Repositories list

• thepanlab.github.io

  Public
  Lab homepage

  SCSS

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 11, 2026Jul 11, 2026

• Aerith

  Public
  R Package for Isotopic Mass Spectra Analysis in Proteomic and Metabolomic Stable Isotope Probing

  proteomicsmetabolomicsisotope+ 4

  proteomicsmetabolomicsisotopelc-msmsisotope-labeling-experimentsstable-isotope-mass-spectrometrystable-isotope-tracing

  C++

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• WinnowNet

  Public
  Deep-learning PSM rescoring for proteomic stable isotope probing data from Sipros5 outputs

  deep-learningproteomicsmass-spectrometry+ 3

  deep-learningproteomicsmass-spectrometrymicrobiomenerual-networkstable-isotope-mass-spectrometry

  Python

  •

  GNU General Public License v3.0

  •44 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• NACHOSv2

  Public
  Pytorch implementation of NCV, HPO, and HPC

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• habit-coach

  Public
  Python

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• sipros5

  Public
  Sipros5, a proteomics tool designed for identifying and quantifying isotopically labeled proteins—especially 13C-15N-18O-2H-labeled—in complex microbial communi…

  proteomicsmass-spectrometrylc-ms+ 4

  proteomicsmass-spectrometrylc-msmetaproteomicsstable-isotopesstable-isotope-mass-spectrometrystable-isotope-tracing

  C

  •

  Other

  •22 forks•44 stars•1010 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• NPHVI

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•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

  •

  MIT License

  •00 forks•22 stars•66 issues•00 pull requests•Updated Dec 2, 2025Dec 2, 2025

• Sipros4

  Public
  Sipros 4 for stable isotopic mass spectrum metaproteomics proteomics

  proteomicsmass-spectrometrylc-ms+ 4

  proteomicsmass-spectrometrylc-msmetaproteomicsstable-isotopesstable-isotope-mass-spectrometrystable-isotope-tracing

  C

  •

  MIT License

  •11 fork•99 stars•33 issues•00 pull requests•Updated Nov 17, 2025Nov 17, 2025

• SNPBench

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 10, 2025Nov 10, 2025

• ProStoichiometric

  Public
  A multi-layer metod to study the microbial interactions and metabolic activities

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 1, 2025Aug 1, 2025

• Raxport.net

  Public
  .net version of Raxport for scan extraction of raw file

  C#

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 14, 2025May 14, 2025

• paper-redaction-guidelines

  Public
  This repository will compile all tools that are useful to write a paper.

  00 forks•00 stars•00 issues•00 pull requests•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"

  segmentationoctnnunet

  segmentationoctnnunet

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2024Aug 7, 2024

• Supercomputing_Instructions

  Public
  Useful information to use the supercomputers

  Shell

  •33 forks•44 stars•00 issues•00 pull requests•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…

  nlpdecodingsmoking-cessation+ 2

  nlpdecodingsmoking-cessationprompt-engineeringllms

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 20, 2024Mar 20, 2024

• WetlandSoil

  Public
  Stoichiometric model and scripts used in wetland soil project

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 30, 2023Dec 30, 2023

• GattacaNet2

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•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""

  tensorflowkerascnn+ 2

  tensorflowkerascnnmedical-imagingimage-classification

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•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

  •11 fork•00 stars•00 issues•00 pull requests•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…

  00 forks•00 stars•00 issues•00 pull requests•Updated May 26, 2023May 26, 2023

• LINA

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•33 stars•00 issues•00 pull requests•Updated May 9, 2023May 9, 2023

• Community_stoichiometric_model

  Public
  MATLAB

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•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"

  pythonmedical-imagingimage-classification+ 3

  pythonmedical-imagingimage-classificationcnn-kerasocttensorflow2

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 26, 2022Sep 26, 2022

• Seq2MAG

  Public
  Metagenomics workflow from sequencing data to Metagenome-Assembled Genomes (MAGs)

  Python

  •

  GNU General Public License v3.0

  •33 forks•1010 stars•11 issue•00 pull requests•Updated May 27, 2022May 27, 2022

• ukb_scripts

  Public
  Scripts to download, process and merge ukb SNPs data

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 24, 2022Jan 24, 2022

• Endoscopic_OCT_Veress_Needle

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 11, 2021Nov 11, 2021

• gcloud

  Public
  Google Cloud tutorial and setup

  183183 forks•00 stars•00 issues•00 pull requests•Updated Jan 14, 2021Jan 14, 2021

• DeepLearningTutorials

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 6, 2020Oct 6, 2020