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ad4bea5849ec22427942ce3462a666d7bd5ed7eae532337c9bbd8b9324e8f72d | Text | 2,287 | 82 | # TASC-DMD
MATLAB implementation of **Time-Augmented, Space-Contracted Dynamic Mode Decomposition (TASC-DMD)**.
> **Paper:** *[TASC DMD Paper — title and citation to be added after publication]*
---
## Repository Structure
```
TASC-DMD/
├── src/
│ ├── DMD_exact.m Core DMD solver with time-delay ... |
c399b012eb8c87c46a40eb293f221828eabf34799afdcbfaba89cb2215477f25 | Text | 2,295 | 53 | This is the code associated with the following research work:
Savadjiev et al. (2025) Automated diagnosis of usual interstitial pneumonia on chest CT via the mean curvature of isophotes. medRxiv preprint: https://doi.org/10.1101/2025.02.28.25322740
If you use this code, please cite the above preprint
* Input file o... |
edbb7ba9ef84522b30898b444bcb1d501da46b27523c2d603698d2226541f714 | Text | 2,300 | 80 | Data-driven deformation correction in X-ray spectro-tomography with implicit neural networks
====
Installation
-------
1. Clone the repository:
```
conda create -n CANet_alignment python=3.12.7
conda activate CANet_alignment
git clone https://github.com/wangting1907/CANet
cd CANet
```
2. Install packages:
```
con... |
51ac742e40b5211dedb022353700d4eec9b5d29266db4efcb197498d619b6aa9 | Text | 2,301 | 51 | # ⚠️ This tool is no longer under development
I recommend migrating to **[movement](https://github.com/neuroinformatics-unit/movement)**, a fantastic tool for drawing ROIs after pose estimation, plus much more.
# DLC ROI tool
A tool for drawing regions of interest (ROIs) on videos and analysing DeepLabCut videos.
__W... |
d28afb0bd019d0d63db84b325fc72376bc0633486fee41b318a9cd6b6154baba | Text | 2,303 | 63 | ClearMap
========
[](https://zenodo.org/badge/latestdoi/59701678)
[](https://twitter.com/intent/follow?screen_name=clearmap_idisco)
ClearMap is a toolbox for the analysis and regist... |
5b4265da94ee02914d1400400b919e80e83b21fa78a08273fc1ca4158c3010aa | Text | 2,309 | 51 |
# BENDNET
This is BendNet, a deep neural network developed for power detection in a tapered seven-core six-mode fiber. It predicts the fiber's bending radius and rotation angle by inputting the power of each core of the tapered seven-core six-mode fiber into the model. The following is the testing and evaluation proc... |
80ff63fbba47f6a2b7802bcce28a0b6a67e13d5634a8a5189bcd2ec534518252 | Text | 2,322 | 19 | # MPD-DF
**01 What is MPD-DF？**
The Multimodal Phenotyping Dataset of Driving Fatigue ** (MPD-DF)** is a publicly available dataset collected from 50 participants through standardized 2-hour driving simulation experiments. This meticulously curated resource integrates multidimensional subjective and objective metrics... |
84fe0765d7eb31739f8cdfddb30c286119cd334a67dee03356a398e25c3f3f1e | Text | 2,322 | 59 | # D-LIM (Direct-Latent Interpretable Model)
# Overview
D-LIM (Direct-Latent Interpretable Model) is a neural network that enhances
genotype-fitness mapping by combining interpretability with predictive accuracy.
It assumes independent phenotypic influences of genes on fitness, leading to
advanced accuracy and insight... |
786bb887c14b5bfc18c6efe2c153f314b029cdc92a33ab08d0852ba127d12e2b | Text | 2,328 | 49 | # Larval-ORN
Data and analysis of fruit fly larvae olfactory receptor neuron (ORN) population responses to a broad panel of odors. This folder contains code and data from the paper, "Structured odorant response patterns across a complete olfactory receptor neuron population."
Quick Links
--------------------
* Raw ... |
b23ef8f2dad0185b369825e96bb27ba86ffb5c022276fa0e9caf9b5e7968cddb | Text | 2,346 | 41 |
<div style="float: left">
<h1> <img src="https://user-images.githubusercontent.com/47796061/97297065-6c161d80-1849-11eb-949b-390894dd41fa.png" width="100" height="100" valign="middle"> ERICA: Emulated Retinal Image CApture </h1>
</div>
## Description
ERICA is a simulation tool for generating synthetic high resol... |
28cf86cd0c40826152428d044ca78d665f983570adea94ecd025c19b86306388 | Text | 2,374 | 61 | # DMFF-DTA: Dual Modality Feature Fused Neural Network Integrating Binding Site Information for Drug Target Affinity Prediction
DMFF-DTA is an innovative dual-modality neural network model that effectively integrates sequence and structural information from both drugs and targets to achieve accurate drug-target affini... |
264a9bc9484f2d4ca2d65c1fa09bc5434282e85f21c59842ea1a2bfa122925bb | Text | 2,378 | 36 | # READMe
This repository contains the models and supplementary data for the paper *A Neural Network Multi-Task Learning Approach to Biomedical Named Entity Recognition* by *Gamal Crichton, Sampo Pyysalo, Billy Chiu* and *Anna Korhonen*.
