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Search results for python proteomics
proteomics
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python
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61 search results found
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
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.
Alphapeptdeep
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81
Deep learning framework for proteomics
Pyfeat
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68
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
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.
Omiclearn
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50
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
Depthcharge
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47
A deep learning toolkit for mass spectrometry
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 🖥🔬✨
Msproteomicstools
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37
Some hopefully useful tools for mass spectrometry applied to proteomics
Tools Devteam
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37
Contains a set of Galaxy Tools mostly written by the Galaxy Team.
Ursgal
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37
Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis
Ms2rescore
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32
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
Moff
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31
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Mokapot
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31
Fast and flexible semi-supervised learning for peptide detection in Python
Deeprtplus
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30
Deep (Transfer) Learning for Peptide Retention Time Prediction
Directlfq
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27
Fast and accurate label-free quantification for small and very large numbers of proteomes
Pyqms
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26
pyQms, generalized, fast and accurate mass spectrometry data quantification
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.
Pyprophet
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25
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
Nmdc Schema
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23
This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.
Alphabase
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20
Infrastructure of AlphaX ecosystem
Psm_utils
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19
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
Maxquant Pipeline
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19
MaxQuant Automated Pipeline
Mzspeclib
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18
mzSpecLib: A standard format to exchange/distribute spectral libraries
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
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.
Enrich_omics
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15
A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)
Geckopy
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14
Enzyme-constrained genome-scale models in python
Sdrf Pipelines
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12
A repository to convert SDRF proteomics files into pipelines config files
Photon
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11
PHOsphoproteomic dissecTiOn using Networks
Pcprophet
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11
Framework for systematic discovery of novel complexes and differential analysis of cofractionation MS datasets
Dart Id
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10
DART-ID: retention time alignment and peptide identification confidence updates
Sequence Database Curator
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10
This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
Pythonproteomics
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9
A collection of available Python tools for Proteomics analysis
Pridepy
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9
Python client for PRIDE Archive Rest API.
Humos
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9
HUMOS is a web application aimed to help teaching Orbitrap mass spectrometry. HUMOS models a mass spectrum of a peptide mixture allowing to investigate the influence of mass spectral acquisition parameters. By changing the parameters and observing the differences one can learn more about mass spectral resolution, duty cycle, the throughput of the analysis, ion accumulation, spectral dynamic range, and get familiar with advanced spectral acquisition methods, such as BoxCar.
Pyproteome
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8
Python library for analyzing mass spectrometry proteomics data.
Specter
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8
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
Pyproct
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8
pyProCT is an open source cluster analysis software especially adapted for jobs related with structural proteomics. Its approach allows users to define a clustering goal (clustering hypothesis) based on their domain knowledge. This hypothesis will guide the software in order to find the best algorithm and parameters (including the number of clusters) to obtain the result that fulfills their expectatives. In this way users do not need to use cluster analysis algorithms as a black box, improving t
Ionmob
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8
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
Xirt
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8
Multi-Dimensional Retention Time Prediction for Linear and Crosslinked Peptides
Psp
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7
Python scripts for data processing and analysis of P100 and GCP data
Curve_curator
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7
Analysis platform for large-scale dose-dependent data
Prospect
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7
Proteomics Mass Spectrometry Datasets for Machine Learning
Pyfeat 2.x
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6
Biological Feature Representation Tool form the Sequences
Splicevista
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6
Splice variant analysis in shotgun proteomics data
Peptagram
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6
HTML5 interactive visualisations of proteomic experiments
Py Pgatk
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6
Python tools for proteogenomics analysis toolkit
Patpat
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6
Patpat: A Python-based framework for searching public proteomics datasets
Peptacular
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5
A spectacularly simple package for working with peptide sequences.
Synthedia
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5
Create synthetic DIA LC-MS/MS for proteomics experiments
Proteomic Data Manager
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5
Proteomic Data Manager is a Web-based integrated plateform to combine data storage/backup, process and visualization of MS-based Proteomics data.
Scavager
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5
Proteinclusterquant
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5
Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).
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