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1ca6cd87100d30fd41ece86dd3782bc5ce305554fae1668f57913fad591f9bec | Text | 4,877 | 104 | # AI-Powered Evaluation of Dementia Severity Based on Clinical Data and Visual Scoring Systems (MTA, ERICA, GCA) from MRI
Deep learning pipeline for dementia classification and visual scores prediction from 3D brain MRI. Three independent training modules share a common dataset structure.
## Repository Structure
```... |
6f64e43004106ba753dc3df06a229c2c250e92f80cf633ac4edd1c7804d6cc3c | Text | 4,879 | 74 | # Remoteness-sensitive-theta-network-dynamics-during-early-autobiographical-memory-access
This repository contains the preprocessing, synchronization, and epoching pipeline for the study on **Remoteness sensitive theta network dynamics during early autobiographical memory access**.
# 1 Preprocessing (Python/MNE)
### P... |
df3bad797401b30b8931b05755eef5ebd4225b1fd50cac44368c43565f813e98 | Text | 4,886 | 107 | <img align="right" src="https://raw.githubusercontent.com/FZJ-INM1-BDA/siibra-explorer/master/docs/images/siibra-explorer-square.jpeg" width="200">
[](https://zenodo.org/badge/latestdoi/109723444)
[![Documentation Status](https://readthedocs.org/projects/siibra-explorer/ba... |
954da9883f94ee9312f7734eaa83b444abbc961b997d60aaf62c79ac1794497a | Text | 4,890 | 124 | # THOI: Torch - Higher Order Interactions
<img src="https://raw.githubusercontent.com/Laouen/THOI/main/img/logo.png" alt="THOI Logo" width="200">
## Description
THOI is a Python package designed to compute O information in Higher Order Interactions using batch processing. This package leverages PyTorch for efficient... |
d9bfa79147fe5ebfe6a1ff4ed5f3e9b78097d67b6e6771229e9db76e49c82305 | Text | 4,907 | 115 | # T-World
T-World is a a human ventricular cardiomyocyte model for simulating membrane voltage, calcium handling, ionic currents, contraction, and beta-adrenergic signalling. The repository includes the core model (Matlab and CellML), helper utilities for parameter handling and post-processing, and example scripts cov... |
616f5248a7f6e0b258aa5335f9cf318c62e9fc538732c0d3ec4859f7867ae095 | Text | 4,908 | 86 | # ENIGMA Sleep Cognition
This repository contains the analysis code for the manuscript “Prediction of cognitive performance by demographics, sleep, and brain morphometry: machine learning findings from the ENIGMA-Sleep Working Group.” The code supports multisite cohort data preparation, leakage-controlled machine lear... |
2db2e455a943e443a98dfcf50c290f9f80fc45859e11661138be576db2624503 | Text | 4,910 | 135 | # Force Analysis – Gimbal Experiment
**Author:** Federico Tessari, PhD
**Affiliation:** Mechanical Engineering Department, MIT
**Contact:** ftessari@mit.edu
**Last Update:** May 7, 2026
---
## Overview
This repository contains the full MATLAB analysis pipeline for the **Gimbal Experiment**, designed to study ... |
ca9839e2c5c368a5c7bac8631bce05bd53802842eb8e1d055ec9077f0edc471b | Text | 4,911 | 92 | # DANT Curation App
[](https://github.com/jiumao2/DANT_UI)
Language：[English](./README.md) | [中文](./README_CN.md)
## Installation
1. Use a new conda environment:
```bash
conda create -n dant python=3.10.6
conda activate dant
```
2. Download... |
84dc3744ab60029367f9fcd2cca233d54f60071e5e8a637f2e54e494b90a543a | Text | 4,913 | 151 | # EEG-based PD Subtyping
This repository implements a **data-driven EEG-based clustering framework** for identifying
**robust neurophysiological subtypes of Parkinson’s disease (PD)** across **resting-state and active walking conditions**.
The project accompanies the manuscript:
> **EEG-Based Clustering Reveals Robu... |
ca55a5d07d46cf43ed3c58c7408a0df7447ccf3ff1ae42de0a0ff6eb26285b83 | Text | 4,926 | 135 | # Force Analysis – Gimbal Experiment
**Author:** Federico Tessari, PhD
**Affiliation:** Mechanical Engineering Department, MIT
**Contact:** ftessari@mit.edu
**Last Update:** May 7, 2026
---
## Overview
This repository contains the full MATLAB analysis pipeline for the **Gimbal Experiment**, designed to study ... |
32ee9a0ea8685f03f939e4aa12eb68860ef58895ae06d3529559f31232555db6 | Text | 4,927 | 149 | # vanWeperenV_2026_EpiduralRTX
Analysis code accompanying:
> van Weperen V.Y.H.\*, Hoang J.D.\*, Jani N., Avasthi S., Chan C.A., Cao K.,
> Lokhandwala Z.A., Emamimeybodi M., Atmani K., Vaseghi M.