The supplementary data can be found in the file *Additional file 1.pdf*.
The... |
5a1e55ff03e3520fb364c440d4a003a167a1655c28ec95ea6865ab2b05476206 | Text | 2,379 | 28 | # 🤖 ALCF Inference Endpoints
> **Unlock Powerful AI Inference at Argonne Leadership Computing Facility (ALCF)**
For the latest documentation, refer to [ALCF Inference Docs](https://docs.alcf.anl.gov/services/inference-endpoints)
If you use ALCF Inference Endpoints or the Federated Inference Resource Scheduling Too... |
d7e082b1f1e60f6cb74176970d4faca2c03068c61257b2cb07adc07546958a15 | Text | 2,384 | 14 | This repository holds the data and source code for the following manuscript:
[Minikel EV, Painter JL, Dong CC, Nelson MR. **Refining the impact of genetic evidence on clinical success.** _Nature_. 2024 May;629(8012):624-629. doi: 10.1038/s41586-024-07316-0. Epub 2024 Apr 17. PMID: 38632401; PMCID: PMC11096124.](https:... |
422130bc769239c671b14b0bc2b6b9d2bfba02991a5e51181b2389526a3f4e92 | Text | 2,389 | 82 |
ChemPotPy, CHEMical library of POTential energy surfaces in PYthon
==================================================================
Jan. 17, 2025
Authors: Yinan Shu, Zoltan Varga, Dayou Zhang, Donald G. Truhlar
University of Minnesota, Minnesota, United States
ChemPotPy is a library for analytic representation o... |
39f289b9b898a9e4aa9dee9bf708619e0921a64887c51b45d30acb053ece0d96 | Text | 2,411 | 26 | This data set is for the following paper:
McManis, A., et al. (2026) Understanding Glioblastoma Dynamics Using 3D Organoids and Engineered Extracellular Matrix, Advanced Science.
Associated Publications:
-Final Article:
McManis, A., Jimenez, C.A., Shirolkar, A., Syed, R.u.R., Mallick, S., Murphy, M., Gaharwar,... |
f87c29a530831274a9e2a49000dbf9837a4723df69a01b108edda0bfdd8ad7e5 | Text | 2,412 | 86 | # Supplementary Material — Code and Derived Results
This repository contains the code and derived outputs associated with the manuscript:
**Claudio Alemán-Morillo, Natalia García-San-Martín, Richard AI Bethlehem et al., "Early deviations from normative brain morphology and cortical microstructure in schizophrenia spe... |
cb505a886cfece277965fb4a12f617c57c2f216e242963acb3132b36316c7a35 | Text | 2,445 | 82 | # easyshiny [](https://lifecycle.r-lib.org/articles/stages.html#experimental)
`easyshiny` is a R package to quickly create an interactive web application to visualise and explore single-cell data.
## Installation
Run the follo... |
645f03661b222974b3e8bd55f9affae7c55d280a280a0e5a46de29a47e5bf034 | Text | 2,451 | 31 | # Modelling part of Manoim-Wolkowitz, Tunc et al.
This repository includes the code for the mushroom body model used for investigating the role of lateral Kenyon cell - Kenyon cell interactions in mediating efficiency and specificity of learning.
## Repository structure
Folder "codes" contains all the scripts, and f... |
a936b3697117d49f9d9ae258eaa6b419dab2193b1a98c8902b847ad9a1eea9ff | Text | 2,453 | 34 | # NARVI: Neural network-Assisted RNA Velocity Imputation
NARVI is a deep learning framework that recovers RNA velocity for genes excluded from calculations using conventional tools.
This framework learns the relationship between the expression patterns and velocities of computable genes.
## Abstract
Existing RNA vel... |
35ccaf6468c063c4540bd49f4377f004ed62706e1d88d4311e3ec468d1974dd2 | Text | 2,457 | 58 | # IBIO-Banyuls2023-Python
## Working with Google Colab
### Opening Colab
Got to [Colab's website](https://colab.research.google.com/), and in the popup window click on **Github**, then in the seach bar paste the following :
```
https://github.com/EmeEmu/IBIO-Banyuls2023-Python
```
You can then select the notebook y... |
c883b9e72f47a8cfb43c03d03b2c4546d633e9efee0e6503f6a2c69da71e4b61 | Text | 2,462 | 55 | # iEEGcomplexity
**Indexing intracranial EEG (iEEG) signal complexity**
This repository contains code and resources to compute, aggregate, visualize, and model intracranial EEG signal complexity markers, with applications to the **MNI-Open iEEG Atlas** dataset.
## Repository structure
### `app/`
Streamlit applicati... |
8733d6b58b718b951a618e66f2f4600d20416f6e02c7b411db013989c83ee76e | Text | 2,470 | 65 | # hybrid-cnn-vit-plant-disease-diagnosis
This repository contains the implementation of a hybrid deep learning framework for plant disease diagnosis using leaf images. The proposed approach integrates a Convolutional Neural Network (CNN) and a Vision Transformer (ViT) to effectively capture both local texture feature... |
00b6ce42c2288651626029d631f1f00f2a99c3a5537651babb0d7a5f38bf2791 | Text | 2,474 | 67 | # MÖBIUS REM-gating analysis code (COMMSBIO-25-8788A)
This package provides a **minimal executable pipeline** to reproduce the reported REM-gating indices and figures from **local derived feature exports**.
