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83880c8521c8a8074337e1f5b8c6be2edca8e342fa55923b9e68f343f4025bd3 | Text | 1,216 | 43 | 
# scOMM
### A Multi-Omics Deep Neural Network for automatic single-cell Label Transfer and approach Benchmarking
- **/tutorials** directory includes jupyer notebook showing how to prepare and run scOMM in both R and Python.
- **/utils*... |
c181c05662b4b8858de9731e4b093ff0d43746704b2e0de0e481f02d4bd0e0ea | Text | 1,237 | 74 | # SCNN_LIFrow
This git contains all the source files around a Spiking Convolutional Neural Network (SCNN) accelerator for FPGA based on LIF neuron model, and complementary sources for testing and demonstrations.
The neuromorphic SCNN was published in TBIOCAS in 2019.
## Citation
If you use this code in your research, ... |
888351c9ed08bbf219aed28912a0ca3570e30faa268bb1a65962fb303ae333b5 | Text | 1,271 | 21 | # miRInter-Trans
miRInter-Trans is a miRNA-ncRNA interaction classifier, based on a Transformer architecture.
# Requirements
A CUDA environment, and a minimum VRAM of 8GB is required.
### Dependencies
```
miRInter-Trans/RNA-FM/environment.yml
```
# Usage
#### Steps of miRInter-Trans execution
```
1. Embeddings etract... |
b20fb789fd4f638cc843004f49e630072863ca71fab9e6d9882c11e9c23fbda4 | Text | 1,374 | 78 | ## Prerequisites
1. Install required libraries
```python
pip install -r requirements.txt
```
2. Install pytorch-3dunet from pytorch-3dunet-master.zip
## Train
- Data Preprocess
Generate mask images from labeled swc files.
```
python PreMakeData.py
```
Cut raw images and mask images int... |
e059910e0b6cec5e68f93b0f2b78bb3a425e714b1a07b9bd3c19b286c0644e80 | Text | 1,383 | 26 | # MS_beta_fatigue
Code for Tatti Benelli et al., 2025 Brain communications
This repository contains MATLAB scripts used for the analysis and figure generation in:
Tatti E., et al. (2025). *Linking Movement-Related Beta Oscillations to Cortical Excitability, Structural Damage and Fatigue in Multiple Sclerosis* Brain C... |
29db08c2a8f3141a1bb333bc69f70faf450ac52737b0282b5cc4d52de4a90b7a | Text | 1,423 | 28 | An improved version of DP5 analysis developed by Howarth (DOI:[10.1039/D1SC04406K](https://doi.org/10.1039/D1SC04406K)). This codebase is refactored for legibility and maintainability.
We strongly recommend using a separate python environment created via `conda`, `uv`, or other solution of your choice to run this prog... |
12a72024e1fc363b1e4bb9940ad92ddf598fab6d70943dec8a640a246e86fd79 | Text | 1,424 | 25 | # Sulcal Phenotype Networks (SPNs)
Code for SPN analysis as described in "A bimodal taxonomy of adult human brain sulcal morphology related to timing of fetal sulcation and trans-sulcal gene expression gradients"
Please find the containerized version of this pipeline at the link below, which uses one command to take yo... |
8bfcfeb27c1149a4416956bf9f3c0e4c73c27d8b63bd7fe40918cc4bd41fa40a | Text | 1,429 | 7 | This repository consists of the code for data analysis and computational modelling carried out in the manuscript:
## Amygdala GABA Neurons: Gatekeepers of Stress and Reproduction in Female Mice ##
### Abstract ###
Stress can disrupt menstrual cycles, impair fertility and cause reproductive disfunction. The posterod... |
9b7751b2c492701ffff2a24cda913a7e9908b5b87afb596f20652fe8e3ceac28 | Text | 1,442 | 28 | # Introduction
The code is used for the work of “Multi-omics analysis reveals associations between gut microbial subgroup alterations and host genetic aberrations in Alzheimer’s disease ”. This code includes two parts, the first part is the LDA topic model, and the second part is about statistical analyses.
# LDA
... |
8febc977ac4dfc829252ac9cb0463f28c3695d6e6db133f6433e379fd6c88ec2 | Text | 1,446 | 33 | # OASIS: Fast online deconvolution of calcium imaging data
Code accompanying the paper "[Fast online deconvolution of calcium imaging data](http://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1005423)".
