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# coTWAS - co-expression TWAS ## Overview This repository contains the computational pipeline used to train and apply multiple gene expression prediction models for brain tissues using RNA-seq and genotype data. The framework integrates both cis-regulatory (CIS, EpiXcan) and trans-regulatory (MODULE, INGENE) approac...
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- <a href="#preface" id="toc-preface">Preface</a> - <a href="#setup" id="toc-setup">Setup</a> - <a href="#figure-5a-workflow" id="toc-figure-5a-workflow">Figure 5a workflow</a> - <a href="#helpers" id="toc-helpers">Helpers</a> - <a href="#quantify-transcript-counts" id="toc-quantify-transc...
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# Finger Force Regression with SNNs Finger force regression from intramuscular EMG motor unit (MU) spike trains using Spiking Neural Networks (SNNs) and Recurrent Neural Networks (RNNs). The repository accompanies the manuscript and supports three main experiments: (i) SNN on clean MU spike trains, (ii) SNN on noisy M...
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## Contents * [Introduction](#introduction) * [Quick Start](#quick-start) * [Install pleioFDR](#install-pleiofdr) * [Data downloads](#data-downloads) * [Data preparation](#data-preparation) * [Run pleioFDR](#run-pleiofdr) * [pleioFDR results](#pleiofdr-results) * [FUMA-defined loci](#fuma-defined-loci) * [Octave suppo...
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# Voxel‑wise Cox Regression for Atlas Imaging (MATLAB) This repository implements a voxel‑wise Cox proportional hazards regression pipeline in MATLAB, designed to map relationships between imaging-derived covariates and survival outcomes. The code accommodates large 3D imaging datasets by slicing into per-slice `.mat`...
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# [ICLR 2025] Reading Your Heart: Learning ECG Words and Sentences via Pre-training ECG Language Model This is the offical implementation of our ICLR 2025 paper "[Reading Your Heart: Learning ECG Words and Sentences via Pre-training ECG Language Model](https://openreview.net/pdf?id=6Hz1Ko087B)". > Authors: Jiarui Jin...
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``` [![DOI](https://zenodo.org/badge/1172485554.svg)](https://doi.org/10.5281/zenodo.18862439) ``` Code Archive GitHub repository: https://github.com/surekhareddy123/AdjLeafGNN Permanent archived release (Zenodo DOI): https://doi.org/10.5281/zenodo.18862439 # AdjLeafGNN: Graph Neural Network Framework for Le...
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<html> <head> <meta name="google-site-verification" content="FC8xEq44yQepn6GHyTtgwE8snz8H4lnnfgcJE16CIHY" /> </head> </html> # SHARE-seq-alignmentV2 Pipeline for demultiplexing and aligning both ATAC and RNA data generated in SHARE-seq.\ The V2 pipeline is much faster than previous version and less demanding. ...
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# MultiGraphEstimationModels.jl <!-- ![Lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)<!-- ![Lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg) ![Lifecycle](https://img.shields.io/badge/lifecycle-stable-green.svg) ![Lifecycle](https://img.shields.io/badge/lifecycle-retired-...
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# PRANA This repository includes in the implmentation of PRANA Preprint is available [here](https://www.medrxiv.org/content/10.64898/2026.07.12.26357860v1). Abstract: Polygenic risk scores (PRSs), which quantify inherited susceptibility to complex traits and diseases, have emerged as valuable tools for risk stratifi...
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# Data repository * /manual_accuracy_evaluation: contains the manual evaluation of the fixations in the iterations (max. 4) of the fixation correction for each participant, including decisions to perform "remove outlier fixations", select a suitable fixation correction algorithm and apply an offset on the x-axis * /p...
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contrastive =================== A python library for performing unsupervised machine learning on datasets with learning (e.g. PCA) in contrastive settings, where one is interested in patterns (e.g. clusters or clines) that exist one dataset, but not the other. Applications include dicovering subgroups in biological an...
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# ExPO: Exposure–Response Neural Operator for Gene Expression Imputation [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/) [![PyTorch](https://img.shields.io/...
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# syglass-multichannel-io-utils Python command-line utilities for exporting large multi-channel microscopy volumes from syGlass projects and generating raw-signal TIFF stacks from selected labelled regions for downstream visualization or analysis in software such as Imaris. The repository contains two independent too...
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# Coordinative Structures as Scale-Free Networks **Simulation code and data for:** > Coordinative structures as scale-free networks: Cascade and percolation dynamics in motor learning with empirical validation Submitted to *PLOS Computational Biology* **Author:** Chulwook Park **Affiliations:** - Department of Phy...
