sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3db84396444b403912245d3cb4f5428ada3854f1a09e435d6165766e1255b012 | Text | 6,678 | 122 | # SMART: Spatial multi-omic aggregation using graph neural networks and metric learning
This repository contains SMART model and jupyter notebooks essential for reproducing the benchmarking outcomes shown in the paper.
## 1. Over... |
04a9e9f1dcb15f490dc3c2e363b90f8b52b83272b4bde308c3e37c8020597820 | Text | 6,681 | 211 | <div>
<img src="https://github.com/skriabineSop/waven/blob/main/img/image1630.png" width="250" align="right"/>
</div>
**Waven**
This project provides a Python package designed to analyze neuronal responses in the visual cortex to visual stimuli. Using a Gabor transform of the stimulus, the package enables users... |
d36d0faeb86419b5a1f729e58a55b0113f4174d5f343a59e807f608af0cc3969 | Text | 6,684 | 84 | # :brain: Global effects in fMRI reveal brain markers of anxiety project
Hello, this repo was created to provide the codes for conducting the analysis reported in the paper, ["Global effects in fMRI reveal brain markers of state and trait anxiety (Medirxn 2025)"](https://www.medrxiv.org/content/10.1101/2025.07.15.25331... |
fbafc967c6fcba6c29b2229d00f1a3164d71c648cf145501f5d1d74838a8e612 | Text | 6,697 | 104 | [](https://github.com/cpp-lln-lab/localizer_visual_motion/actions/workflows/moxunit.yml)
[](https://code... |
0e82531076165fc4b603d6b1c20b2dc14df0809bcfd5bf4d91b454293b1e30c0 | Text | 6,743 | 125 | # DeBCR
**DeBCR** is a Python-based framework for light microscopy data enhancement, including denoising and deconvolution.
As an enhancement core, **DeBCR** implements a multi-scale sparsity-efficient deep learning model [m-rBCR](https://doi.org/10.1007/978-3-031-73226-3_22).
As a framework, **DeBCR** provides user... |
251a52f8cfa3b0ebac2db6d7f3e64e268d86f51e54886475bdcb861dc13ff3e3 | Text | 6,782 | 98 | # fmri-decoder
[](https://www.python.org/downloads/release/python-3100/)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://doi.org/10.5281/zenodo.1186326)
This repository contains:
* The MUUFL Gulfport Hyperspectral and LiDAR Data Collection Files
* The MUUFL Gulfport Hyperspectral Data Scene labels for Campus 1 Image
* Geo-tagged Photographs and Target Ground-tr... |
ab893ba44f7d8864197fcb6d1cf3312f10e7297185259dca9d2f4dbfe47a73f5 | Text | 6,833 | 212 | [](https://github.com/xrobin/pROC/actions?workflow=R-CMD-check)
[](https://github.com/xrobin/pROC/actions?workflow=test-coverage)
[
## Introduction
Welcome to the project page of *DeepVesselGraph* A Dataset and Benchmark for Graph Learning and Neuroscience. <br/>
Biological neural networks define human and mammalian brain function and intelligence and form ultra-large, spatial, structured graphs... |
e1f6bd58b9bfc447fd00430f70bbf6bb46e872ece7950f5366eba4fac2a78463 | Text | 6,896 | 59 | # Base_barrier_cells
## About
The choroid plexus (ChP) is a highly understudied structure of the central nervous system (CNS). The structure hangs in the brain ventricles, is composed of an epithelial cell layer, which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. It encapsulates a stromal m... |
d8e2bec420a4d21412e1a9d24dabf169fb717328d27992369dd45985c342937e | Text | 6,913 | 142 | # Efficient reliability analysis of spatially resolved transcriptomics at varying resolution using SpaSEG
**SpaSEG**, an unsupervised convolutional neural network-based method towards multiple SRT analysis tasks by jointly learning transcriptional similarity between spots and their spatial dependence within tissue. Spa... |
2c5820c1b0ab07a4bcc94c523948316c17cf20b0e0e4ca3ed5ea996c5211cc0f | Text | 6,926 | 133 | # ASAP
Autism Susceptibility Analysis Pipeline with a focus on Structural Variants (SVs). This repository documents the tasks involved in this project, which may be executed either sequentially or asynchronously. The approach used for rare variant or pathogenic candidate discovery in this study can be applied broadly t... |
92bd5a221fa09843dc34eed267fc7d34b21dcd10a9f14a5633a7e39451970b71 | Text | 6,975 | 83 | # An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery
Wei Zhang, Hanchen Huang, Lily Wang, Brian D. Lehmann, Steven X. Chen
This repo contains code associated with the manuscript, our method enhanced the detection of key variables in multi-omics integration.
