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bioconductor.org "Proteomics" keyword

View the packages on the bioconductor.org package registry that are tagged with the "Proteomics" 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
DeProViR 1.4.0
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...
4 versions - Latest release: 2 months ago - 1.78 thousand downloads total - 1 stars on GitHub - 1 maintainer
diffcyt 1.28.0
Differential discovery in high-dimensional cytometry via high-resolution clustering
7 versions - Latest release: 3 months ago - 5 dependent packages - 39.2 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.34.1
Base Functions and Classes for Mass Spectrometry and Proteomics
7 versions - Latest release: 2 months ago - 30 dependent packages - 474 thousand downloads total - 123 stars on GitHub - 1 maintainer
BulkSignalR 1.0.2
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...
2 versions - Latest release: about 1 month ago - 1.67 thousand downloads total - 1 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
Top 0.6% on bioconductor.org
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R
23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
pepXMLTab 1.42.0
Parsing pepXML files and filter based on peptide FDR.
5 versions - Latest release: 3 months ago - 19.3 thousand downloads total - 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
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
fCI 1.38.0
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
5 versions - Latest release: 3 months ago - 16.4 thousand downloads total - 1 maintainer
GraphPAC 1.50.0
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
5 versions - Latest release: 3 months ago - 1 dependent package - 24 thousand downloads total - 1 maintainer
LimROTS 1.0.3
LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for...
3 versions - Latest release: 2 days ago - 1.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
TPP2D 1.24.0
Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
5 versions - Latest release: 2 months ago - 9.04 thousand downloads total - 1 maintainer
MSstatsBioNet 1.0.0
Network Analysis for MS-based Proteomics Experiments
1 version - Latest release: 3 months ago - 1.14 thousand downloads total - 2 stars on GitHub - 1 maintainer
censcyt 1.16.0
Differential abundance analysis with a right censored covariate in high-dimensional cytometry
5 versions - Latest release: 2 months ago - 6.91 thousand downloads total - 0 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
topdownr 1.30.0
Investigation of Fragmentation Conditions in Top-Down Proteomics
5 versions - Latest release: 2 months ago - 13.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
pRolocGUI 2.18.0
Interactive visualisation of spatial proteomics data
5 versions - Latest release: 3 months ago - 24.4 thousand downloads total - 8 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
MAPFX 1.4.0
MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massivel...
3 versions - Latest release: 2 months ago - 3.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
plgem 1.80.0
Detect differential expression in microarray and proteomics datasets with the Power Law Global Er...
5 versions - Latest release: 2 months ago - 1 dependent package - 41.2 thousand downloads total - 1 maintainer
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
PepSetTest 1.2.0
Peptide Set Test
2 versions - Latest release: 3 months ago - 1.98 thousand downloads total - 2 stars on GitHub - 1 maintainer
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
qcmetrics 1.46.0
A Framework for Quality Control
6 versions - Latest release: 3 months ago - 1 dependent package - 25 thousand downloads total - 2 stars on GitHub - 1 maintainer
TargetDecoy 1.14.0
Diagnostic Plots to Evaluate the Target Decoy Approach
5 versions - Latest release: 3 months ago - 6.57 thousand downloads total - 1 stars on GitHub - 1 maintainer
specL 1.42.0
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
5 versions - Latest release: 3 months ago - 20.8 thousand downloads total - 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
mspms 1.0.0
Tools for the analysis of MSP-MS data
1 version - Latest release: 3 months ago - 1.51 thousand downloads total - 0 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
DAPAR 1.40.0
Tools for the Differential Analysis of Proteins Abundance with R
10 versions - Latest release: 2 months ago - 1 dependent package - 26.6 thousand downloads total - 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
PrInCE 1.24.0
Predicting Interactomes from Co-Elution
5 versions - Latest release: 2 months ago - 10.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
isobar 1.54.0
Analysis and quantitation of isobarically tagged MSMS proteomics data
5 versions - Latest release: 3 months ago - 40.7 thousand downloads total - 10 stars on GitHub - 1 maintainer
protGear 1.12.0
Protein Micro Array Data Management and Interactive Visualization
5 versions - Latest release: 3 months ago - 7.62 thousand downloads total - 1 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
GenProSeq 1.12.0
Generating Protein Sequences with Deep Generative Models
