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

bioconductor.org "MassSpectrometry" keyword

Top 8.6% on bioconductor.org
flagme 1.68.0
Analysis of Metabolomics GC/MS Data
7 versions - Latest release: 5 months ago - 50.4 thousand downloads total - 2 maintainers
Top 1.5% on bioconductor.org
xcms 4.10.1
LC-MS and GC-MS Data Analysis
16 versions - Latest release: 4 months ago - 15 dependent packages - 1.03 million downloads total - 234 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: 6 months ago - 23 dependent packages - 1.24 million downloads total - 44 stars on GitHub - 1 maintainer
Top 8.5% on bioconductor.org
RMassBank 3.22.0
Workflow to process tandem MS files and build MassBank records
7 versions - Latest release: 5 months ago - 59.7 thousand downloads total - 1 maintainer
MSstatsShiny 1.14.0
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
12 versions - Latest release: 6 months ago - 19.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
metabCombiner 1.22.0
Method for Combining LC-MS Metabolomics Feature Measurements
7 versions - Latest release: 5 months ago - 24 thousand downloads total - 6 stars on GitHub - 1 maintainer
MetNet 1.30.0
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
9 versions - Latest release: 6 months ago - 32.4 thousand downloads total - 1 maintainer
marr 1.22.0
Maximum rank reproducibility
7 versions - Latest release: 5 months ago - 21.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
MetCirc 1.42.0
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
7 versions - Latest release: 5 months ago - 32.4 thousand downloads total - 1 maintainer
DAPAR 1.44.0
Tools for the Differential Analysis of Proteins Abundance with R
12 versions - Latest release: 5 months ago - 1 dependent package - 47.8 thousand downloads total - 1 maintainer
lipidr 2.26.0
Data Mining and Analysis of Lipidomics Datasets
8 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 36 stars on GitHub - 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: 2 months ago - 30 dependent packages - 677 thousand downloads total - 140 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.52.0
A unifying bioinformatics framework for spatial proteomics
9 versions - Latest release: 5 months ago - 3 dependent packages - 111 thousand downloads total - 16 stars on GitHub - 1 maintainer
sparsenetgls 1.30.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...
7 versions - Latest release: 5 months ago - 21.7 thousand downloads total - 1 maintainer
phenomis 1.14.0
Postprocessing and univariate analysis of omics data
9 versions - Latest release: 5 months ago - 16.9 thousand downloads total - 1 maintainer
sfi 1.0.0
Data analysis for Single File Injections (SFIs) mode LC-MS analysis
1 version - Latest release: 6 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
PTMods 1.0.0
Managing Post-Translational Modifications in R
1 version - Latest release: 6 months ago - 12.2 thousand downloads total - 11 stars on GitHub - 1 maintainer
glycoTraitR 1.0.0
Compute and analyze the glycan structrual traits from GPSM data
1 version - Latest release: 6 months ago - 4.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
QFeatures 1.22.0
Quantitative features for mass spectrometry data
9 versions - Latest release: 5 months ago - 6 dependent packages - 211 thousand downloads total - 29 stars on GitHub - 1 maintainer
MetaboAnnotatoR 1.0.0
Automated Annotation of All-Ion Fragmentation LC-MS Metabolomic Features
1 version - Latest release: 6 months ago - 6.26 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
mzID 1.50.0
An mzIdentML parser for R
7 versions - Latest release: 5 months ago - 5 dependent packages - 488 thousand downloads total - 1 maintainer
MSstatsQCgui 1.32.0
A graphical user interface for MSstatsQC package
7 versions - Latest release: 5 months ago - 20.2 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
MSstats 4.20.0
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experi...
13 versions - Latest release: 5 months ago - 8 dependent packages - 116 thousand downloads total - 1 maintainer
proBatch 2.0.0
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
2 versions - Latest release: about 2 months ago - 21 thousand downloads total - 0 stars on GitHub - 1 maintainer
customProDB 1.51.0
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...
