89 Open source projects that are alternatives of or similar to pyqms

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)

Quantitative features for mass spectrometry data

A complete toolkit for shotgun proteomics data analysis

Public Workflows at GNPS

CoreMS is a comprehensive mass spectrometry software framework

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

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

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

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

The repo for LFQ-Analyst

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

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

Compare different differential abundance and expression methods

No description or website provided.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

Documentation for GNPS and related tools as written in mkdocs

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Ultrafast sequence typing and gene detection from NGS raw reads

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

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

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

A MALDI Mass Spectrometry Bioinformatics Platform

CPM implementation in pure JavaScript

Interpretation of proteomics identification results

Spatial alignment of single cell transcriptomic data.

Contact map analysis for biomolecules; based on MDTraj

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

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

Glycan Analysis and Glycoinformatics Library for Python

Quantum mechanic mass spectrometry calculation program

An R Package for Geneset Enrichment Workflows

Robust and scalable inference of cell lineages from gene expression data.

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

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

RHermes is a semi-targeted metabolomics package to deeply characterize biological and environmental samples.

A curated list of awesome computational cryo-EM methods.

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.

screenlamp is a Python toolkit for hypothesis-driven virtual screening

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

A Curated List of Computational Biology Datasets Suitable for Machine Learning

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

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

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

Collection of scripts for bacterial genomics

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 …

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

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

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

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

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

No description or website provided.

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

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

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

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

📚 🔬 PIA - Protein Inference Algorithms

Quantitative Analysis of Mass Spectrometry Data

Syntax highlighting for computational biology