Biocview "MassSpectrometry"

A collection of tools for imaging MS data processing

Adaptive processing of LC-MS data

A DownStream Chemo-Proteomics Analysis Pipeline

A flexible and comprehensive software for processing omics data.

A Framework for Quality Control

A graphical user interface for MSstatsQC package

Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

All the usefull tools for MS data processing and analysis

All the usefull tools from Xiaotao Shen

A mass spectrometry imaging toolbox for statistical analysis

Analysis and quantitation of isobarically tagged MSMS proteomics data

Analysis of Metabolomics GC/MS Data

Analysis of single and multiple phenomic data sets

Analytical R tools for Mass Spectrometry

Analytical Tools for MassArray Data

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 mzIdentML parser for R

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 R interface to the Ontology Lookup Service

An R package for proteomics data quality control

An R package for the Bayesian analysis of differential subcellular localisation experiments

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 Pipeline Manager

A shiny GUI for MSGFplus

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

A tool for large scale omics datasets evaluation

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

A unifying bioinformatics framework for spatial proteomics

Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Automated Optimization of XCMS Data Processing parameters

Automated parameter selection for untargeted metabolomics data processing

Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Baffling Recursive Algorithm for Isotope distributioN calculations

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioc2014 workshop on R / Bioconductor packages for Proteomics

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

Ciphergen SELDI-TOF Processing

Collection of annotation related methods for mass spectrometry data

Collection of utility functions to work with .gda files in R

common_mz

Complex feature detection using SEC protein chromatograms.

Complexome Profiling Analysis package

Comprehensitive tools for metabolomics data processing and data analysis

Comprehensitive tools for metabolomics data processing and data analysis.

Comprehensitive tools for raw metabolomics data processing

Compute constrained proportional assignments for fractionated protein abundance

Conducts pathway test of metabolomics data using a weighted permutation test

Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

Converting experimental metadata from ISA-tab into Bioconductor data structures

Convert mass spectrometry raw data to othter format 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

cosmiq - COmbining Single Masses Into Quantities

Create and analize networks built from metabolomics Data

Creating and using (Chemical) Compound Annotation Databases

Creating and Using (Chemical) Compound Annotation Databases

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

Data cleaning for LC-MS based metabolomics data

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 normalization by matrix raking

Decomposition of Isotopic Patterns

Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

Diagnostic Plots to Evaluate the Target Decoy Approach

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Differential Abundant Analysis for Metabolomics and Proteomics Data

Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Differential Enrichment analysis of Proteomics data

Direct Access to Orbitrap Data and Beyond

Downstream analysis of the MaxQuant output

Dynamic Programming Based Alignment of MS2 Chromatograms

Effective mobility scale transformation of CE-MS(/MS) data

Encapsulate X!Tandem in R.

Estimate protein complex membership using AP-MS protein data

Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

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

Functionality for Mass Spectrometry Features

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

Generic infrastructure for Bioconductor mass spectrometry packages

getWorklist

Graphical User Interface for IsoCorrectoR

Handling and Managing Peptide Spectrum Matches

High throughput prioritized acquisition and processing of tandem mass spectra

Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Improving metabolome characterization using molecular formula databases

Imputation of label-free mass spectrometry peptides

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Infrastructure for Chromatographic Mass Spectrometry Data

Infrastructure for Ion Mobility enabled mass spectrometry

Infrastructure for Mass Spectrometry Experiments

Integrated Differential Expression and Differential Network Analysis (INDEED)

Integrating Spectra with Python's matchms

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

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

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 Metabolomics Data Processing Utilities

LC-MS/MS Differential Expression Tests

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LiP Significance Analysis in shotgun mass spectrometry-based 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

MassQL support for Spectra

Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Mass spectrometry data backend

Mass spectrometry Data Backend for Bruker TimsTOF Files

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 Metabolomics Feature Clustering and Interpretation

Mass spectrum processing by wavelet-based algorithms

Maximum rank reproducibility

Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.

Metabolite identification based on MS1 and MS2 spectra

Metaboseek platform

Method for Combining LC-MS Metabolomics Feature Measurements

MetNormalizer

Minimal Protein Set Explaining Peptide Spectrum Matches

Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

MRS Data Preprocessing and Normalisation

ms2Plot

MS-based metabolomics annotation pipeline

MsQuality - Quality metric calculation from Spectra and MsExperiment objects

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 metabolomics data

Normalization of Mass Spectrometry Data

Optimized LC-MS Spectra Processing

Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

parser for netCDF, mzXML 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.

Pathway analysis for metabolomics data

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

PeakABro

Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Peak Matrix Processing and signal batch correction for metabolomics datasets

Peak Picking and Annotation of High Resolution Experiments

Peptide correlation analysis

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

Play with databases about mass spectrometry

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Predict metabolic pathway activity based on metabolomics 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

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

Proteomics Label Free Quantification

protrusionproteome

Provides a GUI for DAPAR

Provides a GUI for rTANDEM

Quality assessment of LC-MS based metabolomics data

Quality Control of Protemics Data

Quantitative features for mass spectrometry data

Quantitative Metabolomics Data Processing Tools

RAMClust: a novel feature clustering method enables spectral-matching based annotation for metabolomics data

R/Bioconductor tools for mass spectrometry-based proteomics

Removing Unwanted Variations in Mass-Spectrometry Data.

RIC (RNA interaction capture)

R interface to the pepXML standard

R Interface to the ProteomeXchange Repository

Robust statistical inference for quantitative LC-MS proteomics

R package for mass and molecular formula calculations

S4 generic functions for Bioconductor proteomics infrastructure

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

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Spectra Infrastructure for Mass Spectrometry Data

Spectral Processing for High Resolution Flow Infusion Mass Spectrometry

Spectrum Infrastructure for Mass Spectrometry Data

SQL-based Mass Spectrometry Data Backend

Statistical analysis for LC-MS-based metabolomics data

Statistical analysis of hydrogen deuterium exchange mass spectrometry

Statistical Analysis of Metabolomic Data

Statistical Analysis of Molecular Profiles

Statistical Characterization of Post-translational Modifications

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

System-wise protein turnover curve fitting

Targeted Metabolic and Stable Isotope Tracer.

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Tools for high-throughput metabolomics

Tools for Manipulating the FOBI Ontology

Tools for Metabolomics Data

Tools for qPLEX-RIME data analysis

Tools for quantitative proteomics data analysis

Tools for the Differential Analysis of Proteins Abundance with R

Transform and Filter SWATH Data for Statistical Packages

Translate metabolites ID

Unified Input and Output for Processing of Metabolomic Profiling Experiments

Unified Statistical Modeling of Omics Data

Untargeted LC-MS data annotation

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

Utilities for Annotation of Metabolomics Data

Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Utility Functions from the Eurac Research Computational Metabolomics Team

Visualising and Exploring Spectra Data

Visualization of multiple MS2s for (un)modified peptides

Visualization of multiple MS/MS spectra for modified and non-modified peptides

Viz tool for xcms peak picking parameter optimisation

Web API Framework for Mass Spectrometry Data Transfer

Well Plate Maker

What the package does (short line)

Workflow to process tandem MS files and build MassBank records

Biocview "MassSpectrometry"

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