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47ee0397180e70ab4185aa0682e40724a4dcba059d44d01877871cf88924430c | Text | 1,318 | 17 | # Biclustering_Epistasis
This is a companion repository for the EXTENSIVE GENETIC INTERACTIONS (EPISTASIS) LINKED TO ALCOHOL USE DISORDER IN A HIGH-RISK POPULATION manuscript.
Code related to (bi)clustering of SNP-SNP interaction results into interval-interval; gene-gene; pathway-pathway results.
BiClustering.... |
169b749e9b379ba5387f5178c2ee16aa0bce2fff66f1e49a0dc1abc8f0cb68de | Text | 1,321 | 23 | # Data and code to reproduce figures from the following manuscript
Caccamo, A., Dunstan, D.M., Richardson, M.P., Shaw, A.D., Goodfellow, M. (2025). Dynamics-Informed Priors (DIP) for Neural Mass Modelling. bioRxiv. doi: https://doi.org/10.1101/2025.09.26.678721.
### Prerequisites
The spm12 toolbox is required, please ... |
ff235eb0cc9b74c59472f20ea8cc7b40853fe0169dbce601013a0235868c3706 | Text | 1,321 | 37 | # TadPose: post-SLEAP analysis for tadpoles, frogs and other animals
---
A Python library for post-analysis of SLEAP* pose estimation. TadPose was developed with the Sweeney and Novarino lab at ISTA (Austria). To use TadPose, the original movie and SLEAP .h5 analysis file is required.
## Features
* Alignment of anim... |
5339398df4b5f2712b88c0a4898791a6a36a20799bee9f52c36fc984fda48e64 | Text | 1,322 | 26 | # BN-NeRF: A Fast 3D Reconstruction and Phenotyping Framework for Banana Plants Using Handheld Devices
This repository contains the **official inference code** and **pre-trained model weights** for the paper:
> **"BN-NeRF: A Fast 3D Reconstruction and Phenotyping Framework for Banana Plants Using Handheld Devices"**
... |
0fa0cb8ea184c4cae66ea4d7682255e1a44bf6ddb1f54aad6166504b6ef6a110 | Text | 1,326 | 11 | Welcome to WMQL's source code!
=========================================
[](https://github.com/demianw/tract_querier/actions/workflows/test_package.yaml)
[](https://pypi.org/project/Hydra-tools/)
[](https://sydneybiox.github.io/Hydra/)
![Python](https... |
28871f7aceb2a5797df902506e3bab850c8421c8f11bae26ee65fe9340ab3d8a | Text | 1,334 | 27 | # Semantic Propagation GNN - Bias Free Sentiment Analysis
This repository houses the code along with detailed comments, used to generate the results for the "Reducing Social Biases in Sentiment Analysis using Semantic Blinding and Semantic
Propagation Graph Neural Networks " paper. It proposes a new GNN architecture ... |
d4f6a1cf7d1f20f8b0572cd13bb82c455bba5c672802967928b70fcd824c882e | Text | 1,344 | 22 | # Neural data and analysis code for Miranda, Butler et al. (2025)
This repository contains all neural data, and code to generate the figures, from the study:
`Miranda Bruno, Butler James L, Malalasekera W M Nishantha, Behrens Timothy EJ, Dayan Peter, Kennerley Steven W (2025) Neural signatures of model-based and ... |
48e5e3bc5ac1c87265c8591078b5f94a3122cca7ef17d6e634ef4f43268de37c | Text | 1,345 | 23 | 04/29/2026 4:30PM by Youjie Zeng
A genome-wide association study of Alzheimer’s disease stratified by APOE*4 status. For details on the study cohorts, phenotypes, genotyping, quality control, and association analyses, see Zeng et al., Alzheimer’s & Dementia, 2026.
All variants are reported on the GRCh38 (hg38) geno... |
f8bd36d403043585b0b89d18ee966603621cd2c09ab18f92e198b88b4a705990 | Text | 1,348 | 7 | # RINFO
Embedding-Driven Physics-Informed Neural Network for Predicting Optical Constants Across Materials
We introduce a deep learning framework for predicting the optical constants of materials, specifically the refractive index n(λ) and the extinction coefficient k(λ), as functions of wavelength. Our model uses le... |
71fd05c93ddc0d40d6f6e365d1b390b22bec350b5785388c7772349bca467b3d | Text | 1,349 | 36 | # EasyBrainSurfacePlots 0.0.1
This repository contains some modified functions based on the packages `brainspace`, `neuromaps` to help people who are unfamiliar with existing neuroscience tools in generating nice surface brain plots using only a few lines of code, starting from a vector of real values.
, a new technique for axonal diameter mapping from myelin water diffusion.
* **Demo 1, radial diffusivity of cylindrical surface (zero thickness)**
* **Demo 2, radial... |
f06629096ed425fffc128bff3e0be14834e70643f67a4289723ce138ec996ad6 | Text | 1,359 | 27 | This code repository hosts source code for Vaa3D (vaa3d.org) plugins for numerous different appliations
in bioimage processing, visualziation, especially neuron tracing.
Folder structure:
* released_plugins: contains well-tested plugins that will be released with vaa3d installers
* hackathon: sandbox for plugin dev... |
339ba1ea95b5384f599f12c8a4acc9aaecc8ea4688d9f2f92ba9bc6ef9b7beb9 | Text | 1,361 | 25 | ## How to open the dataset
1. Install HDFView
Download HDFView from the official website (https://www.hdfgroup.org/download-hdfview/). Select the version matching your operating system (Windows, macOS, or Linux) and install it.
