Biocview "MassSpectrometry"

Adaptive processing of LC-MS data
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A Framework for Quality Control
A Framework for Quality Control
A Framework for Quality Control
A mass spectrometry imaging toolbox for statistical analysis
A mass spectrometry imaging toolbox for statistical analysis
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis of Metabolomics GC/MS Data
Analysis of Metabolomics GC/MS Data
Analysis of Metabolomics GC/MS Data
Analytical Tools for MassArray Data
Analytical Tools for MassArray Data
Analyze thermal proteome profiling (TPP) experiments
Analyze thermal proteome profiling (TPP) experiments
Analyze thermal proteome profiling (TPP) experiments
An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.
An interface between R and MS-GF+
An interface between R and MS-GF+
An interface between R and MS-GF+
An interface between R and MS-GF+
An mzIdentML parser for R
An mzIdentML parser for R
An mzIdentML parser for R
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An R interface to the Ontology Lookup Service
An R interface to the Ontology Lookup Service
An R interface to the Ontology Lookup Service
An R package for metabolomic data analysis
An R package for proteomics data quality control
An R package for proteomics data quality control
An R package for proteomics data quality control
A package for the analysis of GC-MS metabolite profiling data
A package for the analysis of GC-MS metabolite profiling data
A package for variant peptides detection and visualization in shotgun proteomics.
A package for variant peptides detection and visualization in shotgun proteomics.
A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Automated Optimization of XCMS Data Processing parameters
Automated Optimization of XCMS Data Processing parameters
Automated Optimization of XCMS Data Processing parameters
Automated Optimization of XCMS Data Processing parameters
Auto Process Chemical Standards
Baffling Recursive Algorithm for Isotope distributioN calculations
Baffling Recursive Algorithm for Isotope distributioN calculations
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioc2014 workshop on R / Bioconductor packages for Proteomics
Böttcher et al. (2004) Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants
chemhelper
Ciphergen SELDI-TOF Processing
Ciphergen SELDI-TOF Processing
Collection of annotation related methods for mass spectrometry data
Collection of annotation related methods for mass spectrometry data
common_mz
common_mz
Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class
Converting experimental metadata from ISA-tab into Bioconductor data structures
Converting experimental metadata from ISA-tab into Bioconductor data structures
Converting experimental metadata from ISA-tab into Bioconductor data structures
convert.waters.raw
cosmiq - COmbining Single Masses Into Quantities
cosmiq - COmbining Single Masses Into Quantities
Creating and using (chemical) compound annotation databases
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Data management and analysis of ion trees from ion-trap mass spectrometry
Data management and analysis of ion trees from ion-trap mass spectrometry
Decomposition of Isotopic Patterns
Decomposition of Isotopic Patterns
Decomposition of Isotopic Patterns
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Encapsulate X!Tandem in R.
Estimate protein complex membership using AP-MS protein data
Estimate protein complex membership using AP-MS protein data
Exploratory Data Analysis of LC-MS/MS data by spectral counts
Exploratory Data Analysis of LC-MS/MS data by spectral counts
Extensions to the xcms package
Fast identification of Cl or Br containing compounds in LC-MS
GaGa hierarchical model for high-throughput data analysis
GaGa hierarchical model for high-throughput data analysis
GC-SIM-MS data processing and alaysis tool
GC-SIM-MS data processing and alaysis tool
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generating SAM file for PSMs in shotgun proteomics data
Generating SAM file for PSMs in shotgun proteomics data
getWorklist
High throughput prioritized acquisition and processing of tandem mass spectra
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Interfaces the tandem protein identification algorithm in R
Interfaces the tandem protein identification algorithm in R
Investigation of Fragmentation Conditions in Top-Down Proteomics
Investigation of Fragmentation Conditions in Top-Down Proteomics
Label-free data analysis pipeline for optimal identification and quantitation
Label-free data analysis pipeline for optimal identification and quantitation
Label-free data analysis pipeline for optimal identification and quantitation
LC/MS and GC/MS Data Analysis
LC/MS and GC/MS Data Analysis
LC/MS and GC/MS Data Analysis
LC/MS and GC/MS Data Analysis
LC/MS and GC/MS Data Analysis
LC-MS/MS Differential Expression Tests
LC-MS/MS Differential Expression Tests
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Longitudinal system suitability monitoring and quality control for proteomic experiments
Longitudinal system suitability monitoring and quality control for proteomic experiments
Managing amino acid modifications for mass spectrometry
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Mass spectrum processing by wavelet-based algorithms
Mass spectrum processing by wavelet-based algorithms
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
MetCleaning
ms2Plot
MS-based metabolomics annotation pipeline
MS-based metabolomics annotation pipeline
MS-based metabolomics annotation pipeline
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
obabel2R
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
Parsing pepXML files and filter based on peptide FDR.
Parsing pepXML files and filter based on peptide FDR.
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
PeakABro
PeakABro
peakAnnotation
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
pIR: Estimating Isoelectric Point (pI) of Peptide and Proteins from Amino Acid Sequence.
Predict metabolic pathway activity based on metabolomics data
Predict metabolic pathway activity based on metabolomics data
Preprocessing of FIA-HRMS data
Preprocessing of FIA-HRMS data
Preprocessing of GC-MS metabolomics data with a GUI and interactive plots.
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for rTANDEM
Provides a GUI for rTANDEM
RAMClust: a novel feature clustering method enables spectral-matching based annotation for metabolomics data
R/Bioconductor tools for mass spectrometry-based proteomics
R interface to the pepXML standard
R interface to the pepXML standard
R Interface to the ProteomeXchange Repository
R Interface to the ProteomeXchange Repository
R Interface to the ProteomeXchange Repository
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions for Bioconductor proteomics infrastructure
showTags2
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Statistical Analysis of Metabolite Profile
Statistical Analysis of Metabolite Profile
Statistical Analysis of Metabolite Profile
Statistical Analysis of Metabolomic Data
Statistical Analysis of Metabolomic Data
Stoichiometry analysis of label-free proteomics data
System-wise protein turnover curve fitting
Tools for high-throughput metabolomics
Tools for high-throughput metabolomics
Tools for high-throughput metabolomics
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
Transform and Filter SWATH Data for Statistical Packages
Transform and Filter SWATH Data for Statistical Packages
Transform and Filter SWATH Data for Statistical Packages
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records