## Scope and governance
- **No PSG/EEG time-series or clinical metadata are distributed**.
- Inputs are **deri... |
bac7fbafd4849bbb2aaaff6bce2e0d704727e79cf5370d6860da4fd3ba8ec04f | Text | 2,478 | 55 | # Reasoning about Self and Others
This repository contains code and links to data from the manuscript: Hierarchical systems in the default mode network when reasoning about self and other mental states
## Description
Humans spend time contemplating the minds of others. But this ability is not limited to external a... |
5433ce76e9e7afccfcae0ce71a35acc42bf99f134a310cc9f96dd9d5fc9bcdf5 | Text | 2,482 | 30 | # README file for Responsibility study
## Contents
This repository contains Matlab code (.m) and data files (.mat, .csv, .nii) required to reproduce the results of the study entitled "A neural mechanism of social responsibility", by Maria Gaedeke, Tom Willems, Omar Salah Ahmed, Bernd Weber, Rene Hurlemann, and Johanne... |
6051141e5a4cf6481c8240197764e24390c952536db4c6483b8476b382c07926 | Text | 2,505 | 112 | # SwinSite: Protein–Ligand Binding Site Prediction
**SwinSite** is a deep learning-based method for predicting protein–ligand binding sites using a hybrid of Swin Transformer and 3D CNN architectures. It processes protein structures in 3D and outputs likely binding regions.
---
## Installation
### 1. Create conda e... |
11343a019061ab0a8363f9b80c073493704cb49db93d28bb8a7f8c5898af334a | Text | 2,506 | 22 | # PlantScannerDataset
This repository provides a curated subset of the MaizeLeaf Health Dataset, a video database capturing maize (Zea mays) plants under controlled conditions to facilitate automated detection of foliar diseases. The capturing and recording device is a plant scanner crafted and developed Faculty of Hea... |
b37242ddde9c148c3bfd91f76d9fa81cdac5f1b138693dec24510e2849bc0238 | Text | 2,507 | 59 | # NTCP Analysis and Machine Learning Pipeline
A five-stage Python pipeline for DVH processing, dose metrics and visualization, NTCP modeling (LKB/RS),
machine-learning prediction (ANN/XGBoost), output QA checks, and clinical factor analyses.
Designed for reproducible research and publication-quality outputs (600 d... |
62c78fa0703f90d8bce2d22c9388d1e6d45ee730dc06bd2da35af722df3fe206 | Text | 2,515 | 39 | Please contact willn2@illinois.edu with questions or requests for additional data.
The .mat files in each folder consist of the data collected directly from experimental measurements: probe force, probe displacement and scan plane RF data.
Each folder has the following .mat files. Our naming convention refers to the... |
eb1e48453aa4d496ba61fbfb15a4f0f5cb39512b48262a8c310989a6a44d1235 | Text | 2,515 | 47 | # AGED
*Attention-Guided Enhanced Deconvolution for Reference-Free Spatial Transcriptomics Analysis*
`AGED` is an analysis tool that integrates probabilistic modeling with neural attention architectures to enable reference-free analysis. In the firs... |
e16eee9e70fbb065d29b18c42b2d6b5924f283aeaeda0d3af7b1f561f50cd4ad | Text | 2,519 | 87 | .. image:: https://travis-ci.org/eltonlaw/impyute.svg?branch=master
:target: https://travis-ci.org/eltonlaw/impyute
.. image:: https://img.shields.io/pypi/v/impyute.svg
:target: https://pypi.python.org/pypi/impyute
Impyute
========
Impyute is a library of missing data imputation algorithms. This library was ... |
457b451f07b3d581ebbcbde9e8ea5b3cda7e49f11f58960a3513a455a401a6ff | Text | 2,527 | 70 | # Functional gradients dissociate between cortical layers
This repository contains the complete pipeline to reproduce the analyses and
figures from the manuscript:
> **Functional gradients dissociate between cortical layers**
> Degutis, J.K. *et al.* (2026)
## Repository structure
```
.
├── src/
│ ├── preprocessi... |
8cce1434b9704366ea46ca875ada15d30e652062a3f86cd87f8e4b9d51eb853d | Text | 2,532 | 90 | # GROMACS 批处理
## 环境
- 系统：Linux
- Sobtop：1.0
## 使用方法
### 下载Sobtop
从[这里](http://sobereva.com/soft/Sobtop/)获取Sobtop，然后将本脚本置于Sobtop目录。在Sobtop目录下运行：
```shell
chmod +x *
```
### 准备文件
1. 准备一个工作目录，首先放入含有蛋白相关文件的文件夹，并将其命名为<code>protein</code>，下面是一个示例：
```plaintext
work_path/
└── protein/
├── posre_Prote... |
cfda145e76c74f0f7e2b6c06b2c45a451004e292497eb1e53d68441ff3d6a11f | Text | 2,532 | 39 | # EpilepsyEpigenetics
This site contains the scripts used for the analyses performed in our research paper, entitled "Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy". This paper is the process of peer review.