> *Spinal nociceptive denervation impedes chronic autonomic remodeling after
> myocardial infarction.* (\*equal contributi... |
163298ff13d2a743445a21110b38ab02152584da245bbe5c9e274bfff1a6a521 | Text | 4,935 | 93 |
# Dynamic Susceptibility Contrast MRI toolbox
## About
Dynamic Susceptibility Contrast (DSC) MRI toolbox is a MATLAB toolbox to analyze DSC-MRI data. The code was implemented by [@peruzzod](https://github.com/peruzzod) and [@marcocastellaro](https://github.com/marcocastellaro). This web page hosts the developmental ... |
9aaf4558c6fe6b226d8532436bb6efb5d876335603a5d492d733f0bae97a29b5 | Text | 4,971 | 39 | # Scripts and behavioral data for *Common and distinct neural correlates of social interaction processing and theory of mind in narratives*
Zizhuang Miao
[](https://doi.org/10.5281/zenodo.18315908)
This repo hosts the codes and behavioral data accompanying the article ti... |
c271802492d6aa95f179e2f8a21ac1cec45acbd5b55dc6831a4ed9cd28a59f55 | Text | 4,977 | 107 | # Code for Figures 2–8 and Supplementary Figures S1–S6
## What this code is for
This repository contains the MATLAB source code used to generate the main simulation figures (**Figures 2–8**) and supplementary figures (**Figures S1–S6**) for the study on stimulus-specific combination sensitivity. The code implements bi... |
702b9f25677daea590f01ef4c2e7bc3a00b13a5e7edac96c758a6405c9deba25 | Text | 4,986 | 111 | # Epilepsy
## Overview
This repository provides the R code used in the study:
"Uncovering the key circuit FOSL2/FOS/EGR3/EGR1 contributing to hyperexcitability of excitatory neurons in epileptic temporal cortex and hippocampus"
Epilepsy is mainly characterized by spontaneous seizures caused by hyperactive n... |
82a161a28145fd25228f6fc5ad877f2cac2d0c89f00fdb3ef3059e8297a40c66 | Text | 4,989 | 105 | # AMOEBA+NN: A Hybrid Neural Network and Polarizable Force Field
**amoeba_nn** is the PyTorch-based repository dedicated to the **Neural Network (NN)** components of the **AMOEBA+NN** hybrid force field, designed to bridge the gap between quantum mechanical (QM) accuracy and molecular mechanics (MM) efficiency.
## ⚠️... |
6b35463e0afd9b4e03898f970d9882f332203484b74e8f9782d4d5287b5a8f83 | Text | 5,003 | 58 | ## GffCompare
* compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).
* collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)
* classify transcripts from one or multiple GTF/GFF3 files as they relate to referen... |
9c7708d225233861fbed56c0ac0e99162a9296179c742a6dfc66a991331d386a | Text | 5,021 | 152 | # vanWeperenV_2026_EpiduralRTX
[]
(https://doi.org/10.5281/zenodo.20711756)
Analysis code accompanying:
> van Weperen V.Y.H.\*, Hoang J.D.\*, Jani N., Avasthi S., Chan C.A., Cao K.,
> Lokhandwala Z.A., Emamimeybodi M., Atmani K., Vaseghi M.
> *Spinal nociceptive denerv... |
d53336f4b946abb366699247927123ffc91d1bd3c48964fcde3008e766bf7f47 | Text | 5,032 | 117 | # CAPSIF2 and PiCAP #
Official repository for Protein interaction of CArbohydrate Predictor (PiCAP) and CArbohydrate-Protein Site IdentiFier2 (CAPSIF2) from the paper:
[`Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay`](https://www.pnas.org/doi/... |
68889039765138f5158a70e36423765bb5fc3ed9fdcd5512d447f2393b47047f | Text | 5,033 | 110 | # Inferring Exon and Intron Annotations from Genome Feature Files (.gff)
## Overview
This pipeline extracts exon and intron metadata from .gff files using only coordinate information. It classifies exons into the following splicing categories:
- **Constitutively spliced exons** (always included in mRNA)
- **Skipped e... |
3dc10d908e846523dcf4bd639deac8fa86d1a89b3012a53e5169bd3a21437a61 | Text | 5,034 | 91 | # DARSI (Deep Learning Adaptable Regulatory Sequence Identifier) Package
The DARSI package trains Convolutional Neural Networks (CNNs) for MPRA (Massively Parallel Reporter Assays) datasets. The trained models predict expression levels from raw DNA sequences and generate saliency maps for each trained model to predi... |
86fdcec6077d7c4765efec1f128ee4eb408264111c43f460b0de7b0cdcab4e7d | Text | 5,048 | 119 | ========================================================
NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
========================================================
.. image:: https://travis-ci.org/nipy/nipype.svg?branch=master
:target: https://travis-ci.org/nipy/nipype
.. image:: https://circleci.com/gh/nipy... |
8107dbe4467566c6f2d14a37d42f1b8ae3bbee5e67fadcbddd7c8009f7cc310a | Text | 5,056 | 91 | # scMethCraft: A versatile toolkit for analysis of single-cell DNA methylation data
## Installation
It's prefered to create a new environment for scMethCraft
```
conda create -n scMethCraft python==3.9
conda activate scMethCraft
```
You can install scMethCraft from GitHub via
git cl... |
bda731e1f5b366fc59ba7b16fb090ef7c349353d622ced9d47e00a5348c60c20 | Text | 5,083 | 100 | # SMaSH framework
## Overview
The ```SMaSH``` (Scalable Marker gene Signal Hunter) framework is a general, scalable codebase for calculating marker genes from single-cell RNA-sequencing
data for a variety of different cell annotations as provided by the user, using supervised machine learning approaches. These annot... |
9e30a7379102e2ce7354f8e60918d0d32c489da25d1464c864b499204553eecf | Text | 5,100 | 35 | # PAGA - partition-based graph abstraction
*Mapping out the coarse-grained connectivity structures of complex manifolds [(Genome Biology, 2019)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1663-x).*
![PAGA for hematopoiesis.](http://www.falexwolf.de/img/paga_paul15.png "PAGA for hematopoiesis.... |
bdf217dfddba911e6f1bde93970286c8667df1a3211ccd5f79721c9f0d74ca24 | Text | 5,105 | 95 | # scMethCraft: A versatile toolkit for analysis of single-cell DNA methylation data
