the PAN lab

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32 repositories

sipros5
Public
Sipros5, a proteomics tool designed for identifying and quantifying isotopically labeled proteins—especially 13C-15N-18O-2H-labeled—in complex microbial communi…
proteomics mass-spectrometry lc-ms metaproteomics stable-isotopes stable-isotope-mass-spectrometry stable-isotope-tracing
C
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Other
•1•2•8•0•Updated Jan 14, 2026Jan 14, 2026
NPHVI
Public
Python
•0•0•0•0•Updated Jan 3, 2026Jan 3, 2026
NACHOS
Public
Pipeline to process images with CNN: NACHOS and DACHOS. From the paper under writing "Integration of nested cross-validation, automated hyperparameter optimizat…
Jupyter Notebook
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MIT License
•0•2•6•0•Updated Dec 2, 2025Dec 2, 2025
Aerith
Public
R Package for Isotopic Mass Spectra Analysis in Proteomic and Metabolomic Stable Isotope Probing
proteomics metabolomics isotope lc-msms isotope-labeling-experiments stable-isotope-mass-spectrometry stable-isotope-tracing
C++
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GNU General Public License v3.0
•1•1•0•0•Updated Nov 19, 2025Nov 19, 2025
Sipros4
Public
Sipros 4 for stable isotopic mass spectrum metaproteomics proteomics
proteomics mass-spectrometry lc-ms metaproteomics stable-isotopes stable-isotope-mass-spectrometry stable-isotope-tracing
C
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MIT License
•1•8•3•0•Updated Nov 17, 2025Nov 17, 2025
SNPBench
Public
Python
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MIT License
•0•0•0•0•Updated Nov 10, 2025Nov 10, 2025
thepanlab.github.io
Public
Lab homepage
SCSS
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MIT License
•1•0•0•0•Updated Oct 30, 2025Oct 30, 2025
ProStoichiometric
Public
A multi-layer metod to study the microbial interactions and metabolic activities
Python
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
NACHOSv2
Public
Pytorch implementation of NCV, HPO, and HPC
Jupyter Notebook
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MIT License
•0•0•1•0•Updated Aug 1, 2025Aug 1, 2025
Raxport.net
Public
.net version of Raxport for scan extraction of raw file
C#
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MIT License
•0•0•0•0•Updated May 14, 2025May 14, 2025
paper-redaction-guidelines
Public
This repository will compile all tools that are useful to write a paper.
0•0•0•0•Updated Sep 13, 2024Sep 13, 2024
Endoscopic_OCT_PCN_guidance
Public
Scripts used for an upcoming paper "Percutaneous Nephrostomy Guidance by a Convolutional-Neural-Network-Based Endoscopic Optical Coherence Tomography System"
segmentation oct nnunet
Jupyter Notebook
•0•0•0•0•Updated Sep 12, 2024Sep 12, 2024
prb_guidance_paper
Public
The code for paper "Automatic renal carcinoma biopsy guidance using forward-viewing endoscopic optical coherence tomography and deep learning"
Python
•0•0•0•0•Updated Aug 7, 2024Aug 7, 2024
Supercomputing_Instructions
Public
Useful information to use the supercomputers
Shell
•3•4•0•0•Updated May 31, 2024May 31, 2024
smoking_cessation_intervention_messages
Public
Scripts for paper "Towards AI-Driven Healthcare: Systematic Optimization, Linguistic Analysis, and Clinicians’ Evaluation of Large Language Models for Smoking C…
nlp decoding smoking-cessation prompt-engineering llms
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Mar 20, 2024Mar 20, 2024
WetlandSoil
Public
Stoichiometric model and scripts used in wetland soil project
MATLAB
•0•0•0•0•Updated Dec 30, 2023Dec 30, 2023
GattacaNet2
Public
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Sep 21, 2023Sep 21, 2023
Endoscopic_OCT_Epidural
Public
Code used for the paper "Epidural anesthesia needle guidance by forward-view endoscopic optical coherence tomography and deep learning""
tensorflow keras cnn medical-imaging image-classification
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Aug 22, 2023Aug 22, 2023
PDN_Autograder
Public
The autograder for Projects 1 through 5 for the CS PDN course taught by Dr. Pan
Python
•1•0•0•0•Updated Aug 6, 2023Aug 6, 2023
timecourseBiomarker
Public
This is the code repository for the GLMM analysis of metabolomic biomarker discovery in the paper “Persistent Biofluid Small Molecule Alterations Induced by Try…
0•0•0•0•Updated May 26, 2023May 26, 2023
LINA
Public
Jupyter Notebook
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MIT License
•0•3•0•0•Updated May 9, 2023May 9, 2023
Community_stoichiometric_model
Public
MATLAB
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MIT License
•0•0•0•0•Updated Jan 8, 2023Jan 8, 2023
FOCT_kidney
Public
Code for the paper: "Deep-learning-aided forward optical coherence tomography endoscope for percutaneous nephrostomy guidance"
python medical-imaging image-classification cnn-keras oct tensorflow2
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Sep 26, 2022Sep 26, 2022
Seq2MAG
Public
Metagenomics workflow from sequencing data to Metagenome-Assembled Genomes (MAGs)
Python
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GNU General Public License v3.0
•3•9•1•0•Updated May 27, 2022May 27, 2022
ukb_scripts
Public
Scripts to download, process and merge ukb SNPs data
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Jan 24, 2022Jan 24, 2022
Endoscopic_OCT_Veress_Needle
Public
Jupyter Notebook
•0•0•0•0•Updated Nov 11, 2021Nov 11, 2021
gcloud
Public
Google Cloud tutorial and setup
185•0•0•0•Updated Jan 14, 2021Jan 14, 2021
DeepLearningTutorials
Public
Jupyter Notebook
•0•0•0•0•Updated Oct 6, 2020Oct 6, 2020
MetagenomicsTree
Public
Data processing tree for metagenomics
Python
•1•0•0•0•Updated Sep 11, 2020Sep 11, 2020
GattacaNet
Public
predictive genomics
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Aug 4, 2020Aug 4, 2020