For details on using the scripts, refer to RScripts/READM... |
9aab77612444818422e9c693210933db3e71404b3c02dd2b9b2576f4a41be52a | Text | 2,534 | 32 | # Modelling part of Manoim-Wolkowitz, Tunc et al. 2026
This repository includes the code for the mushroom body model used for investigating the role of lateral Kenyon cell - Kenyon cell interactions in mediating efficiency and specificity of learning.
Published paper can be found under: https://doi.org/10.1016/j.cub.2... |
6bbd71f03286a270b42e9fe446a37f7d11b28e9370b7a7f87fa7c304cabc828e | Text | 2,538 | 61 | # Neural Network Training for TURBOMOLE-Compatible Local Mixing Functions (n-LMF)
This repository provides a Python script used to train neural networks that serve as local mixing functions (n-LMF) within Density Functional Approximations (DFAs). The script is specifically designed to produce neural-network-derived pa... |
1576509574b07ca2f25786eed503e6b202603b58d5677411e961ee7d127db611 | Text | 2,542 | 81 | # Reconstruct single-cell resolution from spatial transcriptomics with CellRefiner
CellRefiner is a physical model-based method that integrates a scRNA-seq dataset with a paired spatial transcriptomics (ST) dataset to generate single-cell resolution in the imputed ST data. CellRefiner models cells as particles connec... |
a4e9c26292c2d528f775a729662e5c6b7279ccc2dee373e1938526c69ad2f378 | Text | 2,547 | 23 | # immune-cell-profiling-anti-gad65
This repository contains all analysis code associated with the article **"Immune cell profiling reveals expanded stem cell-like memory T cells in anti-GAD65-associated neurological syndromes"**
## Overview
The code in this repository reproduces the main computational analyses in t... |
936245e15bee4c262e61423fcfcc342a8edeb790ec912b55b572416414557cbb | Text | 2,553 | 59 | # connattractor
[](https://github.com/pni-lab/connattractor/blob/master/LICENSE)
[](https://github.com/pni-lab/connattractor/releases/)
[
But if you wait around awhile, I promise you
------------
## ANTsPy/ANTsPyNet
```
import ants
import antspynet
# ANTsPy/ANTsPyNet processing for subject IXI002-Guys-0828-T1
t1_file = "IXI002-Guys-0828-T1.nii.g... |
1e127495bf9fa0068d1a1b6b53c983a1e5cd967186eed60d9dc32edc5f2f48f5 | Text | 2,573 | 93 |
# Equivariant Diffusion Crystal Structure Solution from Powder X-ray Diffraction (XRDSol)
The XRDSol is a equivariant diffusion model to solve crystalline structures by iteratively refining atom coordinates from powder XRD. XRDSol has solved thousands of entries that were previously unresolved or unlabeled. Compared... |
9312610a8c66d24e8d4e0d8e4db793344a3e00982b093ac06a309b7335f911a3 | Text | 2,581 | 54 | # Pseudo Population and RNN Strategy Analysis
## Tested Environment
- Python: v3.10
- OS: Windows 10/11
- No additional software installation required.
## Dependencies
This project requires the following Python libraries:
- `numpy`
- `scipy`
- `scikit-learn`
- `pytorch`
- `pandas`
- `matplotlib`
- `seaborn`
See also... |
9e3bbb271b2b137a1249df86cce6920bf6c541f3d1488e6201d86d795b248ad9 | Text | 2,605 | 37 | <img src="docs/src/assets/logo_main.png#gh-light-mode-only" width=400>
<img src="docs/src/assets/logo-dark.png#gh-dark-mode-only" width=400>
[](https://github.com/Tinggong/Microstructure.jl/actions/workflows/CI... |
e8f272e76d029abf51bd3c89b6849faf0fe4025906767e30932d7c71e048938e | Text | 2,612 | 20 | # CP_tutorial
This public GitHub repository provides a tutorial for setting-up BE-META simulations of cyclic peptides.<sup>1,2</sup>
• To access the step-by-step tutorials, please see the Word documents in the /Tutorials directory, which includes documents with step-by-step explanations for building cyclic peptides i... |
8e25620f9eee9412e9dd0321a45193c20687584e410d67f4e90382e8539e9dd9 | Text | 2,614 | 46 | FmriTools
===
[](https://github.com/haenelt/FmriTools)
[](https://www.gnu.org/licenses/gpl-3.0)
Python package for processing and analyzing high-resolution fMRI data. Various scripts are includ... |
f1cef45e31d0979dff06e91eb08df2f6808adef3323787cfce83b6732c75e1d3 | Text | 2,628 | 31 | 
# MIDOG++: A Comprehensive Multi-Domain Dataset for Mitotic Figure Detection
> The prognostic value of mitotic figures in tumor tissue is well-established for many tumor types and automating this task is of high re... |
11bd3d3bcb252e87998ef1cf8badea43ac5657392a4852fdaccc4d042ac49864 | Text | 2,635 | 84 | # GASHAP: Alzheimer's Disease Prediction via an explainable CNN using Genetic Algorithm and SHAP values
This repository contains the implementation of the **GASHAP** framework introduced in:
> Mohammad Zahedipour, Mohammad Saniee Abadeh, Shakila Shojaei (2025).