## Updates
**v2.0.3** (2026-09-10): Bug fixes.
## Installation
It's prefered to create a new environment for scMethCraft
```
conda create -n scMethCraft python==3.9
conda activate scMethCraft
```
You ... |
1449249aa729813f486955b2c9a2ebe003f4f62559beba863b638857cd5da954 | Text | 5,111 | 155 |
[](https://doi.org/10.5281/zenodo.15595324)
# ColorMyCells
## A Biological Approach to Cell Type Visualization
`colormycells` is a Python package that solves a common problem in single-cell analysis: **creating colormaps where the perceptual distance b... |
bc9b4e0e02536b116a6790be4b9c2feda662c123f7402a4272ee78c6d6ce70a4 | Text | 5,118 | 49 | # UFNet
Official Github repository for the paper "Accessible, At-Home Detection of Parkinson’s Disease via Multi-Task Video Analysis". The paper has been accepted at AAAI 2025 and the published version will appear soon.
Until then, please refer to the arxiv version: https://arxiv.org/abs/2406.14856
## Dataset
Note: W... |
2a191f18e73238dd27bf22de4c6e2a16f135b7683173306d11bad90b38ce310f | Text | 5,119 | 129 | <img src="https://github.com/QinZhou-work/MicNet/blob/586e71edd32e02bfab2a778df043a35b3c6042ee/assets/qbrc_logo.png?inline=false" width="40%"/>
# MicNet
MicNet: Integrating spatially resolved transcriptomes and pathology images by contrastive deep neural network
# Introduction
Exploring the spatial organization of c... |
f67aabed6641de14bd218821d7bf7300ed53d9c9884e15b0abb88f878c20cf96 | Text | 5,127 | 121 | Neural dynamics for working memory and evidence integration during olfactory navigation in Drosophila
Code and simulation materials for Kathman et al., 2025 (bioRxv)
--------------------------------------------------------------------
OVERVIEW
--------------------------------------------------------------------
This r... |
a5887ca79ad80f5fb55f5a1cce47bc46543f4ca05397e686594f778be1f9fb1f | Text | 5,136 | 122 | ## Nnet-survival: A Scalable Discrete-Time Survival Model using Neural Networks
Michael F. Gensheimer and Balasubramanian Narasimhan
Stanford University
mgens@stanford.edu
[Link to PeerJ paper](https://peerj.com/articles/6257/)
Keras version is compatible with Python version 3.7+ and TensorFlow version 2... |
2005940e3a595fef6ecfac4df672d89f7bd5522cc1adc0832a0966e600e88f75 | Text | 5,143 | 113 | # PTB-DDI
## Contents
- [Overview](#Overview)
- [Config PTB-DDI Environment](#Config-PTB-DDI-Environment)
- [Train and Test on the BIOSNAP Dataset](#Train-and-Test-on-the-BIOSNAP-dataset)
- [Train and Test on the DrugBank Dataset](#Tr... |
12af78b426e37a930426c9bc47912c8751d6d8e919b32a1b92f2019a79b00960 | Text | 5,159 | 106 | ViraPipe
==============
ViraPipe is a Apache Spark based scalable parallel pipeline for analysing metagenomes from NGS read data in a computing cluster or on a multi-core standalone machine.