Python: https://github.com/j-friedrich/OASIS
MATLAB: https://github.com/zhoupc/OASIS_matl... |
ceaf09049acb5f90ead555faf272601b2028745ccedafc6b3ed2f4083596b54c | Text | 1,464 | 17 | # BIBSnet
> [!NOTE]
> **Project status: Stable, with periodic model updates and limited maintenance**
>
> BIBSNet remains in active use, but is not under active feature development. Updates generally include new deep learning models retrained with additional data, as well as critical bug fixes, compatibility updates, a... |
e47c085f330c73ccc0eae10512a28e315528759138b59b43920a5ffa258567b6 | Text | 1,467 | 40 | # SLU_Cpb5.0
Supplementally data and materials of Western Painted Turtle (Chrysemys picta bellii) SLU_Cpb5.0 version
## Tissue-spcific protein FASTA files:
- Brain_advanced.filtered.faa.gz
- Duodenum_advanced.filtered.faa.gz
- Hatchling_Brain_advanced.filtered.faa.gz
- Hatchling_Carapace_advanced.filtered.faa.gz
- Hat... |
8c522297ff544fb808c1c79e7b0f28956c9f359cfa5d721d5e3a6cb9f84ec7e9 | Text | 1,469 | 35 | Main Directories
--data_with_postpain_prestim_lmm_new.csv
----contains all the single trial data for each participant that used for formal analysis (for several figures)
--Figure 2
----csv files for Bayesian analyses conducted in JASP with default priors (also contains the data to reproduce the Table S1 in Supp... |
5decfe2bf33848dc5f744b32946579c5b1c1574fb6ca987ac9e140cfe5120732 | Text | 1,498 | 6 | ## Sequence-based modeling of low-affinity transcription factor–DNA binding through deep learning
Multiple layers of determinants and mechanisms affect binding specificities between transcription factors (TFs) and DNA. DNA sequence-based deep learning models using convolutional neural networks (CNNs) and self-attentio... |
09cbaaf56cac36229c95a0b80e2ef15cafaa6f236087a431d96158544fee644f | Text | 1,502 | 25 | # OrganoidMap
This repository contains code for OrganoidMap - a web application allowing to search a database containing results from a systematic literature search for brain organoid models. The **OrganoidMap** is available at: organoidmap.cs.uni-tuebingen.de
Please refer to the original publication (_Link will foll... |
1570e41b94991221c7d04a7ce53eee200393a5b070513c5c8500c1b8e71bc9d2 | Text | 1,531 | 39 | # pcaMethods
R package for performing
[principal component analysis PCA](https://en.wikipedia.org/wiki/Principal_component_analysis)
with applications to missing value imputation. Provides a single
interface to performing PCA using
- **SVD:** a fast method which is also the standard method in R but
which is not app... |
d45dba8ee387a700cf849801f3aeb17e4f62fa0bef16fa10b2cc260380876925 | Text | 1,576 | 34 | # F. prausnitzii Treatment RNA-Seq Analysis
## Project Overview
This repository contains the analysis of Bulk RNA-Seq data from alpha-synuclein overexpressing (ASO) mice, their wild-type (WT) counterparts, and ASO mice treated with F. prausnitzii. The analysis aims to understand the transcriptional changes associated ... |
efd99fc11d70ced598e71d3ea4feabee4b64ab46b57564d3e32df06b27a61fe2 | Text | 1,576 | 34 | ΦID -- Integrated Information Decomposition
===========================================
.. image:: https://github.com/Imperial-MIND-lab/integrated-info-decomp/actions/workflows/tests.yml/badge.svg
:target: https://github.com/Imperial-MIND-lab/integrated-info-decomp/actions/workflows/tests.yml
:alt: Tests Status
... |
515bdb18fddf53f6192e7f64c5f4a15942663c5f7ed57b418710ecb79087e0c7 | Text | 1,578 | 37 | # Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues
## Overview
This repository contains processed single-cell RNA-seq (3’ and 5’) and single-nucleus multiome (RNA + ATAC) data generated as part of the study:
S... |
a716182778c80d436c245b87c73a7fce5b1267f253196c1b6bfe1eb1edf56457 | Text | 1,621 | 33 | # <div align="center"><b> PETWB-REP </b></div>
[**📕zenodo**](https://zenodo.org/records/16789748)
This is the official repository for **PETWB-REP: A Multi-Cancer Whole-Body FDG PET/CT Dataset with Corresponding Radiology Reports**, in which we provide scripts for whole-body image processing.
Preprocessing steps inclu... |
cff70c8f913c909601d4727f17ffa16ea43bc3441646428380b02419c249ba31 | Text | 1,621 | 9 | # Predicting the number of incoming patients in the ED of the Son Espases University Hospital (HUSE)
This repository contains the datasets and code to predict the number of incoming patients at emergency department (ED) of Son Espases hospital. The data and methods are described in the paper *Forecasting emergency dep... |
49d75dcaaaf1e0879712f25aa9ae881984608ea05c51ccfda2b911cf87001c48 | Text | 1,644 | 15 | # High-Fidelity Neural Speech Reconstruction through an Efficient Acoustic-Linguistic Dual-Pathway Framework
## Abstract
Reconstructing speech from neural recordings is crucial for understanding speech coding and developing brain-computer interfaces (BCIs). However, existing methods trade off acoustic richness (pitch,... |
865b6dd20cf422d9363587c6bf9808910fecf89f9a423a537d58f16a0ba1385f | Text | 1,644 | 49 | YASS: Yet Another Spike Sorter
================================
.. image:: https://travis-ci.org/paninski-lab/yass.svg?branch=master
:target: https://travis-ci.org/paninski-lab/yass.svg?branch=master
.. image:: https://readthedocs.org/projects/yass/badge/?version=latest
:target: http://yass.readthedocs.io/e... |
139a34055ef9e8fedf75d1c1737ccc4427872e2d319f8aad2b244228d197e604 | Text | 1,683 | 39 | # Holistic GNNs: Graph Neural Networks Enhanced with Multi-Connectivity Architecture
A novel Graph Neural Network architecture that combines Jumping Knowledge Networks, Virtual Nodes, and Skip Connections for enhanced molecular property prediction and graph-level tasks.