> *Alzheimer’s Disease Prediction via an Explainable CN... |
5a2995808ad649d90ba267f5776d0a8276935caa35016b8c2699710d3b5c423c | Text | 2,635 | 41 | # MRIcron / NPM / dcm2nii
##### About
MRIcron is a viewer for brain imaging data.
##### Installing
You can download the software from several locations:
- Download from [NITRC](https://www.nitrc.org/projects/mricron).
- Download from [Github](https://github.com/neurolabusc/MRIcron/releases).
- Run ... |
a29a29d2d16b6761b0cdb1c0825b4b3b414d5bf3bed43c1c17f4db52b83c53cd | Text | 2,636 | 66 | # ColocalizationDeconv.ijm
**FIJI/ImageJ macro for quantifying colocalisation between two fluorescence channels after deconvolution.**
This macro automates the analysis of colocalisation between two fluorescent markers in microscopy images. It performs iterative deconvolution, applies intensity thresholds, and measur... |
7f2d48b1af9c8000e9cda14f0b6c57c2678057bea24d34c69a7d345a6dba40d1 | Text | 2,638 | 36 | # Oesch_et_al_Trial_History_ACC #
Analyses from "Anterior cingulate neurons combine outcome monitoring of past decisions with ongoing movement signals", Lukas T. Oesch, Makenna C. Thomas, Davis Sandberg, João Couto and Anne K. Churchland: https://doi.org/10.1101/2025.04.11.648398.
This repository contains the analysis... |
1180a6be6c2220eb5f4a4f1193f63f93c7f0a07a519b81aa7d2e5d05f4ee68b5 | Text | 2,643 | 87 | # Neuronal heterogeneity of normalization strength in a circuit model
> Song, D., Ruff, D., Cohen, M., & Huang, C. (2026). Neuronal heterogeneity of normalization strength in a circuit model. Science Advances.
> DOI: [https://doi.org/10.1126/sciadv.adv9396](https://doi.org/10.1126/sciadv.adv9396)
[, in ISMIR 2020.
## Dataset Zip File Structure
* index.xlsx: it contains a list describing the baisc information of each index f... |
10ce728fd0283dc6c482a4e1ba7f831718d0c4009292a420b0294f8d7a886b10 | Text | 2,669 | 48 | # IID4constancy
Code from the study "Deep neural networks trained for estimating albedo and illumination solve lightness constancy differently than human observers."
## Forwords:
The directory is organized in two sub-directories:
- The directory "RENDERINGS" contains the code we used to generate our training and te... |
e5ed36cd822ad70c31efbd60f7ee3400eb4da4070e8453e1ea65c61bea74abbb | Text | 2,679 | 70 | ====================
Changes on this fork
====================
I forked and changed brainspace so that I can return and analyse the transformation matrices
derived in the procrustes alignment (and the number of iterations used for alignment).
====================
BrainSpace
====================
.. image:: https://... |
690f9fd9737ec606ec7658424d9a160d216c6c5aeb93fabde7e66125cd5e133e | Text | 2,713 | 70 | # README #
### Summary: ###
Jupyter Notebook & train data for recreating the normative charts from [Dimitrova et al., (2021)](https://academic.oup.com/cercor/advance-article/doi/10.1093/cercor/bhab039/6206863).
This notebook will allow the user to
* run Gaussian Process Regression (GPR) on the normative volumetri... |
a02180e3183f40732d23bbb485c8e9a930d120bfed8b8b12fdb8157a6a742af8 | Text | 2,714 | 68 | # Deep-Generative-LesionDeficit-3D
3D deep generative lesion–deficit mapping model used in Tangwiriyasakul et al., Deep generative computed perfusion-deficit mapping of ischaemic stroke (Communications Biology, accepted with minor revision)
Companion Code for:
Tangwiriyasakul et al., Deep generative computed perfusion... |
2f5b69d75ddc2f18d1dd65ffa253adc57a5df89a1c0b80b5c5f8aed533d3b3a2 | Text | 2,715 | 35 | # NovaScope
NovaScope is a [Snakemake](https://snakemake.readthedocs.io/en/stable/)-based pipeline designed for processing spatial transcriptomics data generated from [Seq-Scope](https://doi.org/10.1016/j.cell.2021.05.010). Currently, it is optimized for handling spatial arrays produced by the Illumina [NovaSeq 6000](... |
1d2b9cad9fc99ab6f5b981ddff387d4ff651f767fcb6d6d5d44928c505b21d2a | Text | 2,716 | 74 | # EEG-Based Dataset Explicitly Targets the Transitions between Sitting and Standing for Exploring Neural Activation Patterns in Motor Imagery and Execution
A framework for EEG-based Motor Execution (ME) and Motor Imagery (MI) classfication using using the dataset targeting sit-to-stand and stand-to-sit transitions, re... |
87e9cf010bdf2100216c20a567bcd65c64d92dd6dbaeeb1d14b99f7677156d8e | Text | 2,716 | 47 | # EIANN: A framework for training deep neural networks with E/I cell types and biologically-plausible learning rules
[](https://doi.org/10.1016/j.celrep.2026.117159) (Paper)<br>
[... |
2077c733d8bb8ca966e0b7080d2666d9b445a3e7ebb1eab700801108df4962a8 | Text | 2,719 | 68 | # ofc_schemas
This repository contains the analysis and figure-generation code accompanying the manuscript
**“Persistent representation of a prior schema in the orbitofrontal cortex facilitates learning of a conflicting schema.”**
All scripts and notebooks reproduce the primary analyses and figures using the datase... |
3506627e019d8f56e9ef178aa3aadec904d32c6c3669fa8f4f81d302133048bd | Text | 2,729 | 100 | # Equivariant Graph Hierarchy-Based Neural Networks (NeurIPS 2022)
Jiaqi Han, Wenbing Huang, Tingyang Xu, Yu Rong
[](https://github.com/hanjq17/EGHN/blob/main/LICENSE)
[**[Paper]**](https://arxiv.org/pdf/2202.10643.pdf) [**[Poster]**](assets/poster.... |
3e44c740f6cc063a0275e051df84208344699a1593c82f07f416740357c5aa59 | Text | 2,732 | 38 | # `ivim` - An end-to-end python package for intravoxel incoherent motion (IVIM) analysis of diffusion MRI data
[](https://github.com/oscarjalnefjord/ivim/actions)
[ for current links, a list of
contributors, some history, documentation, descriptions, links for our various projects, Javadocs, and more.