### Abstract
High-throughpu... |
badeefdc272c1f8b465ea03706e4b8ea6d43a6a10468a59bd7cb801501dc1593 | Text | 6,984 | 165 | [](https://snakemake.github.io)
<div align="center">
<img src="https://github.com/user-attachments/assets/6d7d5099-aac4-44e2-a3d2-eacf6921a395" alt="image" width="500">
</div>
# 🌉 Multi-omics bridged Kernel Association test (MOKA) Pipeline... |
519a7c29485c0d58d66606e4b651969d263fb6b9104d11f57c2e1aa37abc121a | Text | 7,009 | 166 | # Probabilistic Mapping Extension
The **Probabilistic Mapping Extension** is a Python package designed to facilitate the creation and analysis of probabilistic maps for voxel-based datasets. It provides tools to download experimental data, compute probabilistic maps, and perform optional density transcriptions and vis... |
a5d021756f4d95b8fd3c7bab82b400e73c3408e0508670ee84159631dc2f60b5 | Text | 7,051 | 67 | # Hierarchical-maturation-WM-connectomes-0-to-8-yrs
This repository provides core code and relevant toolboxes for data analysis in the manuscript "Hierarchical maturation of structural brain connectomes from birth to childhood"
## Overview:
Contents include standalone software, source code, and demo data. All d... |
142b594809fb99084cf2d160f28cdaa4cdd522efec6e50d88a5b8b458fabc65c | Text | 7,074 | 145 | # ASAP
Autism Susceptibility Analysis Pipeline with a focus on Structural Variants (SVs). This repository documents the tasks involved in this project, which may be executed either sequentially or asynchronously. The approach used for rare variant or pathogenic candidate discovery in this study can be applied broadly t... |
2ead88212590074b3516a8dbcea56b38871e27cb58d2fc078100c7a4a23fcdf2 | Text | 7,151 | 147 | # :fire: FireANTs: Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration
<div style="text-align: center;">
<img src="assets/overview.png" width="90%" alt="FireANTs"/>
</div>
The FireANTs library is a lightweight, general-purpose registration package for Riemannian diffeomorphic registration ... |
fc5c570341708e93d813da260d138507a29e6650d79542c1a17c02ef3ef8bb5d | Text | 7,184 | 170 |
# biodiscvr: Biomarker Discovery Using Composite Value Ratios
<!-- badges: start -->
[](https://joss.theoj.org/papers/f143631ed4b6459a399248867b0da166)
[](https://doi.org/10.5281/zenodo.1... |
3e468c2b8539d8b4e6036c8253e3bb61290682b4a3d755a8271ca2a9b76a94f9 | Text | 7,214 | 143 | # Drug Mechanism Database (DrugMechDB)
A database of paths that represent the mechanism of action from a drug to a disease in an indication. A preliminary relase of DrugMechDB was published here:
> [**Database of mechanism of action paths for selected drug-disease indications**](https://zenodo.org/record/3708278)
[](https://www.python.org/)
[ by Tetiana Lutchyn, Marie Mardal, Benjamin Ricaud, [ChemRxiv version](https://chemrxiv.org/engage/che... |
e93382ab56339123b46436a85f6e31c807a0651447f721960b9a8bcd2b2ee4fa | Text | 7,317 | 224 | # Blood-Brain Barrier Permeability Prediction and Molecular Docking Analysis
[](https://opensource.org/licenses/MIT)
## Overview
This repository contains the complete dataset, analysis scripts, and trained models for predicting blood-brain barrier (... |
d802cc4363a47a2c54cc8787e2635063f456b52a9c0938299b21e8e1980a0a73 | Text | 7,342 | 123 |
[](https://github.com/Biomed-imaging-lab/SpineTool/blob/main/LICENSE)
[. This interface allows you to easily predict epitope residues without any local installation.
.
As a framework, **DeBCR** provides user... |
7880abec5e4dff7451d602044c2139436f7091cc690f7d30b59c4767ae9d78ae | Text | 7,377 | 53 | Shield: [![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa]
This work is licensed under a
[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].
[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]
[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/
[cc-by-nc-s... |
35db7b355773356eb147f6fdb08d8732a18a332f3844a03e34a58b479f46aa7e | Text | 7,393 | 257 |
# Topic Annotation Tool
This web-based application was developed to facilitate the human evaluation of topic models, specifically designed for the study: **"Exploiting Topic Analysis Models to Explore Psychological Dimensions in Social Media Data"**.
The tool serves as a bridge between automatic topic generation an... |
e74018e1e262440fc80f927f953711774f18cb04d1cd231355104cbf5167ba03 | Text | 7,404 | 141 | # NeuroFM: Toward Precision Neuroimaging with Foundation Models for Individualized Brain Health Estimation
> **NeuroFM is a foundation model trained exclusively on healthy brains that organizes structural MRI into population-level representations of brain health, transfe... |
0d026355657d03c68c154ecc28ae96f7651ff0fa806ddccd5ccc4c6ad396bb8f | Text | 7,426 | 95 | Welcome to the Variformer repository! This repository is meant to fine-tune sequence-to-expression models using paired whole genome sequencing (WGS) and gene expression data. We focus on [Enformer](https://www.nature.com/articles/s41592-021-01252-x), although the code used here can be adapted to other models.