The pipeline is designed especially for viral metagenomes but the software is applicable for any other genome analysis purposes.... |
160c56dbd887de6d5f4d0c2c40b674f6c1e3a678b0c8444fda2df2534fe7a170 | Text | 5,164 | 82 | # Anticipatory EEG during auditory feedback under silence and noise conditions
## Overview
This dataset contains de-identified EEG and behavioral data from a time-estimation task in which auditory feedback was presented either in silence or in background noise. The release is intended to support the revised analyses r... |
98fb03b0e1a30e8d5b46affd61e103ff0e917b62f119d4a33fcdbc762e9f85c9 | Text | 5,166 | 136 | # LG-Transformer
[](https://example.com) [](https://example.com) [
### Data availability
Data can be accessed at the following locations:
| Location | Files |
|-------------|-----... |
3e24e168a06288b211a4460e2cf914448accd8a053282ef3de9aebdd8cad89ef | Text | 5,186 | 53 | # DR.DEGMON
DR.DEGMON: Self-explainable deep neural network for drug-induced cell viability prediction incorporating differentially expressed genes and Gene Ontology
<img src="https://github.com/user-attachments/assets/f2a99ac4-aab7-4f89-b14e-51eeba98ff77" width="450" height="600"/>
# Abstract
Accurate prediction of... |
6b6d045a22baf37a64fbab4486f81d31824a28fbfa40cc850d3a402cd7ff8c9c | Text | 5,191 | 191 | <div align="center">
<div>
<h1>
Spacing effect improves generalization in biological and artificial systems
</h1>
</div>
<div>
<strong>Guanglong Sun</strong>,
<strong>Ning Huang</strong>,
<a href="https://github.com/AnAppleCore"><strong>Hongwei Yan</strong></a>,
<a href="https:... |
63c8c08d4447938f7910909a5a850c17a7e092487d05b305b420f2fcbaa6a155 | Text | 5,220 | 104 | # Molecular evolution of the nonapeptide signalling in Lake Tanganyika cichlid radiation
Pol Sorigue, Walter Salzburger, Rui Oliveira (2025), DOI: **https://doi.org/10.1111/jne.70203**
---
## **Scripts**
The versions refer to the versions used during the analysis.
### **`01.Map_assemblies.sh`**:
Maps raw reads to re... |
c100dcb5b758b296adc279a278bf59516263cc14da48a490c71fc0f3f0023964 | Text | 5,220 | 80 | # DeSMRRest-RestingState-TDLM-Simulation
Code for the resting state analysis and simulation data using TDLM for the paper "Challenges in Replay Detection by TDLM in Post-Encoding Resting State"
For an overview of the experiment and results head to GH-pages: [Paper: Challenges in Replay Detection by TDLM in Post-E... |
e8017512dee9a51f872789b6f7e14ac5a9ed158813601845948fa9400ee07815 | Text | 5,253 | 170 | # FEDUPP — FED3 Users Processing Package
Official implementation for the paper *"The development of FEDUPP: Feeding Experimentation Device Users Processing Package to Assess Learning and Cognitive Flexibility"* from Nature Translational Psychiatry.
[](htt... |
61dbcb60ff368d7ce78d577acb3a504a7c32fc016ce149c2f49b97c852c0f50d | Text | 5,281 | 131 | # Coordinated Hand Movement Sensation – Analysis & Figure Code
This repository contains the **exact MATLAB code and data** used to generate the figures and tables for the manuscript:
**“Coordinated hand movement sensation revealed through an implanted magnetic prosthetic kinesthetic interface.”**
All data in this re... |
9edccf6e3862cdcae85b8b46f5755dd3f064acd1a1db1b2dea992fde6dd954de | Text | 5,292 | 97 | <img src="NS-Forest-sticker.png" width="110" height="125">
# NS-Forest v4.2
__Documentation:__ https://ns-forest.readthedocs.io/en/latest/
__Citation:__ Liu A, Peng B, Pankajam A, Duong TE, Pryhuber G, Scheuermann RH, Zhang Y. (2024) Discovery of optimal cell type classification marker genes from single cell RNA seq... |
bccb5660ce8612f9f8c36df80940ec9e1abc2b4321f4c6560ecb6b5d6a0cc87f | Text | 5,304 | 123 | ## Introduction
The **E-CloudBind** project consists of a **preprocessing part** and a **demo testing part**. Its structure is as follows:
```bash
├─ E-CloudBind/
│ ├─ E-CloudBind/ # Demo execution code; dataset assembly; model architecture and implementation
│ ├─ Preprocess/ # Procedures for ligand electron-... |
9866ee889a1c9dd0579c6fa8029228bcce945e260ba36b49456ea9c5dadeabb6 | Text | 5,314 | 153 | # Memory Storage and Accessibility after Sleep Deprivation
## Analysis Code and Reproducibility Package
**Zenodo DOI:** 10.5281/zenodo.20786380
**Associated manuscript:**
> Sánchez-López S, Delgado-Caro C, Poveda-Bautista R, Moll-López S (2026).
> *Disentangling Memory Storage and Accessibility after Sleep Deprivati... |
a905c372bfac909617819d529b7327c595bef516728087f81c9f2373d8cd216e | Text | 5,315 | 57 | # Figure Ground Segregation in Texture Stimuli
MATLAB code utilized for data acquisition in the psychophysics experiment described in the article:
Karimian, A., Roberts, M.J., De Weerd, P., & Senden, M. (n.d.). Gamma Synchrony Mediates Figure Ground Perception. *Manuscript submitted*.
