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The Top 22 Jupyter Notebook Proteomics Open Source Projects

Open source projects categorized as Jupyter Notebook Proteomics
Categories > Data Processing > Jupyter Notebook
Categories > Proteomics
Ckg ⭐ 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
most recent commit 2 years ago
Alphapeptdeep ⭐ 81
Deep learning framework for proteomics
dependent packages 1total releases 25most recent commit 3 months agopypi peptdeep} Downloads
Alphamap ⭐ 66
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
total releases 10most recent commit 3 months ago
Alphapeptstats ⭐ 37
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
total releases 31most recent commit 5 months ago
Proteomicsml ⭐ 33
Community-curated tutorials and datasets for ML in proteomics
most recent commit 10 months ago
Directlfq ⭐ 27
Fast and accurate label-free quantification for small and very large numbers of proteomes
most recent commit 3 months ago
Fava ⭐ 23
Functional Associations using Variational Autoencoders
most recent commit 5 months ago
Omicsintegrator2 ⭐ 20
Prize-Collecting Steiner Forests for Interactomes
total releases 16most recent commit 5 years ago
Alphabase ⭐ 20
Infrastructure of AlphaX ecosystem
most recent commit 3 months ago
Autort ⭐ 16
AutoRT: Peptide retention time prediction using deep learning
most recent commit 10 months ago
Kineticlearning ⭐ 13
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
most recent commit 4 years ago
Mmtf Proteomics ⭐ 11
Methods for mapping proteomics data on 3D protein structure.
most recent commit 4 years ago
Isoprot ⭐ 11
Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering
most recent commit 5 years ago
Pymultiomics ⭐ 9
Python toolbox for multi-omics data mapping and analysis
total releases 5most recent commit a year ago
Irs_normalization ⭐ 9
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
most recent commit 5 years ago
Shannonmets ⭐ 9
** Blood metabolome predicts gut microbiome α-diversity in humans**
most recent commit 5 years ago
Amp_phase1_ra ⭐ 8
🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.
most recent commit 4 years ago
Ald Study ⭐ 8
ALD study data analysis
most recent commit 2 years ago
Tmt_analysis_examples ⭐ 7
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
most recent commit 4 years ago
Cohorts ⭐ 7
A python package for standardized and reproducible processing, analysis, and integration of clinical proteomics data
most recent commit 9 months ago
Phage Host Prediction ⭐ 7
Published in PLOS ONE. We show that using embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features for phage-host interaction prediction — with the highest performance obtained using the transformer-based protein language model ProtT5
most recent commit 3 months ago
Cptac Proteomics Pipeline ⭐ 5
The research and processing repo for import of CPTAC data into cBioPortal
most recent commit 6 years ago
The 5 Latest Releases In Jupyter Notebook Proteomics Open Source Projects
Alphapeptdeep ⭐ 81
Deep learning framework for proteomics
dependent packages 1total releases 25latest release September 09, 2023most recent commit 3 months agopypi peptdeep} Downloads
Alphapeptstats ⭐ 37
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
total releases 31latest release August 21, 2023most recent commit 5 months ago
Pymultiomics ⭐ 9
Python toolbox for multi-omics data mapping and analysis
total releases 5latest release March 24, 2022most recent commit a year ago
Omicsintegrator2 ⭐ 20
Prize-Collecting Steiner Forests for Interactomes
total releases 16latest release February 14, 2019most recent commit 5 years ago
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