## 🔬 Overview
HolisticGNNs introduces a mul... |
ad64684f37dc67ae97d6705d817b05de167e7fc24339c00c7b38c6439b87478c | Text | 1,683 | 28 | # PC-Astrocyte
This repository holds `MATLAB` codes for numerical bifurcation analysis using `MATCONT` toolbox, as presented in the article
*Astrocyte-Induced Dynamics of a Pyramidal Cell with a Dendrite-Connected Astrocyte* by Lenka Přibylová, Jan Ševčík, Anastasia Egorova, Štěpán Husa, Lucia Kajanová, Eva Kopřivová,... |
0316be9ffc363b0f5d7f417bd339ba3b8a4e5a9e4aa6bbe6d12d0acd1444cfd6 | Text | 1,723 | 23 | # AIMS - An Automated Immune Molecule Separator
# Description
This particular repository is specifically for recreating the analysis in all manuscripts published thus far using AIMS. If you'd like to use AIMS to run your own analysis, please see:
https://github.com/ctboughter/AIMS
The AIMS github has its own program... |
de63da6a54d054a64eb22e109b309280e4d45e9b1af9b4eebb8c8d26c3f61548 | Text | 1,756 | 13 | This repository introduces an open-access 31P Nuclear Magnetic Resonance (NMR) shift database designed to bridge the gap between commercial and open-access resources. With 43,317 entries encompassing 39,107 distinct molecules from 6,853 references, this database offers a comprehensive repository of organic and inorgani... |
fc617d485e69da7c98d887a943b114206248329a990c4adc7cc41fd8caa7cc1f | Text | 1,756 | 35 | # Parietal-Hippocampus
Preprint: https://www.biorxiv.org/content/10.1101/2025.06.08.658503v1
Both the code for concurrent TMS-iEEG preprocessing and the preprocessed TMS-fMRI dataset (/TMS-fMRI_data) are provided (see the preprint for details). Instructions for using the preprocessing code are described below.
## Aim... |
041ce05c143b78da36890d31f817428dde51dd640cbbbef98e523e6c357683db | Text | 1,793 | 23 | # Opatz Lab ROSA toolbox
Welcome to the Hanganu-Opatz ROSA toolbox!
The goal is to collect all the most relevant scripts for preprocessing/analysis that one might need as a lab member.
IMPORTANT: everything here is under development, and should be treated like that. If you find something that needs... |
bdc8ac024963f4cb9ab3730ecf33a514624c772014f24c09708d0713699e1535 | Text | 1,801 | 43 | # Docking-Validation
KNIME workflows for the validation of docking protocols, using metrics such as AUC, Enrichment Factor (EF), and Boltzmann-Enhanced Discrimination of the Receiver Operating Characteristic (BEDROC).
## 🔬 Overview
This repository provides tools to validate docking protocols based on a selected scor... |
a1806f6083c74db8bab0bf0191f7a6145124f33e0cd2d9666d3b8c96444272b6 | Text | 1,806 | 17 | # Dynamic Transcriptomic Remodeling in Grafted Human Neural Progenitor Cells Uncovers Mechanisms for Vision Preservation in a rat model of Retinitis Pigmentosa
** Shahin et al. 2025 **
Human neural progenitor cells (hNPCs) show promise in slowing retinal degeneration and are currently being tested in clinical trials ... |
8ea09c8d3594ae7aa9c4da10f3b8d0450d155680ec3d9f5693dadc9b623e6c12 | Text | 1,824 | 16 | # EEG/MEG Study
## Prediction, Syntax and Semantic Grounding in the Brain and Large Language Models
This repository explains the preprocessing and methods used to analyze the EEG and MEG data. The data was recorded using combined EEG and MEG measurements while the participants listened to an hour of the science fictio... |
60fc3ff3e55c0813add840d108e42f8c556c241e40e8e45d51226789a780de39 | Text | 1,825 | 49 | # Inkube: An All-in-One Solution for Neuron Culturing, Electrophysiology, and Fluidic Exchange
This repository contains all code associated with the Inkube system, which integrates neuron culturing, electrophysiological measurements, and fluidic exchange into a single platform. Below is an overview of the repository s... |
2db928a04bc314a320f9fef580df005068080119ebc73d7a56e519d755dfa5e4 | Text | 1,829 | 53 | # DyPheT
DyPheT is an Assembloid analysis tool, which is a Python-based application designed for automated tracking and analysis of rotating 3D cell structures (assembloids) in time-lapse microscopy videos. It aligns video frames using robust translation and rotation correction, applies polar image warping for rotation... |
f6234cd901b5572a94f09e6cdf6d4ace42eb27787229b53d1cfd7fb15fcef73d | Text | 1,832 | 30 | # MOLEXA <br><br>
<img width="1811" height="1417" alt="Fig_1_annotated" src="https://github.com/user-attachments/assets/7f85b150-135e-45dc-ab69-08114cdc4096" />
<br><br>
MOLEXA is a deep generative neural network capable of reconstructing molecular geometries from ion momentum measurements in X-ray-based Coulomb explos... |
5e08eff54e8c3a6cc1b233672400d406f48b7612d069a4f0eb334bce330984c6 | Text | 1,864 | 50 | # AdaLi
This repository is the official PyTorch implementation of the paper: Towards Adaptive and Lightweight Backpropagation for Training Spiking Neural Networks.