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<img src="images/logo.png" align=mid /> # MedicalNet This repository contains a Pytorch implementation of [Med3D: Transfer Learning for 3D Medical Image Analysis](https://arxiv.org/abs/1904.00625). Many studies have shown that the performance on deep learning is significantly affected by volume of training data. The...
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[![DOI](https://zenodo.org/badge/1172485554.svg)](https://doi.org/10.5281/zenodo.18862439) ![License](https://img.shields.io/badge/license-MIT-blue.svg) ![Python](https://img.shields.io/badge/python-3.9+-blue.svg) Code Archive GitHub repository: https://github.com/surekhareddy123/AdjLeafGNN Permanent archived rel...
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# Local Gyrification Index ## Description The amount of cortical folding, or gyrification, is typically measured within local cortical regions covered by an equidistant geodesic or nearest neighborhood-ring kernel. However, without careful design, such a kernel can easily cover multiple sulcal and gyral regions that m...
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# Neuropixels Opto Network Effects Dataset ## Overview This dataset contains neuropixels opto recordings from mouse cortex and stimulation data. This data supports analysis of spatially-resolved neural responses to optogenetic activation and inactivation across different power levels and emitter locations. Mice e...
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# Local connectivity model A stochastic graph model that captures non-random trends in local connectivity of neuronal circuitry. With a proof-of-concept extension to long-range connectivity. The model defines a way to build a graph on top of the structure of another graph. We call this a *stochastic spread graph*. A st...
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[![PyPI](https://img.shields.io/pypi/v/paste-bio.svg)](https://pypi.org/project/paste-bio) [![Downloads](https://pepy.tech/badge/paste-bio)](https://pepy.tech/project/paste-bio) [![Documentation Status](https://readthedocs.org/projects/paste-bio/badge/?version=latest)](https://paste-bio.readthedocs.io/en/stable/?badge=...
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# PIE-Model-Experiments This repository provides a guide and the necessary resources for reproducing the experimental results of the publication: [A Physics-Informed Eikonal Model for Simulating Arrhythmias in the Human Heart in Real-Time](https://www.researchsquare.com/article/rs-7741556/v1). ## Description The `setu...
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20055048.svg)](https://doi.org/10.5281/zenodo.20055048) # Local connectivity model A stochastic graph model that captures non-random trends in local connectivity of neuronal circuitry. With a proof-of-concept extension to long-range connectivity. The model defines a ...
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# shinobi_fmri fMRI analysis pipeline for the [cneuromod.shinobi](https://github.com/courtois-neuromod/shinobi_access) dataset. ## Installation This package requires Python 3.8+. ### Quick Setup (Recommended) Use the automated setup script: ```bash # Clone the repository git clone https://github.com/courtois-neur...
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# Efficient Gillespie algorithms for spreading phenomena in large and heterogeneous higher-order networks > [!NOTE] > Code implemented using the [Fortran Package Manager](https://fpm.fortran-lang.org/). > > Main paper: *Efficient Gillespie algorithms for spreading phenomena in large and heterogeneous higher-order netw...
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<!-- README.md is generated from README.Rmd. Please edit that file --> # ggVennDiagram <!-- badges: start --> [![](http://cranlogs.r-pkg.org/badges/grand-total/ggVennDiagram)](https://cran.r-project.org/package=ggVennDiagram) [![](http://cranlogs.r-pkg.org/badges/last-month/ggVennDiagram)](https://cran.r-project.or...
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.19486642.svg)](https://doi.org/10.5281/zenodo.19486642) # Repository for "Latent Neural Architecture Organizing Shared Aesthetic Evaluations of Visual Artworks" Authors: Xinyu Liang, Kaixiang Zhuang, Yun Wang, Yueting Su, Jianfeng Feng, Zhou Feng, Benjamin Becker and...
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<p align="center"> <a href="http://mlatom.com"><img src="assets/img/banner.png" alt="MLatom" width="720"></a> </p> <p align="center"> <a href="https://pypi.org/project/mlatom/"><img src="https://img.shields.io/pypi/v/mlatom.svg" alt="PyPI version"></a> <a href="https://pepy.tech/project/mlatom"><img src="https:/...
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# broccolini GPU-accelerated spatial normalization (image registration) for NIfTI volumes. Extracted from [BROCCOLI](https://github.com/wanderine/BROCCOLI) (Eklund et al., 2014) with a pluggable backend architecture supporting CUDA, Metal, OpenCL, and WebGPU. ## Features - Phase-based multi-scale registration (not ...