3. Troubleshooting
If HDFView fails to launch or shows an error:
- Install JDK 22, d... |
280500df718d46d0863dd36053f99c84d9250dd44db40194ff6762afb43cd5c8 | Text | 1,363 | 13 | # Dexras1_Behavioural_Sleep
This repository is to supplement the paper: "Molecular correlates of sleep deprivation in the mouse brain identified by meta-analysis of microarray data"
The repository contains methods for the analysis of passive infrared sensing of Dexras1 knockout and C57 wild-type mice. The original m... |
dbaba7f0982d7c724f48c5b4b087f02d90553cb4bf4d1045f92872b8a7cb70e7 | Text | 1,364 | 59 | # PsychAD Scientific Data supplement
This relates to the publication: **Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution**
doi: TBA
## Creating virtual environment
Using [anaconda](https://conda.io/projects/conda/en/latest/index.html), and the *env.yaml* file provided h... |
9622a900b1afa7a94b85d04a1f03d650951d017cab1f7b33f6d2fa6fac4a06de | Text | 1,366 | 14 | # mouse_abi_tool
Tool to pull gene expression from Allen Brain Institute API in Common Coordinate Framework v2 space. This code was used to obtain gene expression data for Brynildsen et al. 2020 (https://www.pnas.org/content/early/2020/07/20/2003601117).
View `code/misc/packages.R` to find the prerequisite packages.
... |
c26dbee4f1e21ad33dea4768644cac84279c16a8ae2ce4d70492ec2fdb5e2e3b | Text | 1,368 | 27 | Welcome to Intrinsic Physiology Feature Extractor (IPFX)
==========================================
IPFX is a Python package for computing intrinsic cell features from electrophysiology data. With this package you can:
- Perform cell data quality control (e.g. resting potential stability)
- Detect action potentials a... |
81393f3ef552273a60501a1322a6a1c617d03ff35d2e86924583388da17d668d | Text | 1,380 | 54 | # MeRIT - Mendelian Randomization for Identification of Targets
__version__: `0.6.0a1`
This package allows users to perform Mendelian randomisation (MR) analysis and all the data manipulation steps that are required before the analysis. Whilst the focus is on *cis*-MR it can also be used for traditional genomewide-... |
9bdf38e13f6e68dd9128abec84a0a33d726dd92ddc4a0270124173305768ba26 | Text | 1,380 | 17 | # Modelling-of-Memory-in-Unmyelinated-Axons
An efficient model to predict conduction velocity changes in unmyelinated axons, based on "memory" where prior activity modulates subsequent action potential speeds. Incorporating linear long-term and non-linear short-term memory components, it predicts propagation speeds usi... |
2fd00ce152411b4f53a00027375992331061d7319dffe1e22673500f54a0c98a | Text | 1,383 | 39 | # Multi-fiber array (MFA)-based photometry system
This page provides resources for the publication on MFA development
## system
The folder contains an Excel file with a parts list to construct the optical system.
## grids
The folder contains three .stl files and a Python-based FreeCAD macro.
## fabrication
There is ... |
b133e85508421f938391e0c7b2bab044d4759f26fa226a0f94cb6c9836fd3495 | Text | 1,385 | 39 | *This repository is not maintained by ANTs developers*
# SlicerANTs
This extension implements [ANTs](https://github.com/ANTsX/ANTs) Registration into [Slicer](https://github.com/Slicer/Slicer)
## Dev
CDash: [SlicerPreview](https://slicer.cdash.org/index.php?project=SlicerPreview&filtercount=1&showfilters=1&field1=b... |
c65bf56b61e852a80b45c3b27794e5946704d5fc27d056a38f5b58285f465197 | Text | 1,385 | 52 | # mlip-neuraldft
## About the code
This repository contains code to train and perform neural density functional theory calculations in a framework for ab initio multiscale modeling of liquids.
## Citation
Please find the associated paper with the code:
***A. T. Bui, S. J. Cox, **"A unified machine learning framew... |
b93234eda85ecf0ddb8e53e123ce9cbb1ac25398cd52ff5c3158ab554ff2d39b | Text | 1,396 | 16 | [](https://zenodo.org/badge/latestdoi/511173381)
*Burden Heritability Regression* (BHR) is a method to estimate the heritability explained by mutational burden in each gene, as well as gene-se... |
241c5dc0aae3caa5664d3b69304f1abc6f4708993c91cd8fbdd646c34c2ae314 | Text | 1,400 | 45 | 
### python liftover utility
Converts point coordinates between genome assemblies.
