Zhang Lab

All

47 repositories

xlranker
Public
prioritization tool for ppi-xl data
bioinformatics ppi protein-protein-interaction cross-linking ppi-xl
Python
•
MIT License
•0•0•0•0•Updated Aug 6, 2025Aug 6, 2025
PepQueryMHC
Public
PepQueryMHC: Rapid and Comprehensive Tumor Antigen Prioritization from Immunopeptidomics Data
proteogenomics immunopeptidomics
Java
•
Other
•0•2•2•0•Updated Aug 5, 2025Aug 5, 2025
nf-docker
Public
docker files for pipeline steps
docker
R
•1•0•0•0•Updated Aug 2, 2025Aug 2, 2025
webgestaltpy
Public
Python package for WebGestalt
Rust
•
GNU General Public License v3.0
•0•1•1•0•Updated Jul 29, 2025Jul 29, 2025
metasage
Public
feature importance to identify interesting analytes
Python
•0•1•0•0•Updated Jul 28, 2025Jul 28, 2025
customprodbj
Public
Java
•
GNU General Public License v3.0
•5•3•0•1•Updated Jul 12, 2025Jul 12, 2025
WebGestaltR
Public
R package for WebGestalt
R
•14•37•15•1•Updated Apr 25, 2025Apr 25, 2025
funmap
Public
generate gene co-function networks using omics data
Python
•
MIT License
•4•7•1•1•Updated Apr 22, 2025Apr 22, 2025
DeepMVP
Public
Python
•0•1•0•0•Updated Apr 12, 2025Apr 12, 2025
webgestalt_rust
Public
Rust implementation of WebGestalt
Rust
•
Apache License 2.0
•0•3•1•0•Updated Apr 8, 2025Apr 8, 2025
webgestalt_tutorial
Public
Tutorial of how to start from abundance data to using WebGestalt for Enrichment Analysis
R
•0•0•0•0•Updated Mar 28, 2025Mar 28, 2025
CoPheeMap
Public
Co-regulation map of phosphosites
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated Feb 28, 2025Feb 28, 2025
neoflow
Public
NeoFlow: a proteogenomics pipeline for neoantigen discovery
proteogenomics nextflow-pipeline neoantigen-prediction novel-peptide-identifications neoantigen-discovery
Nextflow
•12•25•9•0•Updated Nov 16, 2024Nov 16, 2024
sumer
Public
SUmmarizing Multiple Enrichment analysis Results
R
•4•8•0•0•Updated Nov 14, 2024Nov 14, 2024
AutoRT
Public
AutoRT: Peptide retention time prediction using deep learning
proteomics lc-msms peptide-retention-time deep-learning
Jupyter Notebook
•
GNU General Public License v3.0
•8•28•1•0•Updated Jul 31, 2024Jul 31, 2024
neoflow2
Public
Nextflow
•0•0•0•0•Updated Jul 22, 2024Jul 22, 2024
clinicalomicsdbR
Public
R package for interfacing with ClinicalOmicsDB
R
•
Other
•0•4•0•0•Updated Jun 26, 2024Jun 26, 2024
funmap_aml
Public
HTML
•0•0•0•0•Updated May 21, 2024May 21, 2024
DeepRescore
Public
DeepRescore: rescore PSMs leveraging deep learning-derived peptide features
machine-learning deep-learning proteomics peptide-identification msms
Nextflow
•3•7•4•0•Updated May 10, 2024May 10, 2024
deep_learning_in_proteomics
Public
A list of tools on proteomics using deep learning
24•97•0•0•Updated May 5, 2024May 5, 2024
PepQuery
Public
PepQuery: a targeted peptide search engine
proteomics mass-spectrometry peptide-identification proteogenomics
Java
•
GNU General Public License v3.0
•1•12•24•0•Updated May 1, 2024May 1, 2024
NetSAM
Public
Network Seriation And Modularization R package
R
•3•3•0•0•Updated Apr 2, 2024Apr 2, 2024
COSMO
Public
COSMO: COrrection of Sample Mislabeling by Omics
R
•5•9•4•0•Updated Mar 19, 2024Mar 19, 2024
TAAPrediction
Public
R
•0•0•0•0•Updated Mar 4, 2024Mar 4, 2024
bzhanglab.github.io
Public
Zhang Lab
HTML
•0•0•0•0•Updated Feb 20, 2024Feb 20, 2024
funmap_visualization
Public
HTML
•0•0•0•0•Updated Feb 15, 2024Feb 15, 2024
DeepRescore2
Public
DeepRescore2: deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification
deep-learning phosphoproteomics
Python
•0•2•0•0•Updated Nov 2, 2023Nov 2, 2023
SEPepQuant
Public
SEPepQuant: a graph theory-based approach enables comprehensive protein isoform characterization in shotgun proteomics
R
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Apache License 2.0
•2•4•2•0•Updated Jul 26, 2023Jul 26, 2023
py-pgatk
Public
Python tools for proteogenomics analysis toolkit
Python
•
Apache License 2.0
•12•0•0•0•Updated Jun 21, 2023Jun 21, 2023
OmicsEV
Public
A tool for large scale omics datasets evaluation
R
•4•25•0•0•Updated Jun 14, 2023Jun 14, 2023