## Abstract
Gamma synchrony is... |
5bda808ce4bc85b7f3f6b9a70a9e82867d6db8022546b6ece85f257fd2354738 | Text | 5,316 | 164 | # PPF-CSC: Privacy-Aware Federated Congestion-Signal Coordination for Home Energy Management
[](LICENSE)
Code and data for the paper:
> **Privacy-Preserving Federated Congestion-Signal Coordination for Coordinated Home Energy Management Systems**
-... |
7bec00f8407259514522354ae48445f31ce5890b60350504e88499d91dcef53f | Text | 5,322 | 185 | # nnUNet Tree-Semantic Extension
Tree-semantic and hierarchy-aware training extensions for `nnUNet v2`, packaged as a lightweight add-on repository (without re-uploading the full `nnUNet` source).
## 1. Create Virtual Environment
```bash
python3.11 -m venv nnunet_env
source nnunet_env/bin/activate
```
## 2. Install... |
44b6b6eea6f514bb1c08523bde370c4165aac34b216081b2ec0510a0a8aec1a5 | Text | 5,350 | 49 | # CCA/PLS Toolkit
This is a __MATLAB__ toolkit to incorporate __Canonical Correlation Analysis (CCA)__, __Partial Least Squares (PLS)__ and their different variants to investigate __multivariate associations__ between multiple modalities of data, e.g., brain imaging and behaviour. These models find pairs of weights (o... |
40b7d47ea7fa5b58b1250f330c08e351b746f3105b011edac1b2da03409715f1 | Text | 5,354 | 133 | # Keras 3: Deep Learning for Humans
Keras 3 is a multi-backend deep learning framework, with support for JAX, TensorFlow, PyTorch, and OpenVINO (for inference-only).
Effortlessly build and train models for computer vision, natural language processing, audio processing,
timeseries forecasting, recommender systems, etc.... |
93eb9e244054018ee653947553d4a097f71a4cbdccfa9ca99971a10050b85fff | Text | 5,371 | 97 | # Data repository for the RAW to ACES Utility
## Table of Contents
1. [Introduction](#introduction)
2. [Package Contents](#package-contents)
3. [JSON Schema for Spectral Datasets](#schema)
4. [License](#license)
## Introduction
This is the data repository for the RAW to ACES Utility or `rawtoaces` (https://github.co... |
4f4b7360428adf1f886db1f2d1867a5c47011d66ff90a32f985f02b5aec0eb0f | Text | 5,402 | 177 | # BMI-Dynamic Models
Gene expression prediction models with BMI-gene interactions using glinternet.
[](https://opensource.org/licenses/MIT)
------
## Overview
This repository provides pre-trained models for **predicting BMI-dynamic tissue-specific... |
ea08fb16adb0292d6f2df1088388453d46a53ab7fec34cc452834db28c436bd2 | Text | 5,404 | 138 | # TF-DWGNet
## A Directed Weighted Graph Neural Network with Tensor Fusion for Multi-Omics Cancer Subtype Classification
---
## Introduction
This repository provides the implementation of **TF-DWGNet**, a Graph Neural Network framework that integrates tree-based directed weighted graph construction with tensor fusion... |
e477963f370b1402914ad0c994fe6775b1fc5b79bac5eed96c77654abd904710 | Text | 5,419 | 94 | # KiTS23
The official repository of the 2023 Kidney Tumor Segmentation Challenge
[Challenge Homepage](https://kits23.kits-challenge.org/)
**Current Dataset Version: `0.1.4`**
Most recent change (`0.1.3` -> `0.1.4`) was updating a dependency only.
## Timeline
- **April 14**: Training dataset release
- **July 14**:... |
6cd6b5466119dc36d55fe6ac76677057741a08f1aaf0661a2fe0ba8e78e9bb4d | Text | 5,425 | 92 | Connectome Computation System (CCS)
===
If you use or are insp... |
cbafd2209d9561a68acb364d0fc7e78eea52c2c98d0c9d0ab3219210707b3384 | Text | 5,440 | 149 | # NL-HSIM
**NL-HSIM** is a nonlinear high-dimensional set-based inference framework designed to detect group-level effects under complex correlation structures.
This repository provides fully reproducible code for：
simulation studies (Cases 1–3)
real data analysis
and a minimal end-to-end tutorial of the full NL-HSI... |
cd87dd175b1393fa9f1996e3750190cce9e45d725dc1e056df9fe34e203baa1f | Text | 5,449 | 96 | # EfficientPose
This is the official implementation of [EfficientPose](https://arxiv.org/abs/2011.04307).
