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

bioconductor.org "MassSpectrometry" keyword

Top 1.5% on bioconductor.org
xcms 4.10.1
LC-MS and GC-MS Data Analysis
16 versions - Latest release: 3 months ago - 15 dependent packages - 1.02 million downloads total - 234 stars on GitHub - 1 maintainer
wpm 1.22.0
Well Plate Maker
7 versions - Latest release: 4 months ago - 15.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
glycoTraitR 1.0.0
Compute and analyze the glycan structrual traits from GPSM data
1 version - Latest release: 5 months ago - 4.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
lcmsPlot 1.0.0
Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package
1 version - Latest release: 5 months ago - 6.67 thousand downloads total - 3 stars on GitHub - 1 maintainer
Aerith 1.0.1
visualization and annotation of isotopic enrichment patterns of peptides and metabolites with sta...
2 versions - Latest release: 4 months ago - 7.16 thousand downloads total - 5 stars on GitHub - 1 maintainer
limpa 1.4.0
Quantification and Differential Analysis of Proteomics Data
8 versions - Latest release: 5 months ago - 12 thousand downloads total - 24 stars on GitHub - 1 maintainer
ncGTW 1.26.0
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misali...
7 versions - Latest release: 5 months ago - 16.7 thousand downloads total - 1 maintainer
ptairMS 1.20.0
Pre-processing PTR-TOF-MS Data
7 versions - Latest release: 5 months ago - 16.1 thousand downloads total - 7 stars on GitHub - 1 maintainer
SWATH2stats 1.42.0
Transform and Filter SWATH Data for Statistical Packages
9 versions - Latest release: 5 months ago - 27.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
notameStats 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: 5 months ago - 3.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
pgca 1.36.0
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
7 versions - Latest release: 5 months ago - 18.4 thousand downloads total - 1 maintainer
rgoslin 1.16.0
Lipid Shorthand Name Parsing and Normalization
7 versions - Latest release: 5 months ago - 13.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
SIMAT 1.44.0
GC-SIM-MS data processing and alaysis tool
7 versions - Latest release: 5 months ago - 27.4 thousand downloads total - 1 maintainer
scDataviz 1.22.0
scDataviz: single cell dataviz and downstream analyses
7 versions - Latest release: 5 months ago - 19.6 thousand downloads total - 68 stars on GitHub - 1 maintainer
bandle 1.16.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
7 versions - Latest release: 5 months ago - 14.2 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.5% on bioconductor.org
MassSpecWavelet 1.78.2 💰
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
9 versions - Latest release: 3 months ago - 2 dependent packages - 348 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
rols 3.7.1
An R interface to the Ontology Lookup Service
10 versions - Latest release: 5 months ago - 3 dependent packages - 92.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
artMS 1.29.0
Analytical R tools for Mass Spectrometry
7 versions - Latest release: 5 months ago - 22 thousand downloads total - 1 maintainer
notame 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
3 versions - Latest release: 5 months ago - 5.73 thousand downloads total - 6 stars on GitHub - 1 maintainer
FeatSeekR 1.12.0
FeatSeekR an R package for unsupervised feature selection
7 versions - Latest release: 5 months ago - 9.98 thousand downloads total - 2 stars on GitHub - 1 maintainer
MsQuality 1.12.0
MsQuality - Quality metric calculation from Spectra, MsExperiment and Chromatograms objects
10 versions - Latest release: 5 months ago - 14.9 thousand downloads total - 9 stars on GitHub - 1 maintainer
squallms 1.6.0
Speedy quality assurance via lasso labeling for LC-MS data
4 versions - Latest release: 5 months ago - 8.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
CalibraCurve 1.2.0
Calibration curves for targeted proteomics, lipidomics and metabolomics data
2 versions - Latest release: 5 months ago - 5.41 thousand downloads total - 5 stars on GitHub - 1 maintainer
cliqueMS 1.26.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
8 versions - Latest release: 5 months ago - 20.7 thousand downloads total - 1 maintainer
MsBackendSql 1.12.0
SQL-based Mass Spectrometry Data Backend
7 versions - Latest release: 5 months ago - 12.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
qcmetrics 1.50.0
A Framework for Quality Control
8 versions - Latest release: 5 months ago - 1 dependent package - 36.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
mspms 1.4.0
Tools for the analysis of MSP-MS data
3 versions - Latest release: 5 months ago - 7.74 thousand downloads total - 1 stars on GitHub - 1 maintainer
MsDataHub 1.12.1
Mass Spectrometry Data on ExperimentHub
8 versions - Latest release: about 1 month ago - 2 dependent packages - 17.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
hdxmsqc 1.8.0
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
6 versions - Latest release: 5 months ago - 8.77 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
rpx 2.20.0
R Interface to the ProteomeXchange Repository
8 versions - Latest release: 5 months ago - 3 dependent packages - 86.5 thousand downloads total - 7 stars on GitHub - 1 maintainer
MSstatsBioNet 1.4.1