# Dependencies
- Python >= 3.9
- spikingjelly==0.0.0.0.14
- torch==2.4.1+cu121
- tensorboard==2.17.1
- numpy==2.0.2
# Training
The bounda... |
944ef009e1eb06bca2eb93f157216f9c1d98d477892b4373dcb81dd6d77e5f19 | Text | 1,887 | 48 | avg_q README
------------
This is avg_q (pronounced "average queue"), a multichannel (EEG/MEG/other
time series) data processor originally developed for analyzing event-related
brain activity. It features built-in methods for filtering, detection,
spectral analysis, Independent Component Analysis, SVD/PCA, convolutio... |
c91e3370009b50200172e629eab4fa74cf645b6d19dc43d7b41c6662f00bbb37 | Text | 1,889 | 42 | # GTree
---
#### Introduction
Global Tree Reconstruction System (GTree) software is a open source software for neuron tracing. GTree is written in C++, and freely available for academic research using. GTree is used to reconstruct neurons in single images and reconstruct neuronal population from brain-wide image stac... |
8780e3411afac05ad3daadc607020852e43603ae36995165ee08a9a3e27bd52a | Text | 1,929 | 65 | # DANN
Repository for the domain-adaptive neural network approach discussed in DeGiorgio, M., Arnab, S.P., Fumagalli, M., *"AI solutions for evolutionary genomics of nonmodel species"*.
# Image dataset generation
Image dataset generation follows Arnab et al. 2025, *"Efficient detection and characterization of targets ... |
8da0bdcd95f4a827f63c07807859ebdfa6b5185c74743ba4686f6a153cd4afd6 | Text | 1,945 | 43 | # Kadobianskyi_et_al_2026
This repository contains data related [to the paper](https://www.biorxiv.org/content/10.64898/2026.03.09.710483):
**Kadobianskyi, Henninger, Markov, Groneberg, Veith, Renz, Atabay, Reddien, Maler, Judkewitz (2026): “Multimodal reference brain atlas of adult *Danionella cerebrum*”**
---
## ... |
b9d168f20e8b2416b679950776ddcc0a549dcefe9bd4693d59866f65a7617de9 | Text | 2,017 | 39 | # Phase Pole Correction
This repository contains scripts to perform experiments and create figures for the paper "Phase-Pole-Free Images and Smooth Coil Sensitivity Maps by Regularized Nonlinear Inversion" by Moritz Blumenthal and Martin Uecker.
To run the scripts, execute:
```
$ ./run_all.sh
```
This script download... |
80b5b5bd44f1ca62b4093fe4d6b65973d37a54d25798706e8de9f7dfa8c9f966 | Text | 2,073 | 42 |
==============================
[Documentation](docs/_build/html)
Project Organization
------------
├── LICENSE
├── README.md <- The top-level README
├── requirements.txt <- The requirements file for reproducing the analysis environment
├── get_started.sh <- bash script to setup the en... |
4e9b4d342a9742765e62b890c08aa9703140c197e76546165c1353ff7c4299aa | Text | 2,080 | 57 | # PISCO Software v2.0
This software corresponds to a newer version of the original PISCO software,
which is available at: http://mr.usc.edu/download/pisco/
## Overview
This MATLAB software performs subspace-based estimation of sensitivity maps
for multichannel MRI reconstruction. It follows a nullspace-based appro... |
6e4f0e262a9065a59ad298773c5b12f88561f69c28f7a182a704b97afbf3957c | Text | 2,082 | 39 | THE REVISED MD17 dataset:
=========================
Citation:
========
Anders S. Christensen and O. Anatole von Lilienfeld (2020) "On the role of gradients for machine learning of molecular energies and forces" arXiv:?????
The molecules are taken from the original MD17 dataset by Chmiela et al., and 100,000 str... |
b9c67308ea0674e1a8a79ead730597f65307202e64cd04fb2fdf368c9355cb92 | Text | 2,084 | 42 | # Cedalion - fNIRS analysis toolbox
A python-based framework for the data-driven analysis of multimodal fNIRS and DOT in naturalistic environments. Developed by the [Intelligent Biomedical Sensing (IBS) Lab](https://ibs-lab.com/) with and for the community.
<p align="center">
<img src="docs/img/cedalion_frontpage... |
5995255b9a33ec6d47cbffd7731759de25392b09470805baca1ac8fed77d8285 | Text | 2,152 | 47 | # GP_with_IFS
Genomic prediction with incremental feature selection
The script determines the optimal number of SNPs to use for genomic prediction by ranking SNPs according to a GWAS and adding them incrementally to a random forest prediction model.