5 versions - Latest release: 3 months ago - 5.43 thousand downloads total - 1 maintainer
infinityFlow 1.18.0
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
5 versions - Latest release: 3 months ago - 8.65 thousand downloads total - 1 maintainer
Cardinal 3.10.0
A mass spectrometry imaging toolbox for statistical analysis
10 versions - Latest release: 3 months ago - 34.9 thousand downloads total - 1 maintainer
Rtpca 1.18.0
Thermal proximity co-aggregation with R
5 versions - Latest release: 3 months ago - 7.78 thousand downloads total - 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
CytoGLMM 1.16.0
Conditional Differential Analysis for Flow and Mass Cytometry Experiments
5 versions - Latest release: 3 months ago - 1 dependent package - 7.55 thousand downloads total - 2 stars on GitHub - 1 maintainer
proDA 1.22.1
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
6 versions - Latest release: about 1 month ago - 1 dependent package - 17.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
iPAC 1.52.0
Identification of Protein Amino acid Clustering
5 versions - Latest release: 3 months ago - 3 dependent packages - 26.6 thousand downloads total - 1 maintainer
qPLEXanalyzer 1.26.0
Tools for quantitative proteomics data analysis
5 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 1 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
koinar 1.2.0
KoinaR - Remote machine learning inference using Koina
3 versions - Latest release: 3 months ago - 2.05 thousand downloads total - 37 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
rScudo 1.24.0
Signature-based Clustering for Diagnostic Purposes
6 versions - Latest release: 3 months ago - 9.68 thousand downloads total - 4 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
vsclust 1.10.0
Feature-based variance-sensitive quantitative clustering
5 versions - Latest release: 3 months ago - 5.01 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
BRAIN 1.54.0
Baffling Recursive Algorithm for Isotope distributioN calculations
5 versions - Latest release: 3 months ago - 2 dependent packages - 41.2 thousand downloads total - 1 maintainer
CNORode 1.50.0
ODE add-on to CellNOptR
5 versions - Latest release: 3 months ago - 1 dependent package - 31.4 thousand downloads total - 1 maintainer
IMMAN 1.28.0
Interlog protein network reconstruction by Mapping and Mining ANalysis
5 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 1 maintainer
immunogenViewer 1.1.1
Visualization and evaluation of protein immunogens
2 versions - Latest release: 2 months ago - 1.45 thousand downloads total - 0 stars on GitHub - 1 maintainer
MsExperiment 1.10.1
Infrastructure for Mass Spectrometry Experiments
6 versions - Latest release: 18 days ago - 2 dependent packages - 42.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
oppti 1.21.0
Outlier Protein and Phosphosite Target Identifier
5 versions - Latest release: 3 months ago - 7.72 thousand downloads total - 2 stars on GitHub - 1 maintainer
bandle 1.12.0
An R package for the Bayesian analysis of differential subcellular localisation experiments
5 versions - Latest release: 2 months ago - 6.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
SpatialOmicsOverlay 1.8.0
Spatial Overlay for Omic Data from Nanostring GeoMx Data
5 versions - Latest release: 3 months ago - 4.87 thousand downloads total - 1 maintainer
ASEB 1.52.0
Predict Acetylated Lysine Sites
5 versions - Latest release: 3 months ago - 30.7 thousand downloads total - 1 maintainer
GeomxTools 3.11.0
NanoString GeoMx Tools
6 versions - Latest release: 3 months ago - 3 dependent packages - 26 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
PECA 1.44.0
Probe-level Expression Change Averaging
5 versions - Latest release: 3 months ago - 1 dependent package - 22.6 thousand downloads total - 1 maintainer
MSstatsShiny 1.10.0
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
9 versions - Latest release: 3 months ago - 7.08 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 8.5% on bioconductor.org
MassSpecWavelet 1.74.0 💰
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
6 versions - Latest release: 3 months ago - 2 dependent packages - 243 thousand downloads total - 10 stars on GitHub - 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
DominoEffect 1.28.0
Identification and Annotation of Protein Hotspot Residues
5 versions - Latest release: 3 months ago - 11.5 thousand downloads total - 2 maintainers
msqrob2 1.16.0
Robust statistical inference for quantitative LC-MS proteomics
6 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 7 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
RCASPAR 1.54.0
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
5 versions - Latest release: 3 months ago - 25 thousand downloads total - 2 maintainers
TPP 3.36.0
Analyze thermal proteome profiling (TPP) experiments
5 versions - Latest release: 3 months ago - 1 dependent package - 24.3 thousand downloads total - 1 maintainer
ReactomeGSA 1.22.0
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
6 versions - Latest release: 3 months ago - 19.4 thousand downloads total - 25 stars on GitHub - 1 maintainer
SpacePAC 1.46.0
Identification of Mutational Clusters in 3D Protein Space via Simulation.