Inspired by [pyliftover](https://github.com/konstantint/pyliftover), this
offers a few advantages:
- ~5X faster, and lower memory requirements, as loadin... |
35e6529a635e0f30e8b64864d4b86ed6a66611802eac03f88813aaf783dc0eaa | Text | 1,404 | 31 | # Script used for the micro Co-activation pattern analysis
1- Data should be saved as describe below:
A. seedmask = A logical vector of number of voxels of whole brain included in the study where 1 indicates the voxel within the initial seed - bilateral thalami in case of test data -(Dimension : nVox x 1)
B. ... |
3f074068322549b83a71d8cf4364c6d38f51a1d3807fae23f1339e339fb9a3ba | Text | 1,405 | 31 | ## Associated Publication
### *Sex and tissue resolved co‑expression networks reveal a female placental–brain axis protective against prenatal PCB exposure* — Chau et al., accepted at Genome Biology (2026)
[](https://doi.org/10.5281/zenodo.19011412)
---... |
b6b47af18236f53906e0499ed0284d2fceda4f98ee5cf526f70208347b64e4dd | Text | 1,408 | 16 | Traffic-Forecasting-Graph-neural-networks-LSTM
----------------------------------------------
Dataset Descriptions; A Real-world traffic speed dataset named PeMSD7. PeMSD7 was collected from Caltrans Performance Measurement System (PeMS) in real-time by over 39, 000 sensor stations, deployed across the major metropol... |
caa6462c22f5d27b84481420671de806590177829fd6b1aac6c491e46528e91d | Text | 1,410 | 62 | # **ProteinNexus: An SE(3)-Equivariant and Dynamic Multi-Modal Engine Advancing from PTM Site Prediction to Network Understanding**
**1.Catalog description**
data: Data storage
src: Main code storage
model/embedding: Weight storage
------
**2.Requirements**
```
pandas
scikit-learn
t... |
2708914650d56cde63de96f3188eb3a3534e137b8a2a085beb46778c07635ba5 | Text | 1,413 | 16 | Loh et al 2026 Neuroimage - Ventral temporal-frontal pathways in the human brain based on diffusion MRI tractography
The shared files are organised as two folders:
1) ProbMaps_26Dec2025
- contains spatial probability maps for the left and right uncinate fasciculus (UF), dTFexcF (dorsal temporal-frontal extreme capsul... |
a15c0439562cf500a99849c6b1d8298c15815a5ed48ff6ac42cbcf80ba9d1dfe | Text | 1,415 | 24 | # CRN Drosophila larva MB benchmark (Bridge-A) — simulation artifacts
This archive contains code, configs, and outputs for the *Drosophila* larva mushroom-body (MB) connectome benchmark used in the CRN manuscript (vNext5).
Primary result reproduced:
- Topology- and coherence-dependent disorder response (DES peak) in ... |
da13d834636fc3712ebc2d62a73ec36f0f560acfabdb1ea1494496c4b416b74f | Text | 1,417 | 54 | # Algorithm-hardware co-design of neuromorphic networks with dual memory pathways
Pengfei Sun* [1], Zhe Su*[2], Jascha Achterberg* [3], Giacomo Indiveri [2] , Dan F.M. Goodman [1], Danyal Akarca [1, 4]
Imperial College London, ETH Zurich, University of Oxford, University of Cambridge
\* These authors contributed equ... |
7a1be946829083b05b86127718bb75dfc7eddfdde65881d16ac472242c661c98 | Text | 1,424 | 22 | # Mouse Human Comparison
This repository contains analysis scripts associated with the paper:
### **A Framework for Comparative Analysis of Human and Mouse Cortical Neuron Dendrites in Corresponding Brain Regions**
Zhixi Yun†, Wen Ye†, Nan Ji†, Yujin Wang†, Jing Rong, Tian Li, Yingxin Li, Qi Shen, Ruilong Wang, Hair... |
ed3a3cb19a87cfbe8de5b10b6446e765e3d1bb107b86e564d55f0aa04ea24521 | Text | 1,431 | 49 | # Scillus
<img align="right" width="108" height="125" src="Scillus.png">
---
[](https://travis-ci.com/xmc811/Scillus)
[](https://ci.appveyor.com/p... |
107c1c26107170cd46d2a56c57fdeee49a8a92860a639a7b4162eb4269411448 | Text | 1,433 | 25 | If this code is used in a publication, please cite the manuscript:
"Single pulse electrical stimulation in white matter modulates iEEG visual responses in human early visual cortex",
by H. Huang, K.N. Kay, N.M. Gregg, G. Ojeda Valencia, M. In, C. Kapeller, Y. Shu, G.A. Worrell, K.J. Miller, and D. Hermes.
The manuscri... |
7495d1d7e2b152ebfd8c7a602a00bf427d25c9251bfbb216507b6d4714ebfecc | Text | 1,435 | 23 | README
***Notes about graphical user interface (GUI)***
To run the GUI, type run_modeling_gui into the MATLAB command window while in the main toolkit directory or after adding it to your path.
To facilitate file and directory selection, you can create a file named "default_paths.mat" in this folder that contains th... |
591c16753f5c2bb732fa37e2108f5f2d08914af326c3e6a0dafadf78b98e50f4 | Text | 1,445 | 26 | # memoslap-denoising-pipeline
# MeMOSLAP-fMRI Denoising using fMRIPrep Preprocessed Data
This repository provides a MATLAB script for **denoising resting-state fMRI data**, based on the **recommended denoising pipeline** described by [Wang et al. (2024)](https://doi.org/10.1371/journal.pcbi.1011942), and **validated ... |
a6e6720178d0e7ae84e1f95188e045ae1793cf05a5d55ef90358794949d98e16 | Text | 1,445 | 35 | # The RESTORE Study
**Study Title:** Insights from nine nights of self-applied, low-density sleep EEG during sleep restriction therapy: a proof-of-concept evaluation
Principal Investigator: Dr Emily Stanyer | University of Oxford
This repository contains the complete analytical pipeline for processing actigraphy, li... |
39d15848aeb28dfe339d58800d3913d6ce7695ba330dc133ebe96568cb571e3d | Text | 1,449 | 17 | # EvaluationSynthesisMethods
Code to help analysis and synthesis of evaluation reports. The colab notebook files in this repository contain the methods described in our paper (preprint):
In our paper, we describe methods to extract data and synthesise information for 64 outcomes from 631 evaluation reports published ... |
1605bc4da4a06d373938e80c38f4fe354de5c44f1ac376c6b36de5c1d437bbe2 | Text | 1,466 | 44 | # Ubiquitination Sites Prediction
This is the official repository of "**A Benchmark for Machine Learning based Ubiquitination Sites Prediction from Human Protein Sequences**" paper.