Genotype and phenotype data needs to be in the binary format used b... |
6f7828d4f093d6d8ac866a94229c88dac01d53c64812aaa3914ac3bedbbc08c7 | Text | 2,153 | 58 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Epoch: Epileptogenic Zone Localization Based on neural Fragility EEG marker
[](https://cran.r-project.org/package=Epoch)
[ or single-nucleus RNA-seq (snRNA-seq) data to spatial transcriptomics data (Stereo-seq). The primary goal is to leverage chromatin accessi... |
e579be55fb87b017264d5af511eb5c1b3798e7cfad2bd27c9c45322d07a1bef2 | Text | 2,318 | 56 | # SPERRFY: A Data-driven Framework for Realizing Sperry's Chemoaffinity Theory in the Neural Connectome
## Overview
This repository provides a complete framework of SPERRFY (Koike et al., 2025). It implements data-driven models including canonical correlation analysis (CCA), connectome reconstruction, gene similarit... |
efcd3b274bfc5a9f1dd08710bec8c83ec3342dd4c47eb783b022146c3b9bdd17 | Text | 2,355 | 43 | # kbstat
A highly configurable statistical library to perform script-based generalised linear model analysis and post-hoc testing. Results and diagnostic plots are saved as Excel and CSV tables, MATLAB, PNG and PDF figures and TXT files to a directory of choice.
## Disclaimer
This library come without any warranty a... |
bb098cd1db28dbfcc4780519283154be81322eada79d09b9c2d5b16a8391a381 | Text | 2,367 | 67 | ## DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms
Official implementation of DTIAM, a unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms.
## DTIAM
<div align="center">
<img sr... |
7a8b54bf2f25b80bedcaeb01cef4208e619500aeab0aed5f76f1f6b10b8def5c | Text | 2,399 | 42 | # Buzzoni_et_al_2026_Platygyra
Data and R code for:\
Persistent legacy effects of marine heatwaves on coral symbioses
Authors:\
D., Buzzoni; A., Van Nynatten; R., Cunning; J. K., Baum.
## Data
- KI_github_basemap_shapfiles (folder of shapefiles for study site map)
- dhw_5km.nc.zip (heat stress accumulation data from... |
6cbc628ff47f427d661f5bca4c5d925a51abd8b269de65f6820609a8af655d4c | Text | 2,416 | 54 | # HybridNDiff-UQ
This repository contains the official implementation of **HybridNDiff-UQ**, an uncertainty quantification framework for hybrid neural differentiable models that integrate numerical representations of known physics with deep neural networks. The proposed approach enables effective and scalable estimatio... |
530e1922e72ff0a1768305ec3da4fddef132c3fde7579eedbe5b5b5d1667ae40 | Text | 2,430 | 62 | # DeepBIT: Deep Learning-Based Brightfield Image Tracking
This project implements DeepBIT, a deep learning-based pipeline for identifying and tracking live and dead cells in brightfield microscopy images using MATLAB. The framework includes modules for training semantic segmentation models, applying them to microsco... |
ad2b1060cf3e6e6352a92bd48ccc526ed071425d4ac6e19a2ab093cd8e184b93 | Text | 2,464 | 61 | YASS: Yet Another Spike Sorter
================================
------------------------------
***[UPDATE Sep 2022]***
Please note that default pyyaml no longer works and the following command needs to be run after all installation steps:
!pip install pyyaml==5.4.1
------------------------------------
***[UPDAT... |
17661908cbfa739957377bf39409213d6e92fc11f17bf1bf45b99851ddc66da6 | Text | 2,514 | 31 |
Paper submitted to Scientific Data - Nature
##################################
"In-vivo probabilistic atlas of human thalamic nuclei based on diffusion weighted magnetic resonance imaging"
##################################
E. Najdenovska*, Y. Aléman-Gómez*, G. Battistella, M. Descoteaux, P. Hagmann, S. Jacquemont, ... |
4c97fe65e5d5530b8bf241cacce1086b79be9775077caf004fd49abe4538992c | Text | 2,518 | 48 | # 🧠 Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset
This repository provides a time-resolved single-cell multi-omics dataset profiling adult hippocampal neurogenesis (AHN) in vitro, with and without Alzheimer’s disease (AD)-related pathology.
Human iPSC-derived n... |
8aa2f96ca4881aea0f3eca0525d21531b7c8f5ff44abba40cf26090fb3da715b | Text | 2,525 | 73 | # Chronological Diagnostic Algorithm for Parkinsonism
Chronognosis is a machine learning-based diagnostic tool for predicting neuropathology in patients with parkinsonism using chronological clinical presentations.
## Key Features
- **Neuropathology-Confirmed**: Trained on 949... |
72f3b14a4966db3c50e77ee76f2386d6b0d9c08d5aa608eedca8f8b76f32e1f2 | Text | 2,587 | 42 | # Scrublet
**S**ingle-**C**ell **R**emover of Do**ublet**s
Python code for identifying doublets in single-cell RNA-seq data. For details and validation of the method, see our paper in [Cell Systems](https://www.sciencedirect.com/science/article/pii/S2405471218304745) or the preprint on [bioRxiv](https://www.biorxi... |
23b0d4a0eff4ec1c1c77f6a3bd1b00b665a6102a378dfb4e5e6e41b552ae6b4e | Text | 2,602 | 29 | 
](https://napari-hub.org/plugins/napari-imc)
[](https://pypi.org/project/napari-imc)
[. Participants were aged between 19 and 27 years. All participants gave informed consent and were free from neurological disorders.