Our prep... |
30add2c6d142bfbd7f9e38516ae1380a8cebf6773a1c5dfbb8b9785e4ae84a75 | Text | 7,439 | 225 | # **segcsvd**
A CNN-based tool for segmentation of white matter hyperintensities (WMH) on FLAIR MRI and enlarged perivascular spaces (PVS) on T1 MRI
## **UPDATES**
* 20260210: PVS paper now published (see citation below)
* 20250731: PVS segmentation now available
## **i) Overview**
* **Purpose and Development**:... |
6115c9adfe6b98444bfe8d0dd04a93738ef106199d5ba7aa93b03e55cb58e5d2 | Text | 7,459 | 168 | # Explainable TGCNN
Visual explainability for TGCNN model for hip replacement risk prediction including Grad-CAM and activation mapping.
## ABOUT
This code produces explainable graphs using the 3D CNN layers from the [TGCNN model](https://dl.acm.org/doi/10.1007/978-3-031-16564-1_34) trained to predict hip replaceme... |
36a63f0471ea3a1ad8752c5bacc0dc0d8da5fb52fd13784a679387bbd2959930 | Text | 7,517 | 97 | [](https://doi.org/10.5281/zenodo.16969871)
Welcome to the Variformer repository! This repository is meant to fine-tune sequence-to-expression models using paired whole genome sequencing (WGS) and gene expression data. We focus on [Enformer](https://www.nature.com/articles... |
e04a61edec09a7bb2233dac4699e67cec68e62e273d829d957453acf9199f6f3 | Text | 7,543 | 223 | # Adspt
Toolbox for the paper: **Cut-SOAP: A Descriptor for Machine Learning–Driven Adsorption Potential Energy Surface Modeling**
## Install dependencies
Most dependencies are included in `environment.yml`:
```yml
channels:
- defaults
dependencies:
- python
- pandas
- numpy
- matplotlib
- scikit-learn
-... |
792e208af7e1439feb111794ab847ce400a9d8c52f32f755edaea9ddb31ba166 | Text | 7,575 | 118 | ==========
ephys anal
==========
**1. PopSpikeAnalClass.py**
------------------------
Analyzes individual experiments in which population spikes are recorded before (baseline) and after (follow-up) LTP induction. The LTP induction is detected automatically as the last gap between pop-spikes greater than induction_gap.... |
4c2ca8de7785e30554b8ae5164ef0b65a241eba00fb9a574e7e738719cbd9bdc | Text | 7,598 | 298 | # AVPENet: Audio-Visual Pain Estimation Network
[](https://opensource.org/licenses/MIT)
[](https://www.python.org/downloads/)
[](https://onlinelibrary.wiley.com/doi/10.1002/mrm.70255) [](conda_env.yml) [](LICENSE)
This is the repository for... |
a5c3baab7ffc834d3e33f175da30e3b47c439bbaa25c3e692c1a8de38e2e2ff1 | Text | 7,641 | 199 | [](https://doi.org/10.5281/zenodo.17038345)
Module for deep learning ingestion of new data and training of U-Nets
## Installation
This ... |
040647129fd711da225b94bb87116703e168932315c54d2f436f66ad60ebcfbb | Text | 7,670 | 99 |
<table align="center">
<tbody>
<tr>
<td align="center" width="1182px">
<img src="https://raw.githubusercontent.com/virelay/virelay/refs/heads/main/design/virelay-logo-with-title.png" alt="ViRelAy Logo"/>
# Visualizing Relevance Analyses
[](https://github.com/virelay/... |
bd85e85106346e3fb4ef97c4f196b11e2014e0fd0d89562acf406283f600a970 | Text | 7,675 | 123 | # Simultaneous acquisition of EEG and NIRS during cognitive tasks for an open access dataset
Tutorial for data processing for Simultaneous acquisition of EEG and NIRS during cognitive tasks for an open access dataset
The authors would be grateful if published reports of research using this code (or a modified version,... |
96944b847fd8fc81b1d687d58be87e8826b2d5edc642c0887af291f95979c044 | Text | 7,727 | 171 | # Simple brain plot
brainPlot is a MATLAB function to create simple line-art brain plots.