Network Analysis for MS-based Proteomics Experiments
4 versions - Latest release: 4 months ago - 9.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
peakPantheR 1.26.0
Peak Picking and Annotation of High Resolution Experiments
9 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 13 stars on GitHub - 1 maintainer
MsBackendMetaboLights 1.6.1
Retrieve Mass Spectrometry Data from MetaboLights
5 versions - Latest release: 3 months ago - 10.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
koinar 1.6.0
KoinaR - Remote machine learning inference using Koina
5 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 57 stars on GitHub - 1 maintainer
Top 2.5% on bioconductor.org
mzR 2.46.0
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
7 versions - Latest release: 5 months ago - 23 dependent packages - 44 stars on GitHub - 1 maintainer
proDA 1.26.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
8 versions - Latest release: 5 months ago - 1 dependent package - 32.9 thousand downloads total - 25 stars on GitHub - 1 maintainer
Pirat 1.6.0
Precursor or Peptide Imputation under Random Truncation
8 versions - Latest release: 5 months ago - 8.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
Doscheda 1.34.0
A DownStream Chemo-Proteomics Analysis Pipeline
7 versions - Latest release: 5 months ago - 23 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.24.0
Core Utils for Mass Spectrometry Data
10 versions - Latest release: 5 months ago - 19 dependent packages - 393 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
plgem 1.84.0
Detect differential expression in microarray and proteomics datasets with the Power Law Global Er...
7 versions - Latest release: 5 months ago - 1 dependent package - 55 thousand downloads total - 1 maintainer
biosigner 1.40.0
Signature discovery from omics data
8 versions - Latest release: 5 months ago - 2 dependent packages - 30.3 thousand downloads total - 1 maintainer
MetaboCoreUtils 1.20.1
Core Utils for Metabolomics Data
9 versions - Latest release: 5 months ago - 5 dependent packages - 144 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.44.0
Generic infrastructure for Bioconductor mass spectrometry packages
7 versions - Latest release: 4 months ago - 20 dependent packages - 1.66 million downloads total - 8 stars on GitHub - 1 maintainer
TargetDecoy 1.18.0
Diagnostic Plots to Evaluate the Target Decoy Approach
7 versions - Latest release: 5 months ago - 14.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
SMAD 1.28.0
Statistical Modelling of AP-MS Data (SMAD)
7 versions - Latest release: 5 months ago - 15.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpectriPy 1.2.1
Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
3 versions - Latest release: 3 months ago - 5.31 thousand downloads total - 13 stars on GitHub - 1 maintainer
MSstatsTMT 2.20.0
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tande...
9 versions - Latest release: 5 months ago - 2 dependent packages - 41.8 thousand downloads total - 1 maintainer
PSMatch 1.16.0
Handling and Managing Peptide Spectrum Matches
7 versions - Latest release: 4 months ago - 2 dependent packages - 122 thousand downloads total - 6 stars on GitHub - 1 maintainer
MsBackendMgf 1.20.1
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
8 versions - Latest release: 2 months ago - 3 dependent packages - 59.5 thousand downloads total - 5 stars on GitHub - 2 maintainers
IsoBayes 1.10.1
IsoBayes: Single Isoform protein inference Method via Bayesian Analyses
6 versions - Latest release: about 2 months ago - 10.9 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
metaMS 1.48.0
MS-based metabolomics annotation pipeline
7 versions - Latest release: 5 months ago - 1 dependent package - 39.5 thousand downloads total - 15 stars on GitHub - 1 maintainer
MsBackendRawFileReader 1.18.0
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
7 versions - Latest release: 4 months ago - 14.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
Chromatograms 1.2.0
Infrastructure for Chromatographic Mass Spectrometry Data
2 versions - Latest release: 5 months ago - 7.43 thousand downloads total - 3 stars on GitHub - 1 maintainer
SpectraQL 1.6.0
MassQL support for Spectra
5 versions - Latest release: 5 months ago - 7.01 thousand downloads total - 10 stars on GitHub - 1 maintainer
MSstatsPTM 2.14.0
Statistical Characterization of Post-translational Modifications
13 versions - Latest release: 5 months ago - 2 dependent packages - 26.2 thousand downloads total - 16 stars on GitHub - 1 maintainer
TargetSearch 2.14.0
A package for the analysis of GC-MS metabolite profiling data
10 versions - Latest release: 5 months ago - 45.2 thousand downloads total - 4 stars on GitHub - 1 maintainer
sfi 1.0.0
Data analysis for Single File Injections (SFIs) mode LC-MS analysis
1 version - Latest release: 5 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
AHMassBank 1.12.0
MassBank Annotation Resources for AnnotationHub
9 versions - Latest release: 5 months ago - 10.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
CompoundDb 1.16.0
Creating and Using (Chemical) Compound Annotation Databases
9 versions - Latest release: 4 months ago - 3 dependent packages - 39.3 thousand downloads total - 19 stars on GitHub - 1 maintainer
PolySTest 1.6.0
PolySTest: Detection of differentially regulated features. Combined statistical testing for data ...
