Biocview "MassSpectrometry"

A collection of tools for imaging MS data processing
Adaptive processing of LC-MS data
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A flexible and comprehensive software for processing omics data.
A Framework for Quality Control
A Framework for Quality Control
A graphical user interface for MSstatsQC package
A graphical user interface for MSstatsQC package
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
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 of Metabolomics GC/MS Data
Analysis of Metabolomics GC/MS Data
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical Tools for MassArray Data
Analyze thermal proteome profiling (TPP) experiments
Analyze thermal proteome profiling (TPP) experiments
An example R package for mass spectrometry
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 mzIdentML parser for R
An mzIdentML parser for R
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
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 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 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 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 tool for large scale omics datasets evaluation
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
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 parameter selection for untargeted metabolomics data processing
Automated parameter selection for untargeted metabolomics data processing
Automated parameter selection for untargeted metabolomics data processing
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
Bioc2014 workshop on R / Bioconductor packages for Proteomics
Ciphergen SELDI-TOF Processing
Collection of annotation related methods for mass spectrometry data
Collection of annotation related methods for mass spectrometry data
Collection of utility functions to work with .gda files in R
common_mz
common_mz
Complex feature detection using SEC protein chromatograms.
Complexome Profiling Analysis paskage
Complexome Profiling Analysis paskage
Comprehensitive tools for metabolomics data processing and data analysis
Comprehensitive tools for metabolomics data processing and data analysis.
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
Core Utils for Mass Spectrometry Data
Core Utils for Mass Spectrometry Data
Core Utils for Metabolomics Data
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
cosmiq - COmbining Single Masses Into Quantities
cosmiq - COmbining Single Masses Into Quantities
Creating and using (Chemical) Compound Annotation Databases
Creating and using (Chemical) Compound Annotation Databases
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Data extraction pipeline for large-scale GC-MS metabolomics datasets
Data management and analysis of ion trees from ion-trap mass spectrometry
Data Mining and Analysis of Lipidomics Datasets
Data Mining and Analysis of Lipidomics Datasets
Decomposition of Isotopic Patterns
Decomposition of Isotopic Patterns
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundant Analysis for Metabolomics and Proteomics Data
Differential Abundant Analysis for Metabolomics and Proteomics Data
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Downstream analysis of the MaxQuant output
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Encapsulate X!Tandem in R.
Estimate protein complex membership using AP-MS protein data
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
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 databases from NGS data for proteomics search
Generating SAM file for PSMs in shotgun proteomics data
getWorklist
Graphical User Interface for IsoCorrectoR
Graphical User Interface for IsoCorrectoR
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
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Infrastructure for chromatographic representation of Mass Spectrometry Data
Infrastructure for Mass Spectrometry Experiments
Integrated Differential Expression and Differential Network Analysis (INDEED)
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
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
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 and GC/MS Data Analysis
LC-MS/MS Differential Expression Tests
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
Mass spectrometry data backend
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
Mass Spectrometry Data Backend for MassBank record Files
Mass Spectrometry Data Backend for NIST msp Files
Mass spectrometry data backends for The Human Metabolome Database
Mass spectrometry data backends for The Human Metabolome Database
Mass Spectrometry Metabolomics Feature Clustering and Interpretation
Mass Spectrometry Metabolomics Feature Clustering and Interpretation
Mass spectrum processing by wavelet-based algorithms
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
Metabolite identification based on MS1 and MS2 spectra
Metabolite identification based on MS1 and MS2 spectra
Metaboseek platform
Metaboseek platform
Metaboseek platform
MetNormalizer
Miscellaneous functions used by Vlad Petyuk for proteomics data analysis
ms2Plot
MS-based metabolomics annotation pipeline
MS-based metabolomics annotation pipeline
MS-based metabolomics annotation pipeline
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Multilevel Model for Multivariate Responses with Missing Values
Multi matrix analysis of multiple proteomics datasets on peptide level
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
Normalization of 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.
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
Peak Matrix Processing and signal batch correction for metabolomics datasets
Peak Matrix Processing and signal batch correction for metabolomics datasets
Peak Picking and Annotation of High Resolution Experiments
Peak Picking and Annotation of High Resolution Experiments
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.
PKG_TITLE
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.
Preprocessing of spectra data from high resolution mass spectrometry
Pre-processing PTR-TOF-MS Data
Processing of adductomic mass spectral datasets
Processing of adductomic mass spectral datasets
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
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for rTANDEM
Quantitative features for mass spectrometry data
Quantitative features for mass spectrometry data
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 package for mass and molecular formula calculations
S4 generic functions for Bioconductor proteomics infrastructure
S4 generic functions for Bioconductor proteomics infrastructure
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
Signal batch correction for (LC)-MS data
Simulation of MSnSet Objects
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Spectra Infrastructure for Mass Spectrometry Data
Spectra Infrastructure for Mass Spectrometry Data
Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
Spectrum Infrastructure for Mass Spectrometry Data
Statistical Analysis of Metabolite Profile
Statistical Analysis of Metabolomic Data
Statistical Analysis of Molecular Profiles
Statistical Analysis of Molecular Profiles
Statistical Modelling of AP-MS Data (SMAD)
Statistical Modelling of AP-MS Data (SMAD)
Stoichiometry analysis of label-free proteomics data
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
System-wise protein turnover curve fitting
Targeted Metabolic and Stable Isotope Tracer.
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Tools for high-throughput metabolomics
Tools for high-throughput metabolomics
Tools for qPLEX-RIME data analysis
Tools for qPLEX-RIME data analysis
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
Translate metabolites ID
Unifying Input And Output For Processing Of Metabolomic Profiling Experiments
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utility Functions from the Eurac Research Computational Metabolomics Team
Visualization of multiple MS2s for (un)modified peptides
Visualization of multiple MS/MS spectra for modified and non-modified peptides
Visualization of multiple MS/MS spectra for modified and non-modified peptides
Well Plate Maker
Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records