[Atlases available](#atlases-available), [Installation](#installation), [Usage](#usage), [Examples](#examples), [Notes](#notes), [References](#references)
## Atlases available
... |
7dc6a05ed27e9b3d1685dd08fbd6a6408ea8a90d90fe3cdbd3b952b20b197f6a | Text | 7,731 | 266 | # Voxelcoder Flow Cytometry Batch Alignment & Voxel Analysis: Command-Line Interface
A command-line tool for aligning flow cytometry batches using autoencoder neural networks and generating voxel occupancy analysis. This tool processes FCS files to correct for batch effects, then performs comprehensive voxel analysis ... |
7a84be2af7b168c3afd227a8865685e260175d70ed74abf4b71ad649f92cd01b | Text | 7,752 | 202 | [](https://github.com/dolphin-acoustics-vip/artwarp/actions/workflows/CI-tests.yml)
[](https://app.codec... |
937e69f48eba6c8a9ec0db131b7c7e04b0323a9fa86e1a1666bf08dda8a45321 | Text | 7,783 | 93 | <p align="center"><img src="img/hctsa_logo_banner.png" alt="hctsa logo" height="180"/></p>
<h1 align="center"><em>hctsa</em></h1>
<p align="center">
<a href="https://github.com/benfulcher/hctsa/actions/workflows/run-unit-tests.yaml"><img src="https://github.com/benfulcher/hctsa/actions/workflows/run-unit-tests.yaml... |
3ebdb743eaa10f4898c282b933fe4b3e6cf51709710ae3324fe7263327b3d334 | Text | 7,799 | 191 | # Leveraging Machine Learning and Network Biology Approaches to Predict Brain Gene Expression from Blood Transcriptomes
## Overview
This repository implements the **Integrative Prediction Strategy (IPS)** — an approach that leverages machine learning and network biology to predict brain gene expression from blood-deri... |
017ef775fe60a2b7b47ecafaac689c4021668ba475c076a1bad4e5e96eb1b3a9 | Text | 7,801 | 203 | [](https://github.com/dolphin-acoustics-vip/artwarp/actions/workflows/CI-tests.yml)
[](https://app.codec... |
d6cfb70900eb8e90b9e99e5efce09d388be5dfed5b1ecb1c29c78098f39b2330 | Text | 7,849 | 160 | # MetaprivBIDS-Assessment
Statistical assessment of MetaprivBIDS https://github.com/CPernet/metaprivBIDS.
Assessed datatset:
1. AOMIC-ID1000-ds003097<br>
link: https://openneuro.org/datasets/ds003097/versions/1.2.1
2. EEG-Study-Alcohol-Imagery-Task-ds004515<br>
link: https://openneuro.org/datasets/ds004515/versio... |
fa2a4f3a41a89dcf1efce66452cab20ddd80eb4ba77e490f3635a3e1d2f7e9f7 | Text | 7,870 | 177 | # Accelerate Flash Removal of PFAS from Soil by Human-guided Bayesian Optimization and Interpretable Machine Learning
A comprehensive machine learning pipeline for PFAS (Per- and polyfluoroalkyl substances) soil treatment optimization using Gaussian Process Regression, XGBoost constraint models, and Human-Guided Baye... |
fecb29289d336b01990c54fc42b8265f636db74cbf2cc0a992669f846e43a810 | Text | 7,898 | 136 | # Osprey
[](https://github.com/schorschinho/osprey/releases)
[](https://github.com/schorschinho/osprey/releases)
[
* [Install MOSTest](#install-mostest)
* [Data preparation](#data-preparation)
* [Run MOSTest](#run-mostest)
* [Other considerations](#other-considerations)
## Introduction
MOSTest is a tool for join genetical analysis of multiple traits, using multivariate analysis to bo... |
f3484097bde19441cede60b32ed88c3dd1b4979926c2b26564bb01e0ec522ed0 | Text | 7,933 | 141 |
<div align="center">
# Quicksetup-ai: A flexible template as a quick setup for deep learning projects in research
<a href="https://pytorchlightning.ai/"><img alt="Lightning" src="https://img.shields.io/badge/-Lightning-792ee5?logo=pytorchlig... |
7ea8954422b3228e87e9110d3b36fc7ff3fa97df69d81be79936aaae9eca8636 | Text | 7,945 | 201 | <div align="center">
<img src="documents/fig_ptq.png" alt="MedPTQ overview" width=70%>
</div>
<h2><p align="center">
MedPTQ: A Practical Toolkit for Real Post-Training Quantization<br>
in 3D Medical Image Segmentation
</p></h2>
<div align="center">
[![MedPTQ Models](https://img.shields.io/badge/MedPTQ-Models-0... |
c4f07370bc8aea78426bc8e0f432041cab3ba4f9cb1d9f3e58de2120050e635d | Text | 7,952 | 187 | <p align="center">
<img src="https://raw.githubusercontent.com/DeepRegNet/DeepReg/main/docs/asset/deepreg_logo_purple.svg"
alt="deepreg_logo" title="DeepReg" width="200"/>
</p>
<table align="center">
<tr>
<td>
<b>Package</b>
</td>
<td>
<a href="https://opensource.org/licenses/Apache-2.0... |
bc754faf76e7e40508fbe5737b3ea2b7537d33591fe93cdb71d36df82d9ec75b | Text | 7,969 | 209 | # nablaColors
This repository accompanies the article “nablaColors: A 3D Benchmark for Optical Property Prediction with Solvent-aware Graph Neural Networks.”