9 versions - Latest release: 5 months ago - 45.5 thousand downloads total - 1 maintainer
lcmsPlot 1.0.0
Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package
1 version - Latest release: 6 months ago - 6.72 thousand downloads total - 3 stars on GitHub - 1 maintainer
topdownr 1.34.0
Investigation of Fragmentation Conditions in Top-Down Proteomics
7 versions - Latest release: 6 months ago - 29.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
TPP 3.40.2
Analyze thermal proteome profiling (TPP) experiments
8 versions - Latest release: 11 days ago - 1 dependent package - 46.2 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
ropls 1.44.0
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
7 versions - Latest release: 5 months ago - 9 dependent packages - 174 thousand downloads total - 1 maintainer
msPurity 1.38.0
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabol...
8 versions - Latest release: 4 months ago - 31.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
MSstatsBioNet 1.4.1
Network Analysis for MS-based Proteomics Experiments
4 versions - Latest release: 4 months ago - 10.1 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: 6 months ago - 23 thousand downloads total - 13 stars on GitHub - 1 maintainer
rawDiag 1.8.0
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
6 versions - Latest release: 6 months ago - 12 thousand downloads total - 37 stars on GitHub - 1 maintainer
treekoR 1.20.0
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
7 versions - Latest release: 5 months ago - 21.6 thousand downloads total - 1 maintainer
CONSTANd 1.20.0
Data normalization by matrix raking
7 versions - Latest release: 6 months ago - 18.7 thousand downloads total - 1 maintainer
rawrr 1.20.0
Direct Access to Orbitrap Data and Beyond
9 versions - Latest release: 5 months ago - 1 dependent package - 29.6 thousand downloads total - 62 stars on GitHub - 1 maintainer
Chromatograms 1.2.0
Infrastructure for Chromatographic Mass Spectrometry Data
2 versions - Latest release: 6 months ago - 8.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
qmtools 1.16.0
Quantitative Metabolomics Data Processing Tools
7 versions - Latest release: 5 months ago - 18.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
INDEED 2.26.0
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis...
7 versions - Latest release: 5 months ago - 18.2 thousand downloads total - 5 stars on GitHub - 2 maintainers
cosmiq 1.46.0
cosmiq - COmbining Single Masses Into Quantities
7 versions - Latest release: 5 months ago - 36 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
apComplex 2.78.0
Estimate protein complex membership using AP-MS protein data
7 versions - Latest release: 5 months ago - 62.5 thousand downloads total - 1 maintainer
msqrob2 1.20.0
Robust statistical inference for quantitative LC-MS proteomics
8 versions - Latest release: 6 months ago - 22 thousand downloads total - 15 stars on GitHub - 1 maintainer
proBAMr 1.46.0
Generating SAM file for PSMs in shotgun proteomics data
7 versions - Latest release: 6 months ago - 30.5 thousand downloads total - 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
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
SmartPhos 1.2.0
A phosphoproteomics data analysis package with an interactive ShinyApp
2 versions - Latest release: 6 months ago - 2.65 thousand downloads total - 5 stars on GitHub - 1 maintainer
notameStats 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: 6 months ago - 3.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
notameViz 1.2.0
Workflow for non-targeted LC-MS metabolic profiling
3 versions - Latest release: 5 months ago - 4.7 thousand downloads total - 0 stars on GitHub - 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
omicsGMF 1.2.0
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
2 versions - Latest release: 6 months ago - 4.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
batchCorr 1.2.0
Within And Between Batch Correction Of LC-MS Metabolomics Data
2 versions - Latest release: 6 months ago - 4.79 thousand downloads total - 0 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
MSstatsLOBD 1.20.0
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
7 versions - Latest release: 5 months ago - 13.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
scp 1.22.0
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