## To Do
- [x] Add end to end training codes.
- [x] Add hybrid training codes.
- [x] Add preprocessing codes.
- [x] Add end to end demo c... |
f73284c76a0449ccee8a7c91ba55c880f80dce6d553405769084977e879946f6 | Text | 1,467 | 28 | # `ComptoxAI`
[](https://zenodo.org/badge/latestdoi/202416245)
[Website](https://comptox.ai/)
A modern data infrastructure for AI research in computational toxicology.
- - -
ComptoxA... |
d03f3f189e6b79cf772cea21e07adeac5d35182d7676efaf50cf39c9bc37a23a | Text | 1,472 | 25 | # mgng_tus_dacc_ains
Analysis code for the scientific article:
Koutsoumpari, N., Algermissen, J., Yaakub, S., den Ouden, H. E., Bault, N., & Fouragnan, E. (2026).
Ultrasound neuromodulation reveals distinct roles of the dorsal anterior cingulate cortex and anterior insula in learning.
PLOS Biology.
MGNG TUS STUDY, ... |
89124c51142f6bd32e2ec2a1347ed8804b46fca2821cad8c4b23f6e754898b9a | Text | 1,474 | 35 | [](https://doi.org/10.5281/zenodo.15020334)
# thoi_tutorials
Tutorials of how to use THOI library.
## Folder Structure and Dependencies
### notebooks
Contains the Jupyter notebooks used to generate the figures using the raw data and the result data.
### data
Contains th... |
25b4e28c8453143a2e91a14f88a4c6f8cd96742bed19b2abb6f550f6ea7574b8 | Text | 1,481 | 20 | This repo holds links and code to browse processed data and reproduce the figures in [Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis](https://www.biorxiv.org/content/10.1101/2025.04.03.647013v1) by Shapira et al. (2025).
Figures can be reproduced in two ways:
1) Manually - d... |
08f6fb6256dcca969d5f3033ad96b43834ff7f9769ecc570318e51b8ecc99479 | Text | 1,490 | 19 | # Global_NMM_parameter_inference
This repository implements model calibration from EEG data in a neural mass model using evolutionary search metaheuristics and approximate Bayesian computation.
The repository contains code to run the algorithms described in Dunstan et al. (2025). doi:10.1101/2025.08.18.670825. If you ... |
6b5b71005526b59ccb31a872dd1360b885e8ff63fd2b96e041ea6e11c5a9a6e9 | Text | 1,500 | 41 | **# Future-prediction**
This is the code repository for the paper "Predicting Future MRI-based Brain Atrophy Based on Longitudinal Data"
This repository contains scripts and models for analyzing brain atrophy/enlargement using Elastic Net Linear Regression (ENLR).
**Workflow**
1. Run Models: Start by defining the ou... |
d5da6368e43963f118f30441f7d041bb557a8e681405415532fb002a16df9e0f | Text | 1,510 | 58 |
# STM MATLAB functions
MATLAB functions to compute **spectrotemporal modulation representations** from audio signals.
This pipeline allows you to:
- compute a **cochlear spectrogram**
- estimate a **spectrotemporal modulation profile** (MPS/MRF)
## Example output
### Spectrogram
![Spectrogram](examples/Spectrogram.pn... |
a9905fbfbdd0bd42d75bdae8164a03885562835b5fc487e8244bed48410af1d3 | Text | 1,511 | 24 | # README
# CCEP\_ASM\_connectivity
## General Info
This folder contains the data analysis and figure generation MATLAB functions and scripts for the Akkol et al. with the title "Anti-Seizure Medications Alter Functional and Effective Connectivity as Measured with Intracranial Electroencephalography". Scripts that ... |
f539eb81ecd3dd9313a47b430ae419330007a1ada5f156b11da67e21c68e748a | Text | 1,519 | 9 | The MR Comparative Anatomy Toolbox (Mr Cat) is a collection of bash shell and Matlab scripts and functions developed by members and collaborators of the Cognitive Neuroecology Lab at the Radboud University Nijmegen and the University of Oxford. It contains code that we have used to process and analyze magnetic resonanc... |
38786f5b1a6bb8774b6006175fdae213b5cbfdf8495144dcb31f2ab623a49dc0 | Text | 1,525 | 30 | # DDParcel
DDParcel: deep learning anatomical brain parcellation from diffusion MRI.