## Installation
Follow these steps to set up the environment and install dependencies.
1) Install Uni-Core and required packages
```bash
# From the repo root
... |
ff315d59592f2a0528ec95e01f046b9d4c4e3b22b9dfc79694c92bb34ba51a96 | Text | 7,983 | 97 | Custom code used in Le Merre and Heining et al. (2024): "A Prefrontal Cortex Map based on Single Neuron Activity" (currently available at [bioRxiv](https://doi.org/10.1101/2024.11.06.622308)).
The custom code was written in **julia** and **python** and is contained in the respective subfolders.
To run the code and fo... |
3aeb8f0d846d159c9ecbd0ac4a09369fb1e75acaa67036042fd28a6718548113 | Text | 7,988 | 150 | # SATURN: Uniting Single-cell Gene Expressions with Protein Sequences for Cross-Species Integration
PyTorch implementation of [SATURN](https://www.biorxiv.org/content/10.1101/2023.02.03.526939v1), a deep learning approach that couples gene expression with protein representations learnt using large protein language mod... |
b4f8a4af3b21661c237fad6b5e415742d645f193d65c5443976e08909079c422 | Text | 7,993 | 109 | # Structure and individuality of navigation in zebrafish larvae
This repository contains the data and code to reproduce the figures from :
*Mattéo Dommanget-Kott, Jorge Fernandez-De-Cossio-Diaz, Monica Coraggioso, Volker Bormuth, Rémi Monasson, Georges Debrégeas, and Simona Cocco*. ‘**Linking brain and behavior sta... |
178533c3790c89b1c719d946db320f6cb0d3fe4bc03021461618454d5b9d9e4c | Text | 8,022 | 89 | Details regarding post-processing steps, etc. can be found in: <https://github.com/jorgenriseth/gonzo>
## Data Records
#### **`mri-dataset.zip`** - Contains the "raw" Nifti1-format MRI images output by `dcm2niix` with meta-data
- **`mri_dataset/`**
- `timetable.tsv` - Timetable of time in seconds the MRI sequence ... |
06e0f4f7fb1ee86e212ae5e9eec399a5619c4238d7acabff9af1b012cf0eb3c4 | Text | 8,057 | 147 | # MonoAlg3D 
The MonoAlg3D is a program for solving the 3D monodomain equation by applying the Finite Volume Method.
# Pre-Requisites
- Linux-based operating system
- Nvidia Driver
- CUDA library
### Setting the environme... |
1c3bfbfcc1f9904f3a36202530d76c7b5ea738d0160dab19c85ad3f55e5397b1 | Text | 8,075 | 208 | # 🔴 ⚠️ SEDEF has been deprecated. Please use [BISER](https://github.com/0xTCG/biser/) (SEDEF's successor) instead. ⚠️ 🔴
# SEDEF: <u>Se</u>gmental <u>D</u>uplication <u>E</u>valuation <u>F</u>ramework
SEDEF is a tool for quick detection of segmental duplications in a genome.
## Paper
SEDEF has been presented at [... |
4dc64b1e877933b16768368b823a27845f8903d274d621e4c31b2317d1ebb19f | Text | 8,084 | 200 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Discrete-Event Simulation Modeling Framework for Cancer Interventions and Population Health in R (DESCIPHR)
- [File directory](#file-directory)
- [Installation](#installation)
- [Citation](#citation)
- [Acknowledgments](#acknowledgments)
This ... |
a4509eaded839f1f597ebb85138587e4bb2f4ab2297188aaf23f8886be061cff | Text | 8,161 | 227 | # AD_PAC: Phase-Amplitude Coupling Analysis in Alzheimer's Disease
This repository contains MATLAB code for analyzing phase-amplitude coupling (PAC) in MEG data from patients with Alzheimer's Disease (AD) and healthy controls.
## Citation
If you use this code in your research, please cite our preprint:
**Preprint:*... |
984f759602c348a5b2fc7caa6faa34f68f54aec0550adf7e98e2d959c437784d | Text | 8,173 | 251 | # README
## How to install
You can install the package via:
```
devtools::install_github("sinomem/CNValidatron_fl")
```
The package depends on two non standard R packages,
R torch (https://torch.mlverse.org/) and BiocParallel
(https://www.bioconductor.org/packages/release/bioc/html/BiocParallel.html).
