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Search results for proteomics mass spectrometry
mass-spectrometry
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proteomics
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61 search results found
Openms
⭐
438
The codebase of the OpenMS project
Sage
⭐
173
Proteomics search & quantification so fast that it feels like magic
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
Philosopher
⭐
104
A complete toolkit for shotgun proteomics data analysis
Msfragger
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83
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
Rforproteomics
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69
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
Alphamap
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66
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
Protti
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50
Picotti lab data analysis package.
Depthcharge
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47
A deep learning toolkit for mass spectrometry
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
Proteomicsml
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33
Community-curated tutorials and datasets for ML in proteomics
Rawdiag
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33
Brings Orbitrap Mass Spectrometry Data to Life; Multi-platform, Fast and Colorful R package.
Moff
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31
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Spectra
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29
Low level infrastructure to handle MS spectra
Mhcquant
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28
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Lfq Analyst
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27
The repo for LFQ-Analyst
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.
Alphabase
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20
Infrastructure of AlphaX ecosystem
Psm_utils
⭐
19
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
Qfeatures
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19
Quantitative features for mass spectrometry data
Scp
⭐
18
Single cell proteomics data processing
Flashlfq
⭐
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
Quantms
⭐
17
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Dlomix
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17
Python framework for Deep Learning in Proteomics
Plink2
⭐
17
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Mscoreutils
⭐
16
Core Utils for Mass Spectrometry Data
Artms
⭐
13
Analytical R Tools for Mass Spectrometry
Pfind3
⭐
12
Sdrf Pipelines
⭐
12
A repository to convert SDRF proteomics files into pipelines config files
Pomashiny
⭐
11
🍎 Web-based User-friendly Workflow for Metabolomics and Proteomics Data Analysis
Dart Id
⭐
10
DART-ID: retention time alignment and peptide identification confidence updates
Pridepy
⭐
9
Python client for PRIDE Archive Rest API.
Promor
⭐
9
A comprehensive R package for label-free proteomics data analysis and modeling
Irs_normalization
⭐
9
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
Sdk
⭐
9
Software solution for common top-down proteomics tasks
Protein Contaminant Libraries For Dda And Dia Proteomics
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9
This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C..(Publication pending) This project aims to provide contaminant protein FASTA and spectral libraries that can be universally applied to DDA and DIA proteomics and freely accessible for the proteomics community.
Quantms
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9
Quantitative mass spectrometry workflow.
Protviz
⭐
9
Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Specter
⭐
8
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
Ionmob
⭐
8
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
Book
⭐
7
R for Mass Spectrometry documentation
Rustyms
⭐
7
A rust library for parsing Pro Forma peptides and matching them against MS spectra
Tmt_analysis_examples
⭐
7
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
Prospect
⭐
7
Proteomics Mass Spectrometry Datasets for Machine Learning
Mzrecal
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6
Recalibrate Mass Spectrometry data in mzML format
Msquality
⭐
6
Msstatsconvert
⭐
6
Converter functions for the MSstats package
Avant_garde
⭐
6
Avant-garde (AvG) is a new tool to refine Data-Independent Acquisition (and Parallel Reaction Monitoring) by removing interfered transitions, adjusting integration boundaries and scoring peaks to control the FDR.
Msviz Backend
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6
A mass spectrometry visualization platform, developed by the PAF & Vital-IT, Swiss Institute of Bioinformatics.
Reproduciblemsguidelines
⭐
6
This project aims at defining a set of guidelines for reproducible mass spectrometry-based experiments.
Py Pgatk
⭐
6
Python tools for proteogenomics analysis toolkit
Protgenerics
⭐
5
S4 generic functions for Bioconductor mass spectrometry infrastructure
Peptacular
⭐
5
A spectacularly simple package for working with peptide sequences.
Synthedia
⭐
5
Create synthetic DIA LC-MS/MS for proteomics experiments
Unimod
⭐
5
Amino acid modifications for mass spectrometry
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R Mass Spectrometry (72)
1-61 of 61 search results
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