# Dependencies
* [3D Slicer](https://www.slicer.org)
* [PNL conversion](https://github.com/pnlbwh/conversion)
# Installation
conda create --name DDParcel python=3.9
conda activate DDParcel
pip install torchvision torch... |
0a83b6496beea5ac009eee07781091d59a37cf73d2651b6fb55860d812e8057a | Text | 1,527 | 60 |
# drosophila-courtship
**An app and python package for the tracking, classification, and analysis of fly behaviors.**
## Repo Structure
<pre>
|-courtship
|-app # code for generating GUI
|-ml # code for creating feature matrices and behavioral... |
6ed0d72d2aa6415dc94d212ac4cd8bad71254311eca4cbdc8c51c5ed116cee24 | Text | 1,548 | 20 | # Application of Machine Learning with MALDI-TOF MS for Rapid Differentiation between Methicillin-susceptible and Methicillin-resistant Staphylococcus aureus
[](https://doi.org/10.5281/zenodo.17395596)
This repository contains code for data processing, model training, eva... |
e55468c50a67179a51917f19eb05469ab0b06ab176b0fb871a243dd7669e730f | Text | 1,556 | 34 | # cogitate-msp1
This repository contains all of the code related to the Cogitate Main Scientific Paper 1 (MSP1). You can find more information below.
Paper Title: "An adversarial collaboration to critically evaluate theories of consciousness"
| Information | Links |
| --- | --- |
| Website | ![Cogitate](https://img.... |
1bb46c4e7f5b9d96011002320ed4691ed1a8fd9a32ac3edf71872d3271ba4717 | Text | 1,578 | 27 | # Rat Datasets for DANT
This repository contains all rat datasets used in DANT in:
> Huang et al., "Density-based longitudinal neuron tracking in high-density electrophysiological recordings"
The repository includes 13 dataset folders. Each folder contains a `spikeInfo.mat` file formatted as input for DANT. These fi... |
59a55547bf31dcd19853f97934062223d2ea9c28c85d55c0c2e1e4d24e4babad | Text | 1,583 | 28 | ## Data-driven network model of CA3 - featuring sequence replay and ripple oscillation with plasticity during offline simulation
Code repository of the The Role of Plasticity in Modulating Replay Dynamics paper (Submitted to NeurIPS 2024)
To run:
git clone https://github.com/sliorbar/ca3net.git
cd ca3net
... |
138800ed42ca1f2f2c7f3fd41d8e944d54f481677b9249b400ae887926f52ca4 | Text | 1,592 | 45 | # Analysis pipeline for GM NODDI
## CODE
## Step 1. Data preprocessing
### Step 1a. PreprocessMPRAGE.sh
- Brain mask and tissue segmentation
- Register to DWI
- Shaeffer parcellation
- Prerequisites: fsl, niftyreg
### Step 1b. Prepare Diffusion
- DWIpreproc: Motion, ringing, bias correct (prev performed)
- Step1b.A... |
945d2b26b9b8a9261fbdb184444db59c8fa4c2492aa33fdb15f1298e3954eeb0 | Text | 1,595 | 12 | # ibb_toolkit
Iowa Brain-Behavior Toolkit: An open-source MATLAB tool for inferential and predictive modeling of imaging-behavior and lesion-deficit relationships
The /tutorials folder contains MATLAB Live notebooks illustrating how to perform different kinds of modeling analyses using the toolkit. These tutorials ill... |
a067ddb96901ce57b720c442c67073ac54a6c40952f040331fcc6173a72ec374 | Text | 1,605 | 43 | # palm-sEMG-doorknob-filtered
## Palm sEMG-based user authentication during doorknob rotation using a convolutional neural network
Yeonjung Shin<sup/>1</sup>, Junghun Kim<sup/>2, *</sup>, Sang-Il Choi<sup/>2, *</sup>
<sup/>1</sup>Department of Computer Software, Daegu Catholic University, Gyeongsangbuk-do, 38430, Re... |
e6f275d205958abea612a41d1e1f78eea57151573bcdf4e5876ee92be4288465 | Text | 1,605 | 22 | # memristor-sde-diffusion
Code for "Resistive memory-based neural differential equation solver for score-based diffusion model"
## Abstract
While AI-Generated Content (AIGC) strives to replicate human imagination, current models like score-based diffusion remain slow and energy-intensive. This inefficiency stems fro... |
a037a3ee4a63e778ce580fe600a2a4854ab4a7fe7d3e501cea883c762d527622 | Text | 1,607 | 17 | # cmrep: Continuous Medial Representation
This software repository contains the source code for the cm-rep algorithms described in a series of papers by Yushkevich et al.
CM-Rep is a method for representing 3D biological objects (e.g, lungs, hippocampi) using a deformable model with predefined medial axis geometry. ... |
8161a695a4ad15f7a9dd428185eb328dbca803f7370f665ed62c50a93db9535e | Text | 1,616 | 31 | # Radiomics-Based Analysis of Emotional Conflict fMRI Predicts Sertraline Response in Major Depressive Disorder
This repository contains code and documentation for a research project that aims to predict treatment outcomes in patients with Major Depressive Disorder (MDD) using sertraline. The project leverages radiomi... |
081fc33f573b7e6e39f04bd8342a632519e0b25d795f7f63fbe134b376ba8597 | Text | 1,628 | 29 | This repository includes all code related to **Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics**, accepted to be published in *Cell Host & Microbe*.