# News
We are trying out a new Tetrad [ReadTheDocs manual](https://tetrad-manual.readt... |
d45d01bfd08f05ba9869adbddbf811adad7bc07871252cd2c852868570831318 | Text | 2,767 | 61 | # Hy_CP_Sorting
This repository contains the MATLAB code developed for the electrophysiological analysis of Multi-Electrode Array (MEA) recording in *Hydra vulgaris*
## Description
The code permits to extract the main electrophysiological parameters, perform the contraction pulse (CP) sorting and compare different d... |
aed29a2e8ab224fee7ae96437c4b074956b52c33b2d5fb2514070a505985f8e4 | Text | 2,789 | 36 | Gene expression matrix dataset of Zeng et al.
H5AD:
2023-05-05-Brain-RIBOmap.h5ad: H5AD file containing the translatomic data of two replicates for RIBOmap
2023-05-05-Brain-combined.h5ad: H5AD file containing the translatomic/transcriptomic data of two replicates for RIBOmap and one replicate for STARmap
Cell c... |
087a124f29abfb6dad40586686f57cc898ee07cc989af4b20a580b40c7be51e6 | Text | 2,804 | 67 | # ProTact
Source code for "Accurate Protein Contact Prediction through Surface-informed Geometric Invariant Learning"
## Install requirements
### PSAIA
Please follow the [DeepInteract#installing-psaia](https://github.com/BioinfoMachineLearning/DeepInteract#installing-psaia) to install the PSAIA tools while the ```p... |
dbccefdb1004a51b7c220ff2aa8c07db8606b070b200e94e7814326bac6a9d8b | Text | 2,808 | 83 | **Unit tests and coverage**
[](https://github.com/cpp-lln-lab/template_PTB_experiment/actions)
[, containing all scripts needed to gen... |
8f9a9411676dfba1a095630062572b0a02e8f63613a99dca79d18c0c95a2053f | Text | 2,861 | 89 | # Reconstruct single-cell resolution from spatial transcriptomics with CellRefiner
CellRefiner is a physical model-based method that integrates a scRNA-seq dataset with a paired spatial transcriptomics (ST) dataset to generate single-cell resolution in the imputed ST data. CellRefiner models cells as particles connec... |
7156f01560c223f1911d319c856d4f6562ee3b00e5dcd4a346d2c6b84a01713d | Text | 2,865 | 64 | # Savas-et-al-2025-Drosophila-SELK
This is code to replicate connectomic & scRNA analyses in Figures: 3D-E, Extended Figures: 2C-F, 7A, 10C, 11C from: <br>
Savas et al. (2025) Feeding Decision-Making by a Single Neuron via Disparate Neurotransmitters <br>
https://doi.org/######
## Getting Started
Download this repos... |
646ac9da8a3eddb6eb7373c62722dbc70b7155d47146efe9ee5fd60e655ac205 | Text | 2,877 | 38 | # VeloVAE - Variational Mixtures of ODEs for Inferring Cellular Gene Expression Dynamics
## Introduction
The rapid growth of scRNA-seq data has spurred many advances in single-cell analysis. A key problem is to understand how gene expression changes during cell development. Recently, RNA velocity provided a new way to ... |
3046aff65902fa7a75944c5f0b46375917f9d47f1ff627238ba8a4f395f76ac6 | Text | 2,879 | 103 | optoBurst.m
Description
optoBurst.m is a MATLAB function for peri-event analysis and optogenetic tagging of in vivo tetrode electrophysiology data. The script aligns single-unit spike activity to behavioral and optogenetic events, computes baseline firing and burst statistics, and extracts spike waveforms and continuo... |
97741413b7a8556d56f3f092ba6f5a069331384304d70aed5dbe3e3aee9c10c8 | Text | 2,900 | 68 | 
# Subcell
Bash script to filter cluster-specific reads from scRNA-seq data.