Paradigm:
The EEG data was recorded during a single paradigm consistin... |
242b884b05b2cece2bca77bf66c18c46ecb915d29c5317e64886c8e7a084a5b9 | Text | 2,659 | 82 | # OpenMX Workflow
A high-throughput workflow for **OpenMX** calculations using [atomate](https://github.com/hackingmaterials/atomate).
This workflow was also employed in our recent work: [arXiv:2505.04862](https://arxiv.org/abs/2505.04862).
This repository is adapted from [openmx-wf](https://github.com/tsaie79/openm... |
64f938a187d9a876115b721483b7d171c99826cc39f791c15b81115009c9649a | Text | 2,716 | 49 | # README
This repository contains code to reproduce the results of "Critical evaluation
of the theory and practice of feed-forward neural networks for genomic prediction"
by Aaron Kusmec, Karlene L. Negus, and Jianming Yu (*submitted*).
### Introduction
This project uses data from maize [Genomes to Fields project]... |
6853106b68f29e537b20acd0ba88a60a5fc428483eb93563fdfc93e4fd3f0365 | Text | 2,740 | 23 | # Mitchell_DCN2026
Code associated with:
Mitchell, J. L., Fuentes-Jimenez, M., Stone, H. L., Yablonski, M., & Yeatman, J. D. (2025). Visual Word Form Area demonstrates individual and task-agnostic consistency but inter-individual variability. Developmental Cognitive Neuroscience, 101703. [https://doi.org/10.1016/j.dcn.... |
2c3473b855098daeb8973fe5ca07141c936c5a63cf720c4f1c8a6fc922d1a70e | Text | 2,753 | 48 | # Deep Learning-Based Physiological Risk Stratification in Night-Shift Hospital Workers
This repository contains the official Python implementation of the analytical pipeline for the manuscript: "Deep Learning-Based Physiological Risk Stratification in Night-Shift Hospital Workers" (Accepted for publication in Scien... |
052e95c5d992717b6cbc6bb7915f0929e0fc076db5781c8d1b124c6cd7fa5172 | Text | 2,775 | 23 | # CAD*opti*
This repository contains MATLAB code for a machine learning algorithm for the detection of functional cell assemblies at their optimal time scale (CAD*opti*) from simultaneously recorded spike trains.
##
The algorithm extends from the cell assembly detection algorithm (CAD) presented in
[*Russo, Durstewit... |
acd6ffd66c70ce16244fb4d55b1ec731dc6b7c41979467a80c796e0a64cbedb1 | Text | 2,799 | 67 | This code was used for the analysis for *"Growth rates for coral reefs peaked at 25 °C through the Holocene"*
by Tonya Macedo and Robert van Woesik.
Some data in this project are derived from Hynes et al. (2024). Please cite their work if you use these data.
---
## Overview
- **Main dataset:** `Holocene_Reef_Gro... |
7d3e6c7156eb012007d3ca835834db863f7965d71e80e1276b8b63538524a0a2 | Text | 2,844 | 120 | # 📘 design_of_promoter_logic
This repository provides an AI tool to propose transcription factor binding site (TFBS) recombination with a promoter sequence to alter its original logic.
---
## 🚀 Getting Started
Follow the steps below to set up your environment and run the code.
### 1. Clone the repository
```bas... |
2d0ae4a65ac499f60e720339808ff45b051681333c2f36c094284fef1e1018bb | Text | 2,860 | 44 | # NetworkControlRichClub
This repository contains MATLAB scripts and example data used in the systematic analysis presented in the research paper "Exploring the Role of the Rich Club in Network Control of Neurocognitive States."
## Prerequisites
### Required MATLAB Toolboxes and External Software
The following MATL... |
fbabb664e2fda0072d8c85b9f74041d6907b2805c2d53a3ced3b82bb7e7324f3 | Text | 2,947 | 65 | # Brain Atlas - FDG
## Overview
This repository contains age-dependent and 3D Hoffman phantom harmonized 18F-FDG brain PET atlases generated using a high-sensitivity short-axial FOV PET/CT system. The atlases are provided in MNI space with different smoothing kernels for various neuroimaging applications.
## Atlas S... |
f20661f1cae0cdda446fdbda834381f09f1d71ee34f190f4b9c06749a932e3a4 | Text | 2,973 | 50 | [](https://github.com/fowler-lab/sbmlcore/actions/workflows/tests.yaml)
[](https://codecov.io/gh/fowler-lab/sbmlcore)
[
and
[IBC webpage](https://individual-brai... |
7ea7f7b4bd3daf8df47c79e029558657eaac34b09b8316c509a17c3d3bf9f0d4 | Text | 3,018 | 52 | # Neural encoding and decoding models for handwriting
## Overview
This repository contains the core codes for the paper Wang et al., 2025 "Cortical representation of multidimensional handwriting movement and implications for neuroprostheses".
## Installation
Set up a new environment with `Python==3.9` and using the pr... |
b1b371dba1cc1866778012bc7e94ba7c9a1f29f2b0ddb6938caccf017a6d4a2b | Text | 3,053 | 55 | # ECLARE: Efficient cross-planar learning for anisotropic resolution enhancement | [Paper](https://doi.org/10.1007/978-3-031-44689-4_12)
ECLARE is a self super-resolution method; no outside training data is required.