Identify Beta-Glucuronidase (GUS) enzymes from a protein FASTA file with [GUS-ID](https://github.com/redinbo... |
3558511ab9f8d942b4697eb2331638de72bdfefbad5ad1db49079cb8ed7abb09 | Text | 1,634 | 16 | Motor imagery-based Brain-computer Interface (MI-BCI) application in stroke rehabilitation aims to match brain activity with real-time feedback, thereby establishing closed-loop neural pathways and providing a basis for evaluating patients' neuroplasticity changes. Thus, constructing EEG datasets under MI paradigms is ... |
bd055f01ec734e5efb77735671e9307b9aebbccb88eaa97466bba0f9442fa9de | Text | 1,639 | 50 | # fibromyalgia-li-rtms-pmcf-dataset
An anonymized representative dataset and supporting documentation associated with a multicenter post-market clinical follow-up (PMCF) program evaluating low-intensity repetitive transcranial magnetic stimulation (Li-rTMS) in patients with fibromyalgia.
## Repository Contents
### d... |
25d01ddf647692bfb2385b201243339635a7e055b65190d6a07c852548a58a4a | Text | 1,667 | 33 | Egg LSCI sexing images dataset
Images of egg blood vessels with sex ground-truth.
Dataset belong to BioPhotonics Lab, California Institute of Technology.
Related publication is S. Mahler et al: Exploring non-invasive sexing of early chick embryos in intact eggs using Laser Speckle Contrast Imaging (LSCI) and Dee... |
65b4477fdde11d2bb6c3a2249eee9613aca98b8c8f6bd4905e84c93b66a37d6b | Text | 1,667 | 25 | # RESCUE: Recovery of unattributed expression patterns
## Overview
We developed a new computational method that can recover the spatial expression patterns missed by standard single-cell inference on spatial transcriptomics (ST) data. RESCUE is based on making a fundamental correction to the class of statistical model... |
1b5373f71d958e6c62ebd3fd776d9f14af8e9a78e83bc8cac06771042a43bb50 | Text | 1,670 | 62 | # SAMap -- version 3.0.0
# Citation
Please cite the following paper if using SAMap: https://elifesciences.org/articles/66747
Tarashansky, Alexander J., et al. "Mapping single-cell atlases throughout Metazoa unravels cell type evolution." Elife 10 (2021): e66747.
> **Requirements:** Python ≥3.11. See `pyproject.toml`... |
5636545fe386d7a8d8b79bea6c2b6e20d3b337350844b35e23426991ea97999e | Text | 1,677 | 34 | # single-nucleus-RNA-seq-code
This repository contains R scripts used for the single-nucleus RNA-seq analyses in:
Iba1 deficiency impairs microglial synaptic remodeling and neuronal survival after axonal injury.
## Contents
- `cluster_vs_rest_deg_volcano_composition.R`: cluster-vs-rest DEG analysis and volcano plot... |
b55c7a17ac2926de7da4d1187d0d2b5e1f2db8987d58f797cef8850063903fa5 | Text | 1,680 | 53 | [](https://software-docs.nanoporetech.com/pod5)
[](https://github.com/nanoporetech/pod5-file-format)
POD5 File Format
================
POD5 File Format
=====... |
82885d516339b19720f66b8ccc4ff5bc19426f3afdbf8ae7e857e318de8463a2 | Text | 1,682 | 33 | Replication Data for: Deep Learning-based Plant Disease Detection using YOLOv8
Overview:
This repository contains the complete dataset, source code, trained model weights, and evaluation results required to replicate the findings of our research paper submitted to PLOS ONE. The study evaluates the performance of a ... |
cd0128032f31f0dfec138485e24434658f40360f145e23353d06c0ac5826dade | Text | 1,682 | 44 | # SpaDC
## Overview
SpaDC is designed to integrate both spatial location and DNA sequence for comprehensive ATAC data analysis.
SpaDC integrates spatial location and DNA fragment. It employs a deep 1D convoluti... |
36502552a3393b26a6bc84f997a02c3854ee043904aa04fe922aa53fe91ffc07 | Text | 1,683 | 35 | # udstyle
Compute complexity metrics from [Universal Dependencies](https://universaldependencies.org/).
Input can be a `.conllu` file, or a plain text file that will be parsed by [Stanza](https://stanfordnlp.github.io/stanza/), if installed and language is specified.
```
Usage: python3 udstyle.py [OPTIONS] FILE...
-... |
831087210d0fd85182f034447b714cd06b9c83a3f6aadd95fb0371c5941bb9a0 | Text | 1,685 | 57 | # Facial expression discrimination emerges from neural subspaces shared with detection and identity
This repo contains the code to decode facial expressions or identity from neural data and ANN features.
## Getting started
Create and activate an environment
```
virtualenv -p python3 ExpressionDecoding
source Ex... |
31498836ca9a84e556a4d24754f9f39c208c0d58b3cfa9b6c5afa6f216620e6e | Text | 1,687 | 59 | # AI-guided Radiation Dose Escalation Pipeline
This repository contains the core scripts required to reproduce the image-processing pipeline used in the study:
**“Personalized Machine Learning-Guided Radiation Dose Escalation in Newly Diagnosed Glioblastoma: A Prospective Early-Stage Clinical Trial.”**
The repositor... |
de7e5e687d7cfc3f3d02828de12c3346deaea4df579746224087da55a8aaef8a | Text | 1,694 | 18 | # sleep_loss_signature
This repository contains code and data for the paper: A neural signature of sleep deprivation in the human brain.
