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: 6 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: 6 months ago - 1.7 thousand downloads total - 1 maintainer
CompoundDb 1.6.0
Creating and Using (Chemical) Compound Annotation Databases
3 versions - Latest release: 6 months ago - 3 dependent packages - 16.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.14.1
Core Utils for Mass Spectrometry Data
4 versions - Latest release: 5 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: 6 months ago - 7.77 thousand downloads total - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 15 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.14.0
Spectra Infrastructure for Mass Spectrometry Data
4 versions - Latest release: 14 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: 6 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: 6 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: 6 months ago - 4.72 thousand downloads total - 1 maintainer
adductomicsR 1.18.0
Processing of adductomic mass spectral datasets
3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 months ago - 5.7 thousand downloads total - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data
3 versions - Latest release: 6 months ago - 1.98 thousand downloads total - 1 maintainer
combi 1.14.0
Compositional omics model based visual integration
3 versions - Latest release: 6 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: 6 months ago - 13.2 thousand downloads total - 1 maintainer
marr 1.12.0
Maximum rank reproducibility
3 versions - Latest release: 6 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: 6 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: 6 months ago - 1.93 thousand downloads total - 1 maintainer
MsFeatures 1.10.0
Functionality for Mass Spectrometry Features
3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 14.9 thousand downloads total - 1 maintainer
MAI 1.8.0
Mechanism-Aware Imputation
3 versions - Latest release: 6 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: 6 months ago - 29.5 thousand downloads total - 1 maintainer
DIAlignR 2.10.0
Dynamic Programming Based Alignment of MS2 Chromatograms
3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 10.7 thousand downloads total - 3 maintainers
MAIT 1.36.0
Statistical Analysis of Metabolomic Data
3 versions - Latest release: 6 months ago - 20.1 thousand downloads total - 1 maintainer
biosigner 1.30.0
Signature discovery from omics data
3 versions - Latest release: 6 months ago - 2 dependent packages - 14.2 thousand downloads total - 1 maintainer
pairkat 1.8.0
PaIRKAT
3 versions - Latest release: 6 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: 6 months ago - 4.88 thousand downloads total - 1 maintainer
FELLA 1.22.0
Interpretation and enrichment for metabolomics data
3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 5 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: 7 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: 7 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: 7 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: 14 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: 7 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: 7 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: 8 days ago - 2.05 thousand downloads total - 1 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: 8 days ago - 15 dependent packages - 852 thousand downloads total - 157 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
SBGNview 1.18.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
3 versions - Latest release: 8 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: 8 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: 13 days ago - 9 dependent packages - 214 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.48.0
GRAPH Interaction from pathway Topological Environment
2 versions - Latest release: 6 months ago - 11 dependent packages - 229 thousand downloads total - 5 stars on GitHub - 1 maintainer
QFeatures 1.14.1
Quantitative features for mass spectrometry data
4 versions - Latest release: 10 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: 16 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: 12 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: 13 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: 13 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: 13 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: 13 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: 13 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: 13 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: 14 days ago - 12.4 thousand downloads total - 15 stars on GitHub - 1 maintainer
MsBackendMsp 1.8.0
Mass Spectrometry Data Backend for NIST msp Files
3 versions - Latest release: 14 days ago - 4.83 thousand downloads total - 4 stars on GitHub - 1 maintainer