You might w... |
67d9f7f93bcfd50cd167442f9236d23ebbbe3fe8addf7a3e88ea1e57448550e5 | Text | 8,226 | 252 | # Transparent AI Assurance & Benchmarking Framework for EEG Seizure Detection (Inference Pipeline)
This repository contains the inference-time pipeline used in the publication:
**"A Transparent AI Assurance and Benchmarking Framework for EEG Seizure Detection on TUSZ Seeded with a Reproducible Gradient-Boosting Ensem... |
ffc9eb64647dae2a7809562dce8930c1e1057af85beb2ee17e7226e0be4ab0e0 | Text | 8,253 | 194 |
# napari-dmc-brainmap
*DMC-BrainMap is an end-to-end tool for multi-feature brain mapping across species.*
This [napari](https://napari.org/stable/) plugin was generated with [Cookiecutter](https://github.com/cookiecutter/cookiecutter) using napari's [cookiecutter-napari-plugin](https://github.com/napari/cookiecutte... |
65baa8dfc9f0f3a89d8bf668fbdc0fb712cc04dcbddd24a370d27d88d69d5211 | Text | 8,334 | 206 | <h1 align="center">
FlowChain VR: A VR Role-Play Game for Inclusive Supply Chain Education
</h1>
<div align="center">
<a href="https://www.youtube.com/watch?v=w-_Mpbzgaeo" target="_blank">
<img src="https://img.youtube.com/vi/w-_Mpbzgaeo/maxresdefault.jpg" alt="FlowChain Video">
</a>
<p>▶ Click the image t... |
8bf39e8af1d7104580135301eaa5976a62e8ca5485a3d9d920a7749fe567f577 | Text | 8,414 | 105 | ## About
This repository includes scripts to process and analyze images from the original 228 individuals in the [Aphasia Recovery Cohort (ARC) Dataset](https://openneuro.org/datasets/ds004512/), as well as the resulting images derived from the processing. The goal of this repository is to provide a minimal starting p... |
2ef761829e84fe8e5e2b49b2028ce64c785a038c7cf3ecbbff51fbe30897b5d5 | Text | 8,461 | 189 | # IFUM
IFUM (***I***n silico evaluation of unfolding ***F***ree energy with ***U***nfolded state ensemble ***M***odeling, 이쁨, was IEFFEUM before)
Please read the [paper](https://www.nature.com/articles/s41467-026-68637-4) before you use IFUM.
We thank those who support open science. Without the... |
383c0016086fc4d6dd2722dccac3c2ddddb8f470a9163b025bc0e4f6bcf508f8 | Text | 8,520 | 97 | # CellAgentChat
## Overview
CellAgentChat constitutes a comprehensive framework integrating gene expression data and existing knowledge of signaling ligand-receptor interactions to compute the probabilities of cell-cell communication. Utilizing the principles of agent-based modeling (ABM), we characterize each cell ag... |
13aaa64d35cca77fc16e9d4eaeeb77d86e2e19c16b2647a251229bf9d8743055 | Text | 8,560 | 158 | # PUMI
Laboratory for Predictive Neuroimaging - University Hospital Essen, Germany
[](https://github.com/codespaces/new?hide_repo_select=true&ref=main&repo=342821467)
#### Status
, segments these structures, and performs quantitative analyses such... |
7c3274d8d80b83fbd488fb9659737d69e967e723c1f888d9d3f4197e14e8cb32 | Text | 8,634 | 107 | Data and code associated with the paper:
*Single-cell delineation of lineage and genetic identity in the mouse brain.*
Rachel C. Bandler\#, Ilaria Vitali\#, Ryan N. Delgado\#, May C. Ho, Elena Dvoretskova, Josue S. Ibarra Molinas, Sophia Maedler, Paul Frazel, Maesoumeh Mohammadkhani, Robert Machold, Shane A. Liddelo... |
d9c6e8ca83096878f0c1c7b488002599082ab983650c56174d995f25d2327363 | Text | 8,695 | 245 | # Spider Anatomy Pipeline
This repository contains the computational pipeline implementing the spider atlas creation process, as published in:
Artiushin Gregory, Corver Abel, Gordus Andrew (2025) A three-dimensional immunofluorescence atlas of the brain of the hackled-orb weaver spider, Uloborus diversus eLife 14... |
16a1b253e0341e2841ea1aed43f97f44b654509be21d8fa4460e1119dbf66fd4 | Text | 8,740 | 166 | <div align="center">
<a href="https://cajigaslab.github.io/Thalamus/">
<img src=".github/assets/banner.png" alt="Thalamus — real-time, closed-loop, multimodal data acquisition" width="100%">
</a>
<p><em>Real-time, synchronized, closed-loop multimodal data acquisition — built for the operating room and the research ... |
07cd606add51ad2bd5376364a4183bd14085e7eb595884c9669b76cb3ce1ee7b | Text | 8,820 | 165 | # NBS-Predict
<p align="center">
<img src="docs/images/NBS-Predict_logo.png" width="480px"/>
</p>
NBS-Predict is a prediction-based extension of the Network-based Statistic (Zalesky et. al., 2010). NBS-Predict aims to provide a fast way to identify neuroimaging-based biomarkers with high generalizability by combin... |
e0d468882b6a85ce0b3a8ecbb6ed1f02b43a153db302f89e89d1827ac53ec792 | Text | 8,851 | 139 | # Splotch
Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) [[1]](#references) data.