- version: 0.5.3
- contact: <ricardo.santos@nms.unl.pt>
## Index
1. [Introduction](#Intro)
2. [Installation](#Installation)
- [Docker image](#Docker-image)
- [Anaconda environment](#Anaconda-environm... |
b6dcc42ce69716a2f648ddfb3141ec614fb004bcc5216a8d6bb52962a092e398 | Text | 2,900 | 72 | # CellRake 🔬
<img src="./CellRake.svg" style="width: 100%;" alt="CellRake">
## Why this package?
**CellRake** is a Python package that analyzes cells in fluorescent images. It provides tools for image segmentation based on [Scikit-image](https://scikit-image.org/stable/), model training and prediction based on [Sci... |
f051a8acac84f409679997415c4656c16ff4982cb40c7cfe398f538b72eee4c4 | Text | 2,901 | 69 | The NAStJA Framework
==================
Neoteric Autonomous Stencil code for Jolly Algorithms
The NAStJA framework provides an easy way to enable massively parallel simulations for a wide range of multi-physics applications based on stencil algorithms.
It supports the development of parallel strategies for high-perfor... |
bb389ec35384318b9730b0fb2169b64992b22dd26d593714bc4656a886082897 | Text | 2,904 | 82 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# About the project:
- this is a repository of an R project containing code and source data
for the paper **Neural Connectome of the Ctenophore Statocyst**.
Contributed by [Jékely
lab](https://www.cos.uni-heidelberg.de/en/research-groups/ga... |
aed1b1569ba6b67722d40fb19152fe1c58a2a21910a62d3c67df2be5f79bf22e | Text | 2,926 | 69 | # LexPredict Legal Dictionaries
==================
## Purpose
Many academic and commercial applications of natural language processing and machine learning to text can benefit from a controlled lexicon of expert-selected terms (i.e., a dictionary). This is especially true of highly technical language, such as legal te... |
3896022fa4be6c4cbc29f5dfa3b4a63d779cc0f1389a6cf60e868dab3dc51e3d | Text | 2,940 | 45 | <p align="center">
<img width="300" height="300" src=https://github.com/TNTurnerLab/HAT/blob/main/doc/logo/small_logo_test_2.png>
</p>
Hare And Tortoise, HAT, are two _de novo_ variant callers developed by the Tychele N. Turner Lab at Washington University in St. Louis Medical School. Hare, as seen in [Ng et al. 2... |
7bf754b9982516bf3b2bfbda08fe4a3e04fa8df3629ebdf718000373f5a85890 | Text | 2,954 | 111 |
# Cluster Haptic Texture Dataset: Haptic Texture Dataset with Variety in Velocity and Direction of Sliding Contacts
The Cluster Haptic Texture Dataset is a comprehensive dataset for haptic texture research. This dataset provides haptic texture data with various sliding velocities and directions.
This repository conta... |
12aee1ca4ae7b07c4027ec467f1a1efc981beec377ee448f7086bab20c9db6f6 | Text | 2,966 | 72 | # Scilpy
[](https://github.com/scilus/scilpy/releases)
[](https://codecov.io/github/scilus/scilpy)
[](https://opensource.org/licenses/MIT)
[](https://pypi.org/project/neuroCombat/)
[![PythonVersion](https://img.shields.io/pypi/pyve... |
2de0b894325716ea459e045e0e121ed129eae910b9394741473d1a5ff3e18b24 | Text | 2,973 | 84 | # sesl - Structural Eigenmode Source Localisation
A Python package for source localisation using the structural eigenmode approach.
## Reference
If you use this code in your research, please cite:
>Siu, P. H., Karoly, P. J., Mansour L., S., Soto-Breceda, A., Kuhlmann, L., Cook, M. J., & Grayden, D. B.
>“Structura... |
8ef195c350ae36e2bfd1251ce65d6a3e3e1efa74aa373b381e84ef05d0d4d1d5 | Text | 2,998 | 35 | <p align="center">
<img width="150" src="./Images/KathleenWang_for_ezTrack.png">
</p>
# Behavior Tracking with ezTrack
This page hosts iPython files that can be used to track the location, motion, and freezing of an animal. For the sake of clarity, these processes are described as two modules: one for tracking an an... |
4ce54fa9aff8be8c09551f945de2693048d190dadcf2dad78b2546bc510c7c67 | Text | 3,000 | 35 | [](https://github.com/wwu-mmll/mccqrnn_docker/actions/workflows/docker-publish.yml)
# MCCQRNN Docker
This repository provides an docker image for the MCCQRNN Model.
## Usage
Make sure you have installed docker and nvid... |
725a015cc49f6539578bb2fcf62e80dd0f6f904ca34bf9fa8d31ffc8765e5796 | Text | 3,003 | 82 | # Biologically Informed code
This is the code for the paper:
C. Sourmpis, C. Petersen, W. Gerstner & G. Bellec
[*Biologically informed cortical models predict optogenetic perturbations*](https://www.biorxiv.org/content/10.1101/2024.09.27.615361v1.full).
