Bioconductor Packages

MassBank Annotation Resources for AnnotationHub

Attribute-Weighted Aggregation

visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics

Baffling Recursive Algorithm for Isotope distributioN calculations

Collection of annotation related methods for mass spectrometry data

Data normalization by matrix raking

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical analysis

Read and write mass spectrometry imaging files

Infrastructure for Chromatographic Mass Spectrometry Data

Complexome Profiling Analysis package

Creating and Using (Chemical) Compound Annotation Databases

Tools for the Differential Analysis of Proteins Abundance with R

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

A DownStream Chemo-Proteomics Analysis Pipeline

FeatSeekR an R package for unsupervised feature selection

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

Automated Optimization of XCMS Data Processing parameters

IsoBayes: Single Isoform protein inference Method via Bayesian Analyses

Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

Graphical User Interface for IsoCorrectoR

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Statistical Analysis of Metabolomic Data

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

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

Base Functions and Classes for Mass Spectrometry and Proteomics

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

MSstats Preprocessing for Larger than Memory Data

Network Analysis for MS-based Proteomics Experiments

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

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

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Statistical Characterization of Post-translational Modifications

Longitudinal system suitability monitoring and quality control for proteomic experiments

A graphical user interface for MSstatsQC package

Statistical Methods for Chemoproteomics Dose-Response Analysis

MSstats GUI for Statistical Anaylsis of Proteomics Experiments

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Analytical Tools for MassArray Data

Peak Detection for Mass Spectrometry data using wavelet-based algorithms

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Utilities for Annotation of Metabolomics Data

Automated Annotation of All-Ion Fragmentation LC-MS Metabolomic Features

Core Utils for Metabolomics Data

Mass Spectrometry Data Backend for MassBank record Files

Retrieve Mass Spectrometry Data from MetaboLights

Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass Spectrometry Data Backend for NIST msp Files

Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files