5 versions - Latest release: 3 months ago - 1 dependent package - 21.6 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
biobroom 1.40.0
Turn Bioconductor objects into tidy data frames
5 versions - Latest release: 3 months ago - 1 dependent package - 35.2 thousand downloads total - 49 stars on GitHub - 1 maintainer
MBQN 2.20.0
Mean/Median-balanced quantile normalization
5 versions - Latest release: 3 months ago - 7.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
MICSQTL 1.6.0
MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
4 versions - Latest release: 3 months ago - 3.94 thousand downloads total - 1 maintainer
Path2PPI 1.38.0
Prediction of pathway-related protein-protein interaction networks
5 versions - Latest release: 3 months ago - 17.2 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
MSstats 4.16.0
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experi...
9 versions - Latest release: 3 months ago - 8 dependent packages - 77.7 thousand downloads total - 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
ProteoMM 1.26.0
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
5 versions - Latest release: 3 months ago - 11.6 thousand downloads total - 1 maintainer
XINA 1.26.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
5 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 1 maintainer
MSstatsPTM 2.10.0
Statistical Characterization of Post-translational Modifications
9 versions - Latest release: 3 months ago - 2 dependent packages - 12.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
ComPrAn 1.16.0
Complexome Profiling Analysis package
5 versions - Latest release: 3 months ago - 6.17 thousand downloads total - 1 maintainer
ROTS 2.0.0
Reproducibility-Optimized Test Statistic
5 versions - Latest release: 3 months ago - 2 dependent packages - 31.5 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
Rcpi 1.44.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
7 versions - Latest release: 3 months ago - 1 dependent package - 39 thousand downloads total - 1 maintainer
cytoKernel 1.14.0
Differential expression using kernel-based score test
5 versions - Latest release: 3 months ago - 6.11 thousand downloads total - 0 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
MSstatsBig 1.6.0
MSstats Preprocessing for Larger than Memory Data
5 versions - Latest release: 3 months ago - 3.93 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
pgca 1.32.0
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
5 versions - Latest release: 3 months ago - 11.7 thousand downloads total - 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
Top 9.6% on bioconductor.org
procoil 2.36.0
Prediction of Oligomerization of Coiled Coil Proteins
5 versions - Latest release: 3 months ago - 34.2 thousand downloads total - 1 maintainer
Related Keywords
Software 196 MassSpectrometry 92 ImmunoOncology 63 Metabolomics 53 DifferentialExpression 49 DataImport 36 Visualization 34 GeneExpression 34 QualityControl 33 Normalization 29 Clustering 29 Transcriptomics 27 Microarray 26 SystemsBiology 25 Infrastructure 25 Regression 24 Preprocessing 24 RNASeq 23 MultipleComparison 21 CellBasedAssays 19 proteomics 19 Sequencing 18 mass-spectrometry 18 Classification 16 Network 16 CellBiology 16 BiomedicalInformatics 16 Genetics 15 GeneSetEnrichment 15 SingleCell 15 r 13 TimeCourse 13 OneChannel 12 Bayesian 12 Pathways 12 bioconductor 11 Transcription 11 FeatureExtraction 10 Cheminformatics 9 Lipidomics 9 GraphAndNetwork 9 FunctionalGenomics 9 BatchEffect 8 FlowCytometry 8 metabolomics 7 StatisticalMethod 7 NetworkInference 7 mRNAMicroarray 7 TwoChannel 7 AlternativeSplicing 6 ExperimentalDesign 6 GUI 6 GO 6 Epigenetics 6 PrincipalComponent 6 ShinyApps 5 Pharmacogenomics 5 Pharmacogenetics 5 MicrotitrePlateAssay 5 KEGG 5 GenePrediction 5 rstats 5 DimensionReduction 5 DataRepresentation 5 ProprietaryPlatforms 5 Coverage 4 SNP 4 Survival 4 GeneTarget 4 bioinformatics 4 GeneSignaling 4 DifferentialSplicing 4 ExonArray 4 Reactome 4 ExperimentHubSoftware 3 WorkflowStep 3 normalization 3 GenomeWideAssociation 3 Annotation 3 Alignment 3 SequenceMatching 3 ComparativeGenomics 3 FunctionalPrediction 3 Bioinformatics 3 MicroRNAArray 3 DNAMethylation 3 proteomics-data 3 Spatial 3 PeakDetection 2 GeneRegulation 2 SomaticMutation 2 DifferentialMethylation 2 StructuralPrediction 2 genomics 2 fast 2 multiplatform 2 ResearchField 2 rpackage 2 Metagenomics 2 visualisation 2