Contact:
[christos.sourmpis@epfl.ch](mailto:christos.sourmpis@ep... |
90439d16e7f6b70c7253ec79f5febea14dc4ec59099eeb916a79e84b5352aa93 | Text | 3,021 | 51 | [](https://doi.org/10.5281/zenodo.7037853)
# 3D_spots_count
## Description
These two scripts allow for different analysis about counting spots.
* [count_3D_FISH.py](https://github.com/imcf-shareables/3D_spots_count/blob/main/count_3D_FISH.py) counts the... |
40dddf01a08bc78508430c391f5316aa785daa152fa14ee7adcecc923c71146f | Text | 3,022 | 55 | # LipidLocator
Shiny App to analyze spatial lipidomics data
> **Note:** If you are using the files directly from GitHub, please download the necessary data files from [https://doi.org/10.5281/zenodo.15112789](https://doi.org/10.5281/zenodo.15112789) before running the app.
> **Test Data** Test data can be downloaded ... |
d6aa5143c71f1d190b7723fc2520acb645c0d9396bbbd2025d68ee17830c7efa | Text | 3,022 | 64 | Deep Ensemble Encoder Network (DEEN)
Overview
Genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with various heritable human traits and diseases. Traditional polygenic risk scores (PRS) capture only simple linear genetic effects across the genome. To a... |
304f25c1c6acb27a7c3877880730bafa244e38c96b0af5d3489e9ea290a212f3 | Text | 3,041 | 91 | # MOF H₂ Storage via ANN + Equilibrium Optimizer (EO)
This repository hosts the MATLAB implementation used in the paper:
> **Accelerating Discovery of MOFs for Hydrogen Storage via Machine Learning in Energy‑Related Applications**
> *S. Fallah Kheirandish et al., YEAR*
> (Add DOI once available)
The code trains/... |
4ef7ab50445f547ec628c0eca46d58c9c74db0eedf8993ec2c2609bb4f536bf2 | Text | 3,043 | 72 | # Multiscale Segmentation using HiP-CT
This is the official repository for the publication entitled **Multiscale Segmentation using Hierarchical Phase-contrast Tomography and Deep Learning**
# Folder Structure
```
├── LICENSE
├── main.py
├── notebooks # Example notebooks
├── pyproject.toml # Python environment r... |
86b2b3bb567c5deabf3184239cc53ef16f98771e6df63059035a1552b2b33e70 | Text | 3,047 | 105 | # Bilingual Reading fMRI Dataset (Chinese–English)
## Summary
This dataset contains BOLD fMRI responses from Chinese–English bilingual human subjects who read a set of natural autobiographical stories in both Chinese and English. Functional data were collected from six subjects, each scanned across four sessions on f... |
05dfdd2be36177aed25a87dc594635abbd86cab42c66a03bf91f54c59eeb7ab6 | Text | 3,054 | 39 | # Overview
This repository contains a brief introduction to an **ex**act **set**-based gene association test statistic (**exset**).
Existing methods to test a gene-based association null hypothesis using the sum of SNP chi-squares in a gene-specific set rely on permutation, simulation, or approximation since the null... |
b262d32ae4002ff3c14ad2642decb3324c17549b6c603f42cd86a7606f63ba7d | Text | 3,059 | 92 | # 颅脑CT高分辨率重建（Brain CT super-resolution）
本代码仓库相当一部分代码来源于https://github.com/leftthomas/SRGAN
训练环境依赖位于environment.yml
## 输入
输入数据已经预先将dcm的格式转为NIFTI格式（.nii），并将像素CT值截断至0-100（常见颅脑软组织CT值密度），具体的转码程序参见我的另一个[代码仓库](https://github.com/hwr9912/ToolBox.git)。
| 代码名称 | 作用 |
| ---------... |
899b0d9a4790003cb58983fcd2d3a0323b2d18f2f2a6b2b14efcc303ed9298a4 | Text | 3,062 | 60 | Code Directory Documentation
This folder contains the core scripts and data templates for processing BIDS-formatted EEG data in CCS and SV tasks. The structure and usage are as follows:
1. Directory Structure
code/
├── Hand_Writing_Imagery_CCS_Data/ # Template: CCS task data structure (0KB placeholders)
├──... |
08350b06f8b8961d7ce54b61b57fbd68358be1dec778d653094e4a48fcf847a5 | Text | 3,075 | 56 | # Blackmer-Raynolds et al., 2025 Code Repository
This GitHub repository contains the code for the paper titled: "Indigenous gut microbes modulate neural cell state and neurodegenerative disease
susceptibility." For a detailed description of the methods and results, please refer to the [paper](#). *Note: The paper is c... |
a810ea73278c68f78102527c9b5ab3426782a35b774b8e2bf08bc6055c8b621b | Text | 3,078 | 72 | Summary Statistics data for Maciel et al (2026) Nature Communications, The genetic landscape of human functional brain connectivity. Summary statistics can be accessed through: https://vu.data.surf.nl/s/KaQp2Bmk4KcTZqB
##########################
# Summary Statistics Information
##########################
A META file... |
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