The only required input is the image itself and the output directory.
The journal manuscript is curren... |
35573cf2b5e0296e7a97446e25aedb2c40f8a2ff33638fe2f7b48b3b5aab57b7 | Text | 3,057 | 55 | <div align="center">
<h1>Changes of cerebellar vascularization in a murine model of apnea of prematurity</h1>
[](https://creativecommons.org/licenses/by/4.0/)
[](https://doi.o... |
dcc84483d45c6d35c2c194337201f6013528db77778c67c692ea4f7d59d678ee | Text | 3,087 | 44 | # NQS4VIB
This is an implementation of modal backflow (MBF) neural quantum states for anharmonic vibrational calculations [1].
The files are organized as follows:
- `nqs_vib.py` contains the MBF neural network design (with and without VSCF extension).
- `opt_tools.py` contains an implementation of the CoRe optimizer [... |
8dcd210061222a6451735e2116d32609f4dab86b4f9d9de9721a257066a751d8 | Text | 3,102 | 86 |
# THINGS-Mooney Database
[](https://doi.org/10.5281/zenodo.15340222)
<img src="/mooney_toolbox/example.gif" alt="Output GIF" width="150"/>
## Overview
The **THINGS-Mooney database** provides a collection of "Mooney-style" distorted images created from ... |
28ea309fab05d24a8e6fa3cad1e40335b608448a1acc042d26ad6c4fd97499a4 | Text | 3,126 | 55 | <div align="center">
<h1>Changes of cerebellar vascularization in a murine model of apnea of prematurity</h1>
[](https://creativecommons.org/licenses/by/4.0/)
[](https://doi.o... |
2dadb3da3648f8307737ae6876455c1956388b2f881f6be1bf8ce3e7a4adb25f | Text | 3,146 | 60 | **mtbi-structure-function-longitudinal**
Analysis code for a longitudinal study investigating structural and functional brain network changes in patients with mild Traumatic Brain Injury (mTBI).
This repository provides a complete pipeline to analyze connectivity evolution and its relationship with cognitive recovery... |
95550a0975542899219d0b2e8850735e62ebf7aac117c48609cd3c4696f14dc7 | Text | 3,167 | 35 | # RNA3DB
A dataset of non-redundant RNA structures from the PDB. RNA3DB contains:
- All RNA chains in the PDB, labelled with non-coding RNA families
- Non-redundant clustering of the above chains, suitable for training and benchmarking deep learning models
We provide periodically updated versions of RNA3DB in [JSON](... |
17a18180d16862ddcda088b4f4614495a421166a3646c4451c68bbba56e72214 | Text | 3,185 | 103 | # TSENN
This repository contains the source code and dataset for the **T**ensorial-**S**pectra **E**quivariant **N**eural **N**etwork (**TSENN**).
## Table of Contents
- [TSENN](#tsenn)
- [Table of Contents](#table-of-contents)
- [Install Dependencies](#install-dependencies)
- [Version-Specific Packages](#ve... |
61a0e82539a3e13119e454a686ef7de10a3c31b77d424e05d7e850d249041f7f | Text | 3,225 | 65 | # Overview
This repository contains the datasets, code scripts, and instructions for running the code implemented in the paper: *"Machine Learning-Based Identification of Abnormal Functional Connectivity in Obesity Across Different Metabolic States."*
Please note that this repository provides MOCK datasets and scripts.... |
a93a17ea44463769a68252ccd2ef0a653fb183d0057ce4fc706db0d639978059 | Text | 3,253 | 109 | ## DiffPharma
This repository provides the source code and pretrained models for the [arXiv](https://chemrxiv.org/engage/chemrxiv/article-details/684c1f943ba0887c3310534d).
