46 Open source projects that are alternatives of or similar to pDeep

A complete toolkit for shotgun proteomics data analysis

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Quantitative features for mass spectrometry data

pyQms, generalized, fast and accurate mass spectrometry data quantification

No description or website provided.

The repo for LFQ-Analyst

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

Quantum mechanic mass spectrometry calculation program

Fast and flexible semi-supervised learning for peptide detection in Python

The Proteomics Experimental Design file format: Standard for experimental design annotation

A MALDI Mass Spectrometry Bioinformatics Platform

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant

Organic/biological mass spectrometry data analysis (development version).

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Brings Orbitrap Mass Spectrometry Data to Life; Multi-platform, Fast and Colorful R package.

LC-MS data processing tool for large-scale metabolomics experiments.

This work was published on Analytical Chemistry: Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

Quantitative Analysis of Mass Spectrometry Data

Reporting and exchange format for mass spectrometry quality control data

Highly adaptable common interface for proteomics search and de novo engines

BACNET is a Java based platform to develop website for multi-omics analysis

Compare different differential abundance and expression methods

Prize-Collecting Steiner Forests for Interactomes

Feature Annotation Location Description Ontology

Open source Java library for computational proteomics

A Comet-based, best practices proteomics pipeline.

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Interpretation of proteomics identification results

📚 🔬 PIA - Protein Inference Algorithms

Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data

CoreMS is a comprehensive mass spectrometry software framework

Mass spectrometry data visualization

Library for mass spectrometry projects

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Public Workflows at GNPS

Haskell library containing isotopic masses and relative abundances for elements from Hydrogen to Bismuth and Thorium and Uranium (excluding Technetium and promethium), i.e., all elements with naturally-occurring isotopes.

Glycan Analysis and Glycoinformatics Library for Python

Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific

A library for deisotoping and charge state deconvolution of complex mass spectra

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be …

Thermo MSFileReader Python bindings