5 versions - Latest release: 5 months ago - 7.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MetaboAnnotation 1.16.0
Utilities for Annotation of Metabolomics Data
10 versions - Latest release: 5 months ago - 26.7 thousand downloads total - 21 stars on GitHub - 1 maintainer
AWAggregator 1.2.0
Attribute-Weighted Aggregation
2 versions - Latest release: 4 months ago - 4.24 thousand downloads total - 0 stars on GitHub - 1 maintainer
MsExperiment 1.14.0
Infrastructure for Mass Spectrometry Experiments
8 versions - Latest release: 4 months ago - 2 dependent packages - 83.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
MSstatsQC 2.30.0
Longitudinal system suitability monitoring and quality control for proteomic experiments
7 versions - Latest release: 5 months ago - 1 dependent package - 22 thousand downloads total - 1 maintainer
omicsGMF 1.2.0
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
2 versions - Latest release: 5 months ago - 4.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
PTMods 1.0.0
Managing Post-Translational Modifications in R
1 version - Latest release: 5 months ago - 12.2 thousand downloads total - 11 stars on GitHub - 1 maintainer
Prostar 1.44.0
Provides a GUI for DAPAR
13 versions - Latest release: 5 months ago - 30.3 thousand downloads total - 1 maintainer
spillR 1.8.0
Spillover Compensation in Mass Cytometry Data
7 versions - Latest release: 5 months ago - 9.02 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.38.1
Base Functions and Classes for Mass Spectrometry and Proteomics
10 versions - Latest release: about 2 months ago - 30 dependent packages - 660 thousand downloads total - 138 stars on GitHub - 1 maintainer
MsBackendMassbank 1.20.0
Mass Spectrometry Data Backend for MassBank record Files
10 versions - Latest release: 5 months ago - 32.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
MsBackendMsp 1.16.0
Mass Spectrometry Data Backend for NIST msp Files
7 versions - Latest release: 5 months ago - 25.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
SmartPhos 1.2.0
A phosphoproteomics data analysis package with an interactive ShinyApp
2 versions - Latest release: 5 months ago - 2.65 thousand downloads total - 5 stars on GitHub - 1 maintainer
notameViz 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
3 versions - Latest release: 4 months ago - 4.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
IPO 1.38.0
Automated Optimization of XCMS Data Processing parameters
7 versions - Latest release: 4 months ago - 34.8 thousand downloads total - 34 stars on GitHub - 1 maintainer
IsoCorrectoR 1.30.0
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isoto...
7 versions - Latest release: 5 months ago - 1 dependent package - 18.4 thousand downloads total - 1 maintainer
MSPrep 1.21.1
Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data
8 versions - Latest release: 5 months ago - 14.8 thousand downloads total - 10 stars on GitHub - 1 maintainer
batchCorr 1.2.0
Within And Between Batch Correction Of LC-MS Metabolomics Data
2 versions - Latest release: 5 months ago - 4.79 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
Rdisop 1.72.0
Decomposition of Isotopic Patterns
7 versions - Latest release: 5 months ago - 2 dependent packages - 156 thousand downloads total - 5 stars on GitHub - 1 maintainer
msPurity 1.38.0
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabol...