7 versions - Latest release: 5 months ago - 31.5 thousand downloads total - 33 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.22.2
Spectra Infrastructure for Mass Spectrometry Data
13 versions - Latest release: 4 months ago - 15 dependent packages - 198 thousand downloads total - 47 stars on GitHub - 1 maintainer
LOBSTAHS 1.38.0
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
8 versions - Latest release: 5 months ago - 24.5 thousand downloads total - 3 maintainers
PepSetTest 1.6.0
Peptide Set Test
4 versions - Latest release: 5 months ago - 8.49 thousand downloads total - 2 stars on GitHub - 1 maintainer
fobitools 1.20.0
Tools for Manipulating the FOBI Ontology
7 versions - Latest release: 5 months ago - 14.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
MSstatsConvert 1.22.1
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
11 versions - Latest release: 3 months ago - 6 dependent packages - 55.1 thousand downloads total - 1 maintainer
wpm 1.22.0
Well Plate Maker
7 versions - Latest release: 5 months ago - 15.4 thousand downloads total - 6 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: 6 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: 6 months ago - 27.1 thousand downloads total - 1 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: 6 months ago - 18.4 thousand downloads total - 1 maintainer
rgoslin 1.16.0
Lipid Shorthand Name Parsing and Normalization
7 versions - Latest release: 6 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: 6 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: 6 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
FeatSeekR 1.12.0
FeatSeekR an R package for unsupervised feature selection
7 versions - Latest release: 6 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: 6 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: 6 months ago - 8.6 thousand downloads total - 3 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: 6 months ago - 20.7 thousand downloads total - 1 maintainer
MsBackendSql 1.12.0
SQL-based Mass Spectrometry Data Backend
7 versions - Latest release: 6 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: 6 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 2 months 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: 6 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: 6 months ago - 3 dependent packages - 86.5 thousand downloads total - 7 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: 6 months ago - 10.1 thousand downloads total - 57 stars on GitHub - 1 maintainer
proDA 1.26.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
8 versions - Latest release: 6 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: 6 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: 6 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: 5 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: 6 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
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: 5 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: 3 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: 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
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 r 15 Regression 15 bioconductor 13 BatchEffect 10 Lipidomics 10 Clustering 9 Classification 9 MultipleComparison 8 GeneExpression 8 StatisticalMethod 8 GUI 8 rstats 7 SingleCell 7 Annotation 7 RNASeq 6 BiomedicalInformatics 6 Transcriptomics 6 ExperimentalDesign 6 ShinyApps 6 PeakDetection 5 OneChannel 5 Bayesian 5 FlowCytometry 4 GeneSetEnrichment 4 FeatureExtraction 4 Sequencing 4 TwoChannel 4 PrincipalComponent 4 DimensionReduction 3 Network 3 Microarray 3 GraphAndNetwork 3 Alignment 3 Genetics 3 Transcription 3 DataRepresentation 3 annotation 2 rpackage 2 infrastructure 2 proteomics-data 2 Coverage 2 visualisation 2 ExperimentHubSoftware 2 r-package 2 GO 2 NetworkInference 2 python 2 Bioinformatics 2 Cheminformatics 2 ImagingMassSpectrometry 2 BiologicalQuestion 2 lc-ms 2 SNP 2 ThirdPartyClient 2 Pathways 2 data 2 feature-detection 2 TimeCourse 2 bioinformatics 2 prostar2 2 multiplatform 2 fast 2 AlternativeSplicing 2 QC-RFSC 1 bioconductor-package 1 dims 1 stable-isotope-tracing 1 fragmentation 1 stable-isotopes 1 lc-msms 1 protein 1 NetworkEnrichment 1 visualization 1 orbitrap 1 precursor-ion-purity 1 amino-acid-modifications 1 proteomexchange 1 quantitative-proteomic-analysis 1 limma 1 KEGG 1 FunctionalGenomics 1 metabolomics-data 1 DNAMethylation 1 lipidomics 1 text-mining 1 ontology 1