## Features
- Supports complex hierarchical experimental designs and model-based analysis of replicates
- Full Bayesian inference with Hamiltonian Monte Carlo (HMC) using the adaptiv... |
67741bb9d528b5aef7b5d8f920cef7d950ec74a9164b08864e859827de6e79b2 | Text | 8,865 | 251 | # kinescope
**Predict clinical and sports scores from human movement video using kinematics.**
*Powered by Pose-JEPA — self-supervised masked embedding pretraining for skeleton sequences.*
`kinescope` is an open-source Python package for extracting kinematic features from pose estimation data and predicting scores (... |
1335b3f671d935e0a0c12aa69d0d09027f67219d51ed1c9d9c6e969b6faa9f9b | Text | 8,889 | 114 | > [!IMPORTANT]
> 🌟 Stay up to date at [opendrivelab.com](https://opendrivelab.com/#news)!
# OpenLane-V1
OpenLane is the first real-world and the largest scaled 3D lane dataset to date. Our dataset collects valuable contents from [public perception dataset](https://waymo.com/open/data/perception/), providing lane and ... |
cf07f34e6fe8fdbaace06b2e53f9c644f48b0c1574d825ab489af7820f06362b | Text | 8,917 | 150 | # scPhase: Exploring phenotype-related single-cells through attention-enhanced representation learning
[](https://opensource.org/licenses/MIT)
[](https://www.python.org/downloads/release... |
dea5d0634c87cdc5d1b5659e139d3fba58ab831fcbb6e0d4e9b5f70bd34c7f2e | Text | 8,956 | 190 | 
[](https://zenodo.org/badge/latestdoi/77548623)
Neuroelectrophysiology object model, data exploration, and analysis in Python.
Overview
========
Nelpy (**N**euro**el**ectro**p**hysiolog... |
a2a201ae68c99345506e91a1ad7778268e94d5b65354e216ab384d4f8c197482 | Text | 9,029 | 241 |
.. image:: docs/images/ogo-logo.png
:alt: Ogo Logo
:align: center
:width: 300px
Ogo
===
Like the `Ogopogo of the Okanagan`_, osteoporosis is elusive.
Help build a fracture free future.
============= ============
Docs Tests
============= ============
|ReadTheDocs| |Azure|
============= =... |
7097e33b9b6144f5cc8b96cc123c5030ecb66cd2b14955653607f75c52894caf | Text | 9,036 | 119 | # Arbor simulation of memory formation and consolidation in recurrent networks of spiking multi-compartment neurons with synaptic tagging and capture
This package employs the [Arbor simulator library](https://arbor-sim.org) to simulate recurrent spiking neural networks consisting of multi-compartment neurons (with som... |
0979ee883f9ae7223cf5b8bbc8c7f0de5c6825887df71a66fc66224f6720f80a | Text | 9,041 | 144 | > ## 🚨 **Important** 🚨 <br>
> ## TAPAS has moved to a new [location](https://github.com/ComputationalPsychiatry). This repository is no longer maintained.
*Version 6.1.0*
T A P A S - Translational Algorithms for Psychiatry-Advancing Science.
============... |
5c34f98d2911f7b5fd619f87264a7a6a0b4c1add8a8118cc07d0c1b60273021c | Text | 9,049 | 83 | **Training Dataset for HNTSMRG 2024 Challenge**
**Overview**
This repository houses the publicly available training dataset for the [Head and Neck Tumor Segmentation for MR-Guided Applications (HNTSMRG) 2024 Challenge](https://hntsmrg24.grand-challenge.org/).
Patient cohorts correspond to patients with histo... |
af37c60eff31d2f3cdf216164082a86a0d2878e000919ea143ddb93ae9b5143d | Text | 9,101 | 243 | # rustybam
[](https://github.com/vollgerlab/rustybam/actions)
[](https://github.com/vollgerlab/rustybam/actions)
[![Actions Status](htt... |
895bc3d5261280bf745b9f1f83d578659de5396d72234775037596366c556d1f | Text | 9,144 | 161 | 15/01/2026
README for information on raw data files relating to manuscript:
"Single molecule counting detects low-copy glycine receptors in hippocampal and striatal synapses" Serena Camuso, Yana Vella, Souad Youjil Abadi, Clémence Mille, Bert Brône, Christian G Specht. eLife 2026, https://doi.org/10.7554/eLife.1094... |
a52f85094168ef912f4d723c946e6a43e8217fd1538a044e1e84eae4b897f2d1 | Text | 9,201 | 177 | # PETRA-TO-CT
[](https://github.com/ucl-bug/petra-to-ct/actions/workflows/ci.yml)
MATLAB toolbox for converting a Siemens PETRA image to a pseudo-CT.