8 versions - Latest release: 3 months ago - 25.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
isobar 1.58.0
Analysis and quantitation of isobarically tagged MSMS proteomics data
7 versions - Latest release: 4 months ago - 52.3 thousand downloads total - 10 stars on GitHub - 1 maintainer
statTarget 1.42.0
Statistical Analysis of Molecular Profiles
7 versions - Latest release: 4 months ago - 37.5 thousand downloads total - 1 maintainer
MSstatsResponse 1.2.0
Statistical Methods for Chemoproteomics Dose-Response Analysis
2 versions - Latest release: 4 months ago - 8.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
PROcess 1.88.0
Ciphergen SELDI-TOF Processing
7 versions - Latest release: 5 months ago - 73.7 thousand downloads total - 1 maintainer
yamss 1.38.0
Tools for high-throughput metabolomics
7 versions - Latest release: 5 months ago - 32.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
gaga 2.58.0
GaGa hierarchical model for high-throughput data analysis
7 versions - Latest release: 5 months ago - 1 dependent package - 54 thousand downloads total - 1 maintainer
metapone 1.18.0
Conducts pathway test of metabolomics data using a weighted permutation test
7 versions - Latest release: 5 months ago - 19 thousand downloads total - 1 maintainer
MAIT 1.46.0
Statistical Analysis of Metabolomic Data
7 versions - Latest release: 5 months ago - 38.6 thousand downloads total - 1 maintainer
adductomicsR 1.27.0
Processing of adductomic mass spectral datasets
7 versions - Latest release: 5 months ago - 22.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
qPLEXanalyzer 1.30.0
Tools for quantitative proteomics data analysis
8 versions - Latest release: 5 months ago - 27.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
rawDiag 1.8.0
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
6 versions - Latest release: 5 months ago - 8.55 thousand downloads total - 37 stars on GitHub - 1 maintainer
omXplore 1.6.0
Vizualization tools for 'omics' datasets with R
9 versions - Latest release: 5 months ago - 12.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
pmp 1.24.0
Peak Matrix Processing and signal batch correction for metabolomics datasets
8 versions - Latest release: 5 months ago - 2 dependent packages - 28.3 thousand downloads total - 1 maintainer
specL 1.46.0
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
7 versions - Latest release: 5 months ago - 36.2 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
msmsEDA 1.50.0
Exploratory Data Analysis of LC-MS/MS data by spectral counts
7 versions - Latest release: 5 months ago - 2 dependent packages - 61.3 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
MassArray 1.64.0
Analytical Tools for MassArray Data
7 versions - Latest release: 4 months ago - 41.4 thousand downloads total - 1 maintainer
pepXMLTab 1.46.0
Parsing pepXML files and filter based on peptide FDR.
7 versions - Latest release: 5 months ago - 31 thousand downloads total - 1 maintainer
ProteoMM 1.30.0
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
7 versions - Latest release: 5 months ago - 25.1 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
msmsTests 1.50.0
LC-MS/MS Differential Expression Tests
7 versions - Latest release: 5 months ago - 1 dependent package - 61.8 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
CAMERA 1.68.0
Collection of annotation related methods for mass spectrometry data
7 versions - Latest release: 4 months ago - 8 dependent packages - 160 thousand downloads total - 1 maintainer
msImpute 1.22.0
Imputation of label-free mass spectrometry peptides
7 versions - Latest release: 4 months ago - 23.8 thousand downloads total - 10 stars on GitHub - 1 maintainer
Related Keywords
Software 162 Proteomics 102 Metabolomics 76 ImmunoOncology 66 QualityControl 39 Preprocessing 33 mass-spectrometry 30 Normalization 30 DataImport 29 Infrastructure 27 Visualization 25 DifferentialExpression 25 proteomics 19 metabolomics 17 Regression 15 r 15 bioconductor 13 BatchEffect 10 Lipidomics 10 Classification 9 Clustering 9 GUI 8 MultipleComparison 8 GeneExpression 8 StatisticalMethod 8 rstats 7 SingleCell 7 Annotation 7 RNASeq 6 Transcriptomics 6 ShinyApps 6 ExperimentalDesign 6 BiomedicalInformatics 6 Bayesian 5 PeakDetection 5 OneChannel 5 FeatureExtraction 4 PrincipalComponent 4 GeneSetEnrichment 4 TwoChannel 4 FlowCytometry 4 Sequencing 4 Genetics 3 Alignment 3 Microarray 3 Network 3 GraphAndNetwork 3 DimensionReduction 3 DataRepresentation 3 Transcription 3 AlternativeSplicing 2 NetworkInference 2 feature-detection 2 proteomics-data 2 fast 2 multiplatform 2 rpackage 2 TimeCourse 2 Cheminformatics 2 infrastructure 2 visualisation 2 BiologicalQuestion 2 GO 2 ImagingMassSpectrometry 2 annotation 2 ExperimentHubSoftware 2 data 2 Coverage 2 r-package 2 Pathways 2 prostar2 2 bioinformatics 2 ThirdPartyClient 2 python 2 SNP 2 lc-ms 2 Bioinformatics 2 NetworkEnrichment 1 metabolomics-data 1 stable-isotopes 1 stable-isotope-tracing 1 stable-isotope-mass-spectrometry 1 low-rank-approximation 1 label-free-proteomics 1 machine-learning 1 deep-learning 1 CopyNumberVariation 1 svg 1 statistics-and-probability 1 statistical-modelling 1 q-value 1 DNAMethylation 1 ReportWriting 1 proteomics-data-analysis 1 protease 1 spectra 1 massbank 1 SystemsBiology 1 ChIPSeq 1 targeted-proteomics 1