We based our work on the Keras EfficientDet implementation [xuannianz/EfficientDet](https://github.com/xuannianz/EfficientDet) which again builds up on the great Keras RetinaNet implementation [fizyr/keras-retinan... |
54ec1774d0804a1813135b2ab85ea62d75ed93945117014498ffe5b7fa7f15b2 | Text | 5,450 | 148 | # Reproducible Benchmark of Wavelet-Enhanced Intrabody Communication Biometric Identification
This repository contains code, processed data, notebooks, and experiment artifacts for the study:
> Jin, S. and Komarov, M. M. (2025). *Reproducible Benchmark of Wavelet-Enhanced Intrabody Communication Biometric Identificat... |
68ebd5167751b21fb0a8e399eb84fa8621bee473a80f325babff7920d5ea2872 | Text | 5,465 | 70 | # Polygenic Priority Score (PoPS) v0.2
PoPS is a gene prioritization method that leverages genome-wide signal from GWAS summary statistics and incorporates data from an extensive set of public bulk and single-cell expression datasets, curated biological pathways, and predicted protein-protein interactions. The PoPS me... |
292c5dbf3265939dfc57bbd909c323e12bbcb37008dafd4a7e8f8d5f351bbf63 | Text | 5,473 | 115 | # Local graph estimation with pathwise feature selection
> **Local graph estimation** is a framework for discovering local graph/network structure around specific variables of interest. **Pathwise feature selection (PFS)** is an algorithm for performing local graph estimation with pathwise false discovery control.
##... |
a97d05f81890eb8dd50781451d5f55b5ab318bcc9a115b7643bdb972733ea835 | Text | 5,476 | 129 | .. image:: https://raw.githubusercontent.com/nipy/nipype/master/doc/_static/nipype-banner-bg.png
:target: https://nipy.org/nipype
:alt: Nipype logo
.. list-table::
:widths: 20 80
:header-rows: 0
* - Code
-
.. image:: https://img.shields.io/pypi/pyversions/nipype.svg
:target: https:/... |
74c8083d14dcce93e8c9790faaae9b9e16bd71fa4103ed7e23b5b4a5adff1035 | Text | 5,477 | 117 | > Note: I am currently not able to actively maintain this repository. Please also checkout more recent implementations, e.g. https://github.com/ai4co/rl4co and https://github.com/cpwan/RLOR.
# Attention, Learn to Solve Routing Problems!
Attention based model for learning to solve the Travelling Salesman Problem (TSP)... |
2cc7549c83b4634cb63849cbd3dc2249f30842f316c007e2259926a85d2ccdb4 | Text | 5,489 | 59 | <!DOCTYPE html>
<html>
<body>
# Overview
This code was developed by Andreas Neef for Igor Pro 7 to 10. It falls into three categories.
The collection inside *Dynamic Gain code* contains all code to compute the dynamic gain function of neurons that fire in response to continuously fluctuating, <i>in vivo</i>-like st... |
e8111e5b0aa7bc7fe3cd36166fa55f3814645f27639344f339708fc34f3a3265 | Text | 5,507 | 147 | # GCTA
GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). Pl... |
2d078c8636fbbb23de88ddf6ee1590e026c24ca944d74000e58ef3cb9f5a8a64 | Text | 5,528 | 126 | # NIFTYSEG PACKAGE #
--------------------------------
1 - WHAT DOES THE PACKAGE CONTAIN?
--------------------------------
This project, lead by Jorge Cardoso at King's College London, contains programs to perform EM based segmentation of images in nifti or analyse format. NiftySeg is an open-source toolkit licensed un... |
131fe357b69d23dd291a4cb5f2478ac33218296182ffef5f1834ebda765f27fd | Text | 5,538 | 133 | # glp1r-reward-circuit
Analysis code and example datasets from the Güler lab for behavioral neuroscience research.
## Overview
This repository contains analysis code and toy datasets used to reproduce key steps of our pipeline for studying how GLP-1R agonists affect home cage behavior (Figure 2).
The core pipeline i... |
b628608dcd40a16bec06a7a52f7eb99fe2a7e8b99bfb2cd3b85d0b58774c8085 | Text | 5,544 | 52 | # TPRoGI: a comprehensive rock glacier inventory for the Tibetan Plateau using deep learning
This is the repository presenting an inventory of 44,273 rock glaciers, covering approximately 6,000 km2, across the Tibetan Plateau, which was compiled using remote sensing and DeepLabv3+, a kind of deep learning model. TPRoG... |
5662c488b996e48d2ea6b29473833755dfc606cb9fd03b0bb0137cc5aca32a80 | Text | 5,557 | 51 | # EMBA: using the Bayesian Brain to investigate the specificity of emotion recognition differences in autism and ADHD
Mutual social interactions require people to be aware of the affective state of their counterpart. An important source for this is facial expressions, which can be indicative of the emotions experience... |
a8fc9cf2e6ce07ba7092075fede382498f18ddeb7af5e9c8bf6e3675707b01e0 | Text | 5,564 | 121 | # ageing_behavioral_and_neural_variability
*Code and data for analyzing age-related changes in behavioral and neural variability in the IBL visual decision-making task.*
This repository contains the code and data used to analyze **age-related changes in behavioral and neural variability** during a visual decision-maki... |
c38b0cad628711cbf395cf478921fe1d6fd96fc12280859f763abe1b1327aef0 | Text | 5,590 | 114 | # Phoradendron velutinum UAV Multispectral and RGB Image Dataset with Segmentation Masks
## Overview
This dataset comprises multispectral and RGB aerial images, along with expert-annotated binary segmentation masks, for the detection of *Phoradendron velutinum* (mistletoe) in a conservation area of Mexico City. T... |
eb796e15721f8c5a5ba37f70bbdc0418badd7dcdc822f3ca7cfe822a1d9ef7f5 | Text | 5,593 | 104 | # GraPhAI-v1
This code is accompanying the paper "GraPhAI: Neural networks for solving centrosymmetric crystal structures".
