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Search results for proteomics
proteomics
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228 search results found
Containers
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621
Bioinformatics containers
Openms
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438
The codebase of the OpenMS project
Training Material
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284
A collection of Galaxy-related training material
Pypdb
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258
A Python API for the RCSB Protein Data Bank (PDB)
Pygeno
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242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Lightdock
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234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Ckg
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184
Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph
Sage
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173
Proteomics search & quantification so fast that it feels like magic
Teachingmaterial
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161
Various teaching material
Diann
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152
DIA-NN - a universal automated software suite for DIA proteomics data analysis.
Fragpipe
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149
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
Alphapept
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136
A modular, python-based framework for mass spectrometry. Powered by nbdev.
Msnbase
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115
Base Classes and Functions for Mass Spectrometry and Proteomics
Percolator
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112
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Galaxytools
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111
🔬📚 Galaxy Tool wrappers
Philosopher
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104
A complete toolkit for shotgun proteomics data analysis
Famsa
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101
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
Plass
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99
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
Pyteomics
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93
Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
Msfragger
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83
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
Alphapeptdeep
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81
Deep learning framework for proteomics
Metamorpheus
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81
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
Rforproteomics
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69
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
Pyfeat
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68
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
Olinkrpackage
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68
Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
Deep_learning_in_proteomics
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68
A list of tools on proteomics using deep learning
Alphamap
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66
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
Proteomics Sample Metadata
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65
The Proteomics Experimental Design file format: Standard for experimental design annotation
Gecko
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54
Toolbox for including enzyme constraints on a genome-scale model.
Awesome Structural Bioinformatics
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54
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Omiclearn
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50
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
Protti
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50
Picotti lab data analysis package.
Depthcharge
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47
A deep learning toolkit for mass spectrometry
Cosmosr
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46
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
Deeplc
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44
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
Astir
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42
astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
Peptide Shaker
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41
Interpretation of proteomics identification results
Ptxqc
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41
A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
Tools Devteam
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37
Contains a set of Galaxy Tools mostly written by the Galaxy Team.
Msproteomicstools
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37
Some hopefully useful tools for mass spectrometry applied to proteomics
Ursgal
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37
Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis
Alphapeptstats
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37
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
Proteus
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36
R package for analysing proteomics data
Searchgui
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36
Highly adaptable common interface for proteomics search and de novo engines
Pdv
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35
PDV: an integrative proteomics data viewer
Tools Galaxyp
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34
Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
Datest
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34
Compare different differential abundance and expression methods
Deep Proteomics
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33
Rawdiag
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33
Brings Orbitrap Mass Spectrometry Data to Life; Multi-platform, Fast and Colorful R package.
Proteomicsml
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33
Community-curated tutorials and datasets for ML in proteomics
Ms2rescore
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32
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
Proteomicslfq
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32
Proteomics label-free quantification (LFQ) analysis pipeline
Babelomics
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31
Mokapot
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31
Fast and flexible semi-supervised learning for peptide detection in Python
Metaboverse
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31
Visualization and analysis platform for metabolic data and network pattern recognition
Moff
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31
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Deeprtplus
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30
Deep (Transfer) Learning for Peptide Retention Time Prediction
Mztab
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29
mzTab Reporting MS-based Proteomics and Metabolomics Results
Spectra
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29
Low level infrastructure to handle MS spectra
Ezaai
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29
EzAAI - High Throughput Prokaryotic AAI Calculator
Mhcquant
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28
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Msqrob
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28
Robust statistical inference for quantitative LC-MS proteomics
Panoply
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28
Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
Lfq Analyst
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27
The repo for LFQ-Analyst
Causalpath
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27
A project for exploring differentially active signaling paths related to proteomics datasets
Directlfq
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27
Fast and accurate label-free quantification for small and very large numbers of proteomes
Faldo
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26
Feature Annotation Location Description Ontology
Compomics Utilities
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26
Open source Java library for computational proteomics
Long Read Proteogenomics
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26
A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
Pyqms
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26
pyQms, generalized, fast and accurate mass spectrometry data quantification
Informed Proteomics
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25
Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
Pyprophet
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25
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
Unipept
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23
A Ruby on Rails application for proteomics data analysis
Fava
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23
Functional Associations using Variational Autoencoders
Nmdc Schema
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23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
Mzidentml
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22
Repository for mzIdentML and the corresponding examples
Do Ms
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22
Modular and extensible visualization of mass-spec data
Omicsintegrator2
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20
Prize-Collecting Steiner Forests for Interactomes
Exon
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20
Exon is an OLAP query engine specifically for biology and life science applications.
Alphabase
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20
Infrastructure of AlphaX ecosystem
Pia
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20
📚 🔬 PIA - Protein Inference Algorithms
Somadataio
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20
The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.
Qfeatures
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19
Quantitative features for mass spectrometry data
Maxquant Pipeline
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19
MaxQuant Automated Pipeline
Psm_utils
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19
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
Flashlfq
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18
Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
Mzspeclib
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18
mzSpecLib: A standard format to exchange/distribute spectral libraries
Container Pwiz
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18
The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis, developed by the Proteowizard Team at http://proteowizard.sourceforge.net/. This repository contains the Docker image to convert from many vendor raw data formats to mzML via Linux WINE.
Scp
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18
Single cell proteomics data processing
Paw_pipeline
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18
A Comet-based, best practices proteomics pipeline.
Dlomix
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17
Python framework for Deep Learning in Proteomics
Thermorawfileparsergui
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17
Graphical user interface for the ThermoRawFileParser
Plink2
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17
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Quantms
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17
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Protigy
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17
Proteomics Toolset for Integrative Data Analysis
Agi Bio
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16
Genomic and Proteomic data exploration and pattern mining
Autort
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16
AutoRT: Peptide retention time prediction using deep learning
Mscoreutils
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16
Core Utils for Mass Spectrometry Data
Pythomics
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16
A library to assist with a variety of -omic analyses. Included are tools for proteomics, transcriptomics, and genomics.
Pyascore
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16
A python package for fast post translational modification localization, powered by Cython.
Related Searches
Python Proteomics (125)
Protein Proteomics (117)
R Proteomics (112)
Bioinformatics Proteomics (78)
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