## Dependencies
### Cuda environment
| Software | Version |
|--------------|---------|
| CUDA | 11.8 |
| cudnn | 8.9.7 |... |
862084bfbc13918371f61e85fff40f5f80d8475eac3411007c39b2efd4a5925d | Text | 3,266 | 24 | # Predict_Calcium_From_ECoG
Use ECoG signals to predict single neuron calcium activity
This Code is based on a previous work: Manley, J., Lu, S., Barber, K., Demas, J., Kim, H., Meyer, D., Martínez Traub, F., & Vaziri, A. (2024). Simultaneous, cortex-wide dynamics of up to 1 million neurons reveal unbounded scaling of... |
f4f280a93de5039867378d9306262dcd0ac1cf32c1df32105701d1e6711916cb | Text | 3,277 | 33 | Use ECoG signals to predict single neuron calcium activity
This Code is based on a previous work:
Manley, J., Lu, S., Barber, K., Demas, J., Kim, H., Meyer, D., Martínez Traub, F., & Vaziri, A. (2024). Simultaneous, cortex-wide dynamics of up to 1 million neurons reveal unbounded scaling of dimensionality with neu... |
1f93f609c67c0680f93bc2bf7bc1d554c785166d91b9f9088e3c586340c18019 | Text | 3,293 | 34 | # *Faecalibacterium prausnitzii*, depleted in the Parkinson’s disease microbiome, improves motor deficits in $\alpha$-synuclein overexpressing mice
Anastasiya Moiseyenko1,2, Giacomo Antonello2,3,4, Aubrey M. Schonhoff1,2, Joseph C. Boktor1,2, Kaelyn Long2,3,4, Blake Dirks7, Anastasiya D. Oguienko1, Alexander Viloria Wi... |
13d5708401a160b9e8f919f8e48364fd6d89eab4f7409c9f9ba136cd083ddf55 | Text | 3,297 | 99 | # Golden Ratio Organization in Human EEG: Analysis Code
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.3389/fnhum.2026.1781338)
## Ov... |
3566880290ab1b23522d58240f485ae90b9809c90f712758c805abb357f6e3c7 | Text | 3,304 | 43 | # ASCENT: Automated Simulations to Characterize Electrical Nerve Thresholds
[](https://github.com/wmglab-duke/ascent/blob/master/LICENSE) [](https://github.com/wmglab-duke/ascent/r... |
6d1638c3b37fa0da5e01f697fd93f40ed1e4c73292786a832836e89a0eb93e32 | Text | 3,304 | 67 | # Impact of CT dose on AI performance
This repository contains the code used to evaluate how CT dose variations affect the stability of radiomic and deep learning features, and their impact on AI model performance. Using a standardized multi-scanner dataset from a 3D-printed anthropomorphic phantom with liver anomalie... |
ad19e955cabd16d248e2fc7433ed17c720337a6d7e9bef37545965712da826b1 | Text | 3,323 | 74 | # Evolutionary Kuramoto dynamics unravels origins of chimera states in neural populations
The repository contains the source code, analysis workflow, and LaTeX manuscript
for the
"Evolutionary Kuramoto dynamics unravels origins of chimera states in neural populations"
paper by Thomas Zdyrski, Scott Pausl, and Feng Fu.... |
cc017aa3de2be7fcb9e204a9fde423f7ace9c82e702b6271f8e20e0d2e27a4dc | Text | 3,333 | 91 | # DPGNNPAM
A deep learning model that integrates path aggregation strategies and prototype-driven mechanisms for effective node classification on biological networks. DPGNNPAM captures both topological and attribute information, improving the prediction of drought-resistant genes in rice.
Below is the algorithm flowch... |
22ac8450aad623a47b7f9155a554fb99491e6edc6cd9cace27c7d80a0324af5b | Text | 3,366 | 99 | Early-Smoke-Fire-Detection
An intelligent vision-based fire and smoke detection framework that integrates a Vision Transformer (ViT) with the YOLOv8 detection architecture.
========================================
------------------------------------------------------------
Project Overview
--------------------------... |
d0cab903d63bce2480cce368a5ad74230f23f3be3a5b433869128207f7e1942c | Text | 3,404 | 47 | # optimap
[](https://cardiacvision.github.io/optimap/)
[](https://github.com/cardiacvision/optimap/actions/workflows/main.yml)
[ "Spatially targeted inhibitory rhythms differentially affect neuronal integration." *eLife*.** doi: [10.7554/eLife.95562](https://doi.org/10.7554/eLife.95562)
## Overview
This repository contains post-processing and analysis code for biophysical simulation... |
7c7ccbee1cc7d897f84feecf327dfb70a51e4e11bf196205f8204cd65e7214f0 | Text | 3,441 | 57 | demixed Principal Component Analysis (dPCA)
===========================================
dPCA is a linear dimensionality reduction technique that automatically discovers and highlights the essential features of complex population activities. The population activity is decomposed into a few demixed components that captu... |
3ab2605bdb0d650640e57b7b8b450e877d5f5825355ae312c9b8ce2923478ea6 | Text | 3,446 | 100 | Early-Smoke-Fire-Detection
An intelligent vision-based fire and smoke detection framework that integrates a Vision Transformer (ViT) with the YOLOv8 detection architecture.
========================================
------------------------------------------------------------
Project Overview
--------------------------... |
928f6eaad11014a12a165de9b3d33de6f48da4b90783e7471dd09f02ac2c8bc6 | Text | 3,463 | 99 | Early-Smoke-Fire-Detection
An intelligent vision-based fire and smoke detection framework that integrates a Vision Transformer (ViT) with the YOLOv8 detection architecture.
========================================
------------------------------------------------------------
Project Overview
-------------------... |
c1dfb5db47243be46c070a992b0f6d5b1c7cc44aa4f771b28d6a16dfe9d3cccd | Text | 3,489 | 32 | # tFUS-ESI-Analysis
These codes were used for the analysis of transcranial focused ultrasound (tFUS) EEG source imaging data as part of the study: Transcranial focused ultrasound induces source localizable cortical activation in resting state humans when applied concurrently with transcranial electric stimulation [1].... |
d126df9fbde51238339abe554168d8842c602ca6de4c058d7e4f02b177788218 | Text | 3,491 | 113 | # TSENN
This repository contains the source code and dataset for the **T**ensorial-**S**pectra **E**quivariant **N**eural **N**etwork (**TSENN**).
## Table of Contents
- [TSENN](#tsenn)
- [Table of Contents](#table-of-contents)
- [Install Dependencies](#install-dependencies)
- [Version-Specific Packages](#ve... |
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