The codes were tested in a PC with Ubuntu 20.04 OS, Python 3.9.18.
The key python toolboxes including jupyterlab 4.0.12, scikit-learn 1.4.0, nilearn 0.10.2, pickle 4.0, numpy 1.26.3,... |
2fc01040724ab8de5c213622c144e6b860dff35b8abd25b91536d5e27404cb28 | Text | 1,695 | 14 | # LAVI
Toolbox to compute the rhythmicity profile and automatic band detection (both sustained and transient bands) of electrophysiological data, introduced in [Universal rhythmic architecture uncovers two modes of neural dynamics](https://www.nature.com/articles/s41467-026-73553-8) (Karvat et al 2026).
The Lagged-Ang... |
d0583ae712a1729eed088807b1f367b9e276554e8ee5384d7ce39ef05de37b72 | Text | 1,695 | 25 | Project Title
Single-cell analysis reveals human-specific oligodendrocyte polarization and conserved neuronal responses after severe traumatic brain injury
Overview:
This repository contains processed data and analysis scripts for the single-cell transcriptomic study of human and mouse traumatic brain injury (TBI)... |
a75f411de99a595068de9c63ff3009961f8aff26133a5aaa922859d8d8560053 | Text | 1,699 | 15 | # Divalent siRNA for prion disease
This repository holds regulatory documents, raw data, source code, and figures for our divalent siRNA drug candidate for prion disease.
## IND
We have made public [101 PDF documents comprising our Pre-IND meeting communications, Investigational New Drug (IND) application, and FDA r... |
b266e89ef88af272da0c3e433cab314d4eec1df1f8591b9b678e392f10b4bd4e | Text | 1,700 | 34 | # REST
# Elite Female Football Athletes Dataset and Analysis Tools
This repository contains various scripts and tools for analyzing a novel dataset of 21 elite female football athletes. The dataset comprises 17 days of actigraphy, well-being, caffeine consumption, screen time, and daily hand strength test data. The a... |
37353c8b322d6695b327aac7ec93e381faafd275787c4a2f9b4397ae0ac5d9c8 | Text | 1,704 | 19 | Demo Matlab code for kernel ridge regression 'Testing_Set227_KRR.m'.
Demo connectivity matrices of 10 subjects 'trans_data_set227_mat_cov_regressed.mat'.
Demo external scores of 10 subjects 'trans_data_all_scores_set227.mat'.
Name of the external measures 'trans_data_set227_all_names.mat'
Demo covariates of 10 subjects... |
08ab2299d71cbb4345c19789006d5dee59d91e1dc99f1f080de32a776cdc87a9 | Text | 1,713 | 56 |
# INRGravity3DInv
Python experiments for 3D gravity inversion with implicit neural representations (INRs).
The scripts in this repository test positional encoding, model capacity, discretization effects, explicit versus implicit regularization, ensemble variability, noise sensitivity, and related inversion settings ... |
3a16104550d994b3e94b69f9f6932caeab2e451c182cda0550865ce9b6cc8aca | Text | 1,716 | 26 | # MEA-bursts
An R script using Spike List csv files to analyse Axion MEA data.
This script generates data about Spike activity and Network bursting for multi-electrode data from Axion Maestro Pro recordings of cyto-view MEA plates.
The script will prompt you to upload a Spike List csv file that can be generated during... |
bf12227d955d3dc4f8602886075a7ff1e313f1cca396fd46963a5e571ac6fc1e | Text | 1,716 | 36 | [](https://github.com/haniffalab/cherita-react/actions/workflows/npm-publish.yml)
[](https://github.com/haniffalab/che... |
145b808898d0ed5eb9ff5ac70641c997f543a10ffc0eabb04379eac57c605d35 | Text | 1,725 | 52 | # Language laterality and cognitive skills: does anatomy matter?
Code repository for the preprint:
**Andrulyte, I.**, Zago, L., Jobard, G., Lemaitre, H., Branzi, F. M., Rheault, F., Petit, L., Keller, S. S.
*Language laterality and cognitive skills: does anatomy matter?*
Preprint DOI: 10.1101/2025.09.06.674566
#... |
dadb6fe87996dc349821261ee6d4097dab2d82993d0eeb161c3cc7bc39b3fb55 | Text | 1,725 | 18 | # Code for "**Dataset of cortical and subcortical single neuron activity **during value-based task**s in macaque monkey**"
London et al., 2025
These scripts are provided as examples of how to access the data using example spk and trialtype matrices. The same logic can be used on the real data, just with different fil... |
46717de0c024a52a540b6cdc5391c9ba62c04f4b3cf7b8e496daca7626011b7a | Text | 1,727 | 29 | # On Network Design Spaces for Visual Recognition
This repository provides the code and data used in the [On Network Design Spaces for Visual Recognition](https://arxiv.org/abs/1905.13214) work, including full training statistics for *over 100,000 models* spanning multiple model families.
<div align="center">
<img ... |
331b7197e2c70f02fa5353952a071d47762fc21a87aa3785b4c1a4b14df2bae6 | Text | 1,742 | 58 | Hi,
This is the GitHub repository for MrBayes, a program used for Bayesian
inference of phylogeny.