AlpsNMR 4.6.0
Automated spectraL Processing System for NMR
3 versions - Latest release: 15 days ago - 4.79 thousand downloads total - 13 stars on GitHub - 1 maintainer
eiR 1.44.0
Accelerated similarity searching of small molecules
3 versions - Latest release: 20 days ago - 15.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
rawrr 1.12.0
Direct Access to Orbitrap Data and Beyond
5 versions - Latest release: 20 days ago - 1 dependent package - 9.26 thousand downloads total - 50 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.44.0
a tool set for pathway based data integration and visualization
3 versions - Latest release: 20 days ago - 9 dependent packages - 505 thousand downloads total - 32 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: 20 days ago - 23 dependent packages - 954 thousand downloads total - 40 stars on GitHub - 1 maintainer
yamss 1.30.0
Tools for high-throughput metabolomics
3 versions - Latest release: 20 days ago - 11 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: 20 days ago - 1 dependent package - 6.13 thousand downloads total - 7 stars on GitHub - 1 maintainer
rawDiag 0.99.34
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
1 version - Latest release: 21 days ago - 67 downloads total - 36 stars on GitHub - 1 maintainer
hdxmsqc 1.0.0
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
1 version - Latest release: 21 days ago - 0 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: 21 days ago - 0 stars on GitHub - 1 maintainer
MsBackendMassbank 1.12.0
Mass Spectrometry Data Backend for MassBank record Files
4 versions - Latest release: 21 days ago - 20.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
MsBackendSql 1.2.0
SQL-based Mass Spectrometry Data Backend
2 versions - Latest release: 7 months ago - 1.27 thousand downloads total - 4 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
ChemmineR 3.54.0
Cheminformatics Toolkit for R
2 versions - Latest release: 6 months ago - 8 dependent packages - 481 thousand downloads total - 13 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis
2 versions - Latest release: 6 months ago - 8.52 thousand downloads total - 7 stars on GitHub - 1 maintainer
CluMSID 1.18.0
Clustering of MS2 Spectra for Metabolite Identification
2 versions - Latest release: 6 months ago - 6.52 thousand downloads total - 9 stars on GitHub - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing
2 versions - Latest release: 6 months ago - 4.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
metaMS 1.38.0
MS-based metabolomics annotation pipeline
2 versions - Latest release: 6 months ago - 1 dependent package - 22 thousand downloads total - 14 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
2 versions - Latest release: 6 months ago - 1 dependent package - 7.17 thousand downloads total - 11 stars on GitHub - 1 maintainer
PepsNMR 1.20.0
Pre-process 1H-NMR FID signals
2 versions - Latest release: 6 months ago - 1 dependent package - 8.64 thousand downloads total - 10 stars on GitHub - 1 maintainer
bioassayR 1.40.0
Cross-target analysis of small molecule bioactivity
2 versions - Latest release: 6 months ago - 24 thousand downloads total - 5 stars on GitHub - 1 maintainer
Related Keywords
Software 106 MassSpectrometry 61 Proteomics 47 ImmunoOncology 29 Infrastructure 21 DataImport 20 Visualization 20 Preprocessing 15 DifferentialExpression 15 Network 14 GraphAndNetwork 14 metabolomics 14 Transcriptomics 13 GeneExpression 13 Pathways 13 mass-spectrometry 13 Regression 13 Sequencing 12 Cheminformatics 12 Microarray 12 Clustering 12 QualityControl 10 Lipidomics 10 MultipleComparison 10 RNASeq 10 BiomedicalInformatics 9 SystemsBiology 9 GeneSetEnrichment 9 Classification 8 Normalization 8 DimensionReduction 7 KEGG 7 proteomics 7 Genetics 7 r 6 bioconductor 6 StatisticalMethod 6 Pharmacogenomics 5 Pharmacogenetics 5 CellBasedAssays 5 MicrotitrePlateAssay 5 PrincipalComponent 5 rstats 5 BatchEffect 5 GeneSignaling 4 Annotation 4 Transcription 4 Epigenetics 4 CellBiology 4 PeakDetection 4 TimeCourse 4 Bayesian 4 FunctionalGenomics 3 bioconductor-package 3 bioinformatics 3 FeatureExtraction 3 TwoChannel 3 OneChannel 3 GeneTarget 3 Alignment 3 ShinyApps 3 GenePrediction 3 ThirdPartyClient 3 GUI 3 Metagenomics 3 GenomeWideAssociation 3 Microbiome 3 r-package 3 Survival 3 ResearchField 2 GO 2 NetworkEnrichment 2 rpackage 2 pathways 2 mRNAMicroarray 2 ProprietaryPlatforms 2 ExperimentalDesign 2 feature-detection 2 AlternativeSplicing 2 DifferentialSplicing 2 MicroRNAArray 2 ExonArray 2 NetworkInference 2 Reactome 2 SNP 2 CopyNumberVariation 2 lc-ms 2 machine-learning 2 Bioinformatics 2 Coverage 2 dims 2 annotation 2 enrichment-analysis 1 multivariate-analysis 1 biological-significance-analysis 1 statistics 1 biological-knowledge 1 univariate 1 massbank 1 spectra 1