## Software requirements
Python version 3.12 is recommended. The required packages and their versions are given in file `graphai-reqs-pip.txt`.
## Training
Representative subsets (10 million ... |
6aa194fa2600f5dc62a6aad865f29b7bba53273688a744c3438f8425866e93b0 | Text | 5,594 | 54 | # Evaluating Spatially Targeted HIV Interventions and Harm Reduction Services Among People Who Inject Drugs in a High-Burden Setting
## Overview
This repository holds the source code to reproduce results in manuscript 'Evaluating Spatially Targeted HIV Interventions and Harm Reduction Services Among People Who Inject ... |
3e3c169690a46a45d1b65dc7a9638bda5e8e727b442d539fc596deda925382cd | Text | 5,605 | 72 | # UniversalProbeFinder
\
Multi-species histology slice processing pipeline and probe alignment program using neurophysiological markers \
\
To install & run, clone this repository and download the atlases you wish to use. Add the main directory to your matlab path and run:\
`UniversalProbeFinder`\
in the matlab promp... |
642465f3c62a0db80a223a8b3020ff00e295aedd424280240743b578e64fe73a | Text | 5,610 | 92 | # T5pKa: a sequence-based model for microstate and pKa prediction
[](https://opensource.org/licenses/MIT)
[](https://huggingface.co/charl... |
5158ffdf917481d9c9d81baae9d4748bbf80ec5ab5bec3d321ceddbb16c98002 | Text | 5,624 | 65 | [](https://doi.org/10.5281/zenodo.8172821)
[](https://github.com/Julie-Fabre/bombcell/blob/master/LICENSE)
[](https://github.com/Julie... |
837e2e56751b1d19564b56ac5e7e99dcbe9aff8890f7d1a50b4dc6141f4c1284 | Text | 5,640 | 123 | # VesiclePy: A Comprehensive Vesicle Analysis Toolbox for Volume Electron Microscopy
[](https://opensource.org/licenses/MIT)
[](https://www.python.org/)
[](https://github.com/arose/ngl/blob/master/LICENSE)
[](https://github.com/arose/ngl/blob/master/CHANGELOG.md)
[](https://... |
15bbc166bc0694f6314080bf7b7c5019a5f26ae85bfb5499bef42758fdb5766a | Text | 5,646 | 69 | # Download and reprocess 10x datasets
<img src="https://github.com/cellgeni/reprocess_public_10x/blob/main/img/seriousman2.png">
This wrapper script can be used for a simple, one-command reprocessing of a publicly available 10x dataset. All you need to do is clone this repo anywhere on Farm, add the location of `repr... |
dc788afcdd8ae7c9b37c8cce2e3599ac8b370e6b63a0e4cef7739fe89a86305d | Text | 5,647 | 118 | # Genotype-by-Environment Prediction for Rye
This repository contains the code for the methodology presented in the manuscript:
**"Tailoring AI and ML Models for Genotype-by-Environment Prediction Leveraging Environmental Covariates: A European Rye Example"**
Authors:
Wera Eckhoff, Florence Parat, Gennady Bracho-Muj... |
5fb658f1a4117833a7f9586e59f550986ca3df812024635b2f9f7e41a9059fb5 | Text | 5,655 | 200 |
# Few-Shot Deployment of Pretrained MRI Transformers
This repository contains the official implementation of the paper:
**Few-Shot Deployment of Pretrained MRI Transformers in Brain Imaging Tasks**
Mengyu Li, Guoyao Shen, Chad W. Farris, Xin Zhang
Department of Mechanical Engineering & The Photonics Center, Bost... |
5658da771b592dce14b1d5c2169fd2973d4e35b0072050dbc08bb46ee9a49004 | Text | 5,657 | 108 | # Sustainable Science Mapping: Green AI vs. Transformers 🌿
[](https://www.python.org/)
[](https://pytorch.org/)
[](https://gradio.app/)
[](https://doi.org/10.1101/2025.05.27.656468)
---
## Abstract
Advan... |
3c9d32c77db6790c19e61a40ffa12945895919e8f88112e3f3249441d2c573a7 | Text | 5,669 | 100 | # dcm2bids
Your friendly DICOM converter.