Build instructions, very very short version (would install MrBayes as
"/usr/local/bin/mb" on a Unix system):
git clone --depth=1 https://github.com/NBISweden/MrBayes.git
cd MrBayes
./configure
make && ... |
8e741d8ecf7ed5bc1e84cdf445f7359d4cb28291baf002f36b3a3995742d5e00 | Text | 1,755 | 16 | # Instructions
When creating these scripts, we used Matlab 2021A, with toolboxes listed in instructions.txt at the top level directory in the accompanying zip file.
Scripts are separated by figure numbers, but in some cases, data and functions are shared across folders, so it is not recommended to take subdirectories ... |
df0223044793d701b8d5d6219399364afb33f9cf01cafec1c012b4c4c4bcc34c | Text | 1,760 | 38 | ### Context & Citation:
## Unmated queens show worker-like behaviour and gene expression in polygynous colonies of the ant _Stigmatomma pallipes_
This repository contains scripts related to the assessment and assembly of ONT reads for the ant _Stigmatomma pallipes_. Findings of the analysis are reported in the follo... |
0186b3c70a6bbf3c9f8f97f1423fc8367ff9305fd358440d704e1450a1c78624 | Text | 1,778 | 27 | This multishell diffusion MRI dataset was collected from three traveling subjects with identical acquisition setting in ten imaging centers. Both of the scanner type and imaging protocol for anatomical and diffusion imaging were well controlled.
Pre-processing Environment:
The dataset was pre-processed on a CentOS 6.... |
9f08b79d7ee9b1e4f61e212efb8e7235be3c3df5792aa89190cd0d947137a259 | Text | 1,780 | 64 | Introduction
------------
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or
FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be
optionally compressed by gzip. To install `seqtk`,
```sh
git clone https://github.com/lh3/seqtk.git;
cd seqtk; make
```
The only librar... |
c3ec332bae916e0c124bab7d820a63cd043675aaad973f9f9def8c2973d9e63e | Text | 1,782 | 56 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# `CroCoNet` <img src="man/figures/logo.png" align="right" width="17.5%" /> <br/> Cro<span style="font-weight:normal">ss-species</span> <br/> Co<span style="font-weight:normal">mparison of</span> <br/> Net<span style="font-weight:normal">works</sp... |
22bf535dec42bc0c3da888f9b23ffff6c1246e567794f90b3a44c3f7e29b9559 | Text | 1,793 | 31 | _____ _____
/ ___| / ___|
\ `--. __ _ _ __ ___ _ __ \ `--. __ _ _ __ ___ _ __
`--. \/ _` | '_ ` _ \| '_ \ `--. \/ _` | '_ ` _ \| '_ \
/\__/ / (_| | | | | | | |_) /\__/ / (_| | | | | | | |_) |
\____/ \__,_|_| |_| |_| .... |
4b05ba76c285de74c63d97fe8850cf0a266735c8bf1fda6df000b4b1de512d60 | Text | 1,795 | 34 | This dataset was used in the paper "Adsorptive Gas Sensor Response Forecasting to Enable Breath-by-Breath Analysis."
===================================
Each .csv file in the dataset includes data taken from one breath sample.
After a short start-up period, a vacuum pump is activated for 90 seconds, which expos... |
28b77d73ec2e704ae0973666dc6842b8c8a9709b68aca17c83bfa8aee0d018ad | Text | 1,797 | 39 | # 🍃 Deep Learning for Classification and Severity Estimation of Coffee Leaf Biotic Stress
This repository is intended to develop the work supported by the Latin America Research Awards 2018.
The work is divided into two parts:
* [Classification](classification/README.md): This folder have the solution developed in ... |
1e09690f99a249074fc8b5ccf35231b5cd7ed6e9597a449ebc78fbdd97123b0b | Text | 1,798 | 79 | ## Installation
You can install kxa_analysis using either Conda or pip. Follow the steps below based on your preferred package manager.
### Using Conda
1. **Clone the Repository:**
```bash
git clone git@github.com:kxa_analysis.git
cd kxa_analysis
```
2. **Create and Activate the Conda Environment:** ... |
cfb175bf7514b515eec849da48b8991107c93815a0437c3b904d99fad2889bc6 | Text | 1,808 | 84 | # Dual-Task fMRI Brain-Behavior Association Study – Analytic Code Repository
## Overview
This repository contains analytic code and processed behavioral summary measures associated with the cognitive–motor dual-task fMRI study investigating age-related differences in motor–cognitive interference and functional networ... |
b115cfa838946da63b7eb991b3f6b4eac9974cabe7948cc4694859a202bdce6f | Text | 1,810 | 56 | # SliceTCA
This library provides tools to perform [sliceTCA](https://www.biorxiv.org/content/10.1101/2023.03.01.530616v1).
___
<p align="center">
<img width="700" src="https://raw.githubusercontent.com/arthur-pe/slicetca/fb51e536afad9bfab60b5fc1def764ad6af1983c/img/decomposition.svg">
</p>
## Installation
```co... |
7b256cb03ce8351fe35b0b172bd77cbcb6413174dcfabcf0393b6f9ee1c81478 | Text | 1,812 | 34 | # Non-Destructive ANN Model for *Epinephelus costae* in Syria (2025)
**Author**: Nader Iskandar Hamwi
**Affiliation**: Department of Animal Production, Latakia University, Syria
**Contact**: nader836@gmail.com
**Manuscript**: Submitted to *PeerJ* (2025)
## 📌 Description
This repository contains:
- Ori... |
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