:warning: *This repository is still under development. Breaking changes may occur!*
##... |
324ce5a9b97d1878b148f1c8f69264c743db467c2997f6e30fbc3fe42f3d6e05 | Text | 9,254 | 318 | # Fuse Melanoma Classification
A deep learning framework for melanoma classification using multi-modal data (images and clinical measurements) built on top of [FuseMedML](https://github.com/BiomedSciAI/fuse-med-ml) and PyTorch Lightning.
## Features
- **Multi-modal classification**: Combines image data with clinical... |
0708ff68932abd32c5015d13deee02415ff62862458819abec84fba7dc2c364b | Text | 9,262 | 170 | [](https://github.com/cpp-lln-lab/localizer_visual_motion/actions)
<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
[](... |
10caa2ffa641dc9246e894f0067447fbe1eb74a3bd67f93ffe61787cb4b7ee24 | Text | 9,272 | 133 | <p align="center">
<img src="docs/source/_static/img/EIR_logo.svg", width="500">
</p>
<p align="center">
<a href="LICENSE" alt="License">
<img src="https://img.shields.io/badge/License-AGPL_v3-5B2D5B.svg" /></a>
<a href="https://github.com/arnor-sigurdsson/EIR#citation" alt="Citation">
<img sr... |
8d09ad39f1a3eef4451975d47a69c33f4883e96a97583fb04613efe341113a7a | Text | 9,302 | 124 | # Arbor simulation of memory formation and consolidation in recurrent spiking neural networks with synaptic tagging and capture
This package serves to simulate recurrent spiking neural networks, consisting of single-compartment (approximate leaky integrate-and-fire) neurons connected via current-based plastic synapse... |
3a9ca719f3288dbd9408c8795c039abf810b065d101dcd548b2181cc60af687b | Text | 9,352 | 118 | # [FeTA: Fetal Tissue Annotation and Segmentation Challenge in MICCAI 2024](https://fetachallenge.github.io/)
## Docker Submission Guidelines and Template
Use this repository to build your Docker container for the FeTA challenge. Your Docker container will be used to evaluate your algorithm on the test data.
**Please... |
1f7224b3619e414e6585db3c4cdc3ac755f63694603534fe81d746810855dd88 | Text | 9,406 | 135 | # CATERPillar
## **Introduction**
CATERPillar (**Computational Axonal Threading Engine for Realistic Proliferation**) is an advanced computational framework designed to simulate natural axonal growth using overlapping spheres as fundamental building blocks. By employing a biologically inspired approach, CATERPillar e... |
e9d0e84c6711b6ccb04941c8a99ae2647039cbc47fb6d13b7f881ac1eb3eff08 | Text | 9,430 | 130 | # neonate_hypothalamus_seg
An automatic pipeline for segmentation of the newborn hypothalamus.
The following materials are provided to guide the reader through the installation and use of a fully automated registration-based pipeline for the segmentation of the newborn hypo... |
039418fd23b359f63dd31c93b40e4c8f09164d32ee71fea101aa9094d8ef2a0f | Text | 9,467 | 233 | # aicspylibczi
[](https://github.com/bioio-devs/aicspylibczi/actions)
[](https://github.com/bioio-devs/ai... |
fe8c25be1dbfa0b7bb13c5b851eba60c3d3eb14a44458c727a8615e8e2239826 | Text | 9,504 | 324 | .. image:: https://pepy.tech/badge/mygene
:target: https://pepy.tech/project/mygene
.. image:: https://img.shields.io/pypi/dm/mygene.svg
:target: https://pypistats.org/packages/mygene
.. image:: https://badge.fury.io/py/mygene.svg
:target: https://pypi.org/project/mygene/
.. image:: https://img.shields.i... |
e6eed78b8e3121c91ec20852c95604841db396f7c5643c77f11a234730559d1a | Text | 9,512 | 137 | [](https://github.com/yingkaisha/keras-unet-collection/graphs/commit-activity) [](https://www.nature.com/articles/s41598-025-33803-z) [ and automatically predicts the age of the subject. The model was trained on more than ... |
078f74db79568804c91e38ab45e06181b8b41a90f52afc716b497e97bf2f55a5 | Text | 9,547 | 226 | # OHBA Software Library: Dynamics Toolbox
[](https://pypi.org/project/osl-dynamics/)
[](https://osl-dynamics.readthedocs.io)
[![License](https://img.shields.io/badge/license-A... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.