[](https://unfmontreal.github.io/Dcm2Bids)
[](https://zenodo.org/badge/latestdoi/59581295)
[   [![CI x64](https://github.com/macs3-project/MACS/actions/workfl... |
d8e39b9fed568e7834bf8540ddb504e50cd07a03957f4aa46a1f3e78729fe0f8 | Text | 5,675 | 138 | # HD-BET
This repository provides easy to use access to our HD-BET
brain extraction tool. HD-BET is the result of a joint project between the
Department of Neuroradiology at the Heidelberg University Hospital, the Divison
for Computational Radiology & Clinical AI, University Hospital Bonn and the
Division of Medical ... |
8cab4a871a26773253f84cb629f19fb0978be5d6d35c395a0d9fa8e60186b491 | Text | 5,679 | 172 | <div align="center">
# BA-Pred
**Protein-Ligand Binding Affinity Prediction using Graph Neural Networks**
[](https://www.python.org/downloads/)
[](https://pytorch.org/)
[ simulation results** and **optical mapping** experiments. Moreover, plotting scripts for creating graphs for pub... |
5c27d71cc6d343d0efd77960d897571bacd1ef13ef08cb8f08a2e1e5d6ae8427 | Text | 5,687 | 173 | # FEDUPP — FED3 Users Processing Package
Official implementation for the paper *"The development of FEDUPP: Feeding Experimentation Device Users Processing Package to Assess Learning and Cognitive Flexibility"* from Nature Translational Psychiatry.
[](htt... |
0007367ffe5387a144e8576af51c2fc92e3a7fc5efb5f7f4c6568579a4e43e8f | Text | 5,692 | 69 | # PCNtoolkit braincharts
[](https://gitter.im/predictive-clinical-neuroscience/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [... |
9297f41b74e0fd1852d1114f86718178c4ee3c56a6c6e9760974d65a2c88207c | Text | 5,696 | 21 | [](https://opensource.org/licenses/Apache-2.0)
# siibra-tutorials
Some tutorial notebooks for programmatic use of the [EBRAINS human brain atlas](https://ebrains.eu/service/human-brain-atlas) with [siibra-python](https://github.com/FZJ-INM1-BDA/sii... |
6b1d78294c12ee515bc82150322ff4a1f00f096e65f6de0124c5bde8fabafcf7 | Text | 5,697 | 86 | # The Brain And Nerve Cord fly connectome
The BANC (said "the bank") is the Brain And Nerve Cord, a connectome of a female adult _Drosophila melanogaster_'s central nervous system generated from a GridTape transmission electron microscopy dataset.
- Read our bioRxiv preprint: **["Distributed control circuits across a ... |
063c2084280c7509db75fbbbd646626e8052bc4ef38a5b6401a4bf9e531e4f2b | Text | 5,715 | 111 | <!-- badges: start -->
[](https://natverse.github.io)
[](https://www.tidyverse.org/lifecycle/#experimental)
[![Release Version](https://img.shield... |
cfc99fca880f743cc1a90e445aa75dcbfad02cc67664f75c6a492debe7d7c69a | Text | 5,715 | 102 | # Foundation Model Rectal MRI
This repository contains the research code accompanying the article "A pre-trained foundation model framework for multiplanar MRI classification of extramural vascular invasion and mesorectal fascia invasion in rectal cancer". The code covers pelvic MRI preprocessing, segmentation-assiste... |
c4e3c43586d6516c39a1d9098947ee0fa40d3d90cc0d21d7ccbaa43d7863e1fe | Text | 5,729 | 78 |
# Arousal modulates functional connectivity through structured and hemispherically asymmetric community architecture during wakefulness
[](https://doi.org/10.7554/eLife.110294)
[](http... |
123d8523675fbbcd1287ac88c8ce15309f41155f731afa4b38305c2f85a0abc0 | Text | 5,755 | 160 | # simcat
`simcat` uses coalescent simulations and a neural-network classifier to infer a
directional introgression edge on a fixed species-tree topology from unlinked SNP
site-pattern frequencies.
This is an early research-software release. Version 0.0.7 supports Python 3.10
and the dependency versions listed in `set... |
6f43854473ad534769b1d7d09a319464c9c23437601aed8fc1816d27dbede40f | Text | 5,782 | 128 | # wes_chd_ukbb
## Meta-analysis of a large-scale wes dataset using Hail
This repository contains a series of pipelines (mostly command-line tools) to analyse the
CHD case-control exome cohort linked to the published study:
*"Assessing the contribution of rare variants to congenital heart disease through
a large-scale... |
60b373ce49438dc7fe927e92ce4a254941612654d53d2f65b203791053557789 | Text | 5,789 | 150 | # Benchmarking Machine Learning Approaches for Polarization Mapping in Ferroelectrics Using 4D-STEM
This repository contains the implementation and benchmarking suite for automating polarization direction detection in ferroelectric (KNN) materials using 4D-STEM diffraction patterns.
## 🔬 Overview
Four-dimensional s... |
f3c10696586148dbc23cfea508ae2b8abb1de2ddfc507e39282ad708347e1f9a | Text | 5,795 | 38 | # Overview
cvVectorStats is a set of functions for using cross-validation to estimate Euclidean distances between the means of multivariate distributions (and for estimating other statistics that require Euclidean distance, such as Pearson's correlation). Using cross-validation substantially reduces bias and makes it ... |
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