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# Lesion based Disconnectomes We provide the implementation of lesion based disconnectome graph modelling from an atlas-based approach. In clinical practice, high-quality diffusion MRI is rarely acquired due to time constraints. To enable the estimation of connectivity damage resulting from brain lesions without requ...
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# Coordinative Structures as Scale-Free Networks [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20694466.svg)](https://doi.org/10.5281/zenodo.20694466) **Simulation code and data for:** > Coordinative structures as scale-free networks: Cascade and percolation dynamics in motor learning with empirical validation...
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# Tissue-autonomous pharmacological direction and the Tissue Direction Index (TDI) — analysis code and data for the hemostatic proof-of-concept This repository contains all analysis code, prepared input structures, and derived result datasets supporting two associated manuscripts: > Chen H, Chen Q, Wang Y. *Tissue-au...
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# Hierarchical Spherical Deformation for Cortical Surface Registration ## Description We present hierarchical spherical deformation for group-wise shape correspondence to address template selection bias and to minimize registration distortion. In this work, we aim at a continuous and smooth deformation field to guide ...
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# PsiAudit: Auditing Symmetry-Organised Complexity in Quantum Neural Networks *PsiAudit: A Reproducible Toolkit for Symmetry-Organised Complexity in Equivariant Quantum Neural Networks*, by H. Ugail and N. Howard. Parameterised quantum circuits are usually evaluated with diagnostics for expressibility, gradient behav...
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[![build](https://github.com/rgcgithub/regenie/actions/workflows/test.yml/badge.svg)](https://github.com/rgcgithub/regenie/actions/workflows/test.yml) ![GitHub release (latest by date)](https://img.shields.io/github/v/release/rgcgithub/regenie?logo=Github) [![install with conda](https://img.shields.io/badge/install%20w...
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# RICE toolbox (Rotational Invariants of the Cumulant Expansion) RICE is a representation-based framework for understanding and estimating diffusion MRI cumulant tensors from arbitrary B-tensor encodings, enabling protocol-independent inference beyond conventional LTE-based DTI and DKI. This '[MATLAB toolbox](https:...
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<img src="https://raw.githubusercontent.com/openbraininstitute/eFEL/master/docs/source/logo/eFELBanner.png" alt="eFEL banner" /> <table> <tr> <td>Latest Release</td> <td> <a href="https://pypi.org/project/efel/"> <img src="https://img.shields.io/pypi/v/efel.svg" alt="latest release" /> </a> </td> </t...
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# PIE-Model-Experiments This repository provides a guide and the necessary resources for reproducing the experimental results of the publication: [A Physics-Informed Eikonal Model for Simulating Arrhythmias in the Human Heart in Real-Time](https://doi.org/10.1038/s41467-026-76050-0). ## Description The `setups` direct...
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# Data repository: Charting Higher-Order Models of Brain Function Beyond Pairwise Interactions **Authors:** Andrea Santoro, Matteo Neri, Simone Poetto, Davide Orsenigo, Matteo Diano, Marilyn Gatica, Giovanni Petri This repository contains the processed fMRI timeseries (raw data) and all higher-order interaction (HOI)...
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# Figures For Paper — ISRGDF15 Project This folder contains all scripts and data needed to reproduce the main figures in the paper. --- ## First download necessary RNAseq files and put into proper folders GTEx v8 RNAseq data is available through the GTEx Portal (https://gtexportal.org/home/downloads/adult-gtex/bulk...
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# neuroPASC-scRNA-seq-data-analysis This repository contains R scripts for processing and analyzing single-cell RNA sequencing (scRNA-seq) data derived from brain CD45+ immune cells collected from a neuroPASC mouse model. ## Table of Contents - [Overview](#overview) - [Requirements](#requirements) - [Installation](#in...
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# SpatiotemporalSCModel Code repository to fit linear-nonlinear models, spatial contrast models and STC-bases subunit models to responses of retinal ganglion cells under spatiotemporal stimulation. It accompanies the paper: **Sridhar S, Vystrčilová M, Khani MH, Karamanlis D, Schreyer HM, Ramakrishna V, Krüppel S, Zap...
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# Fast spike sorting for hundreds of channels # Implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings. Very fast when a GPU is available, but can also run on the CPU side. Described in this NIPS paper Pachitariu M, Steinmetz NA, Kad...
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# Representational Tuning Paper [![DOI](https://img.shields.io/badge/DOI-coming%20soon-red)](add%20link%20when%20available) This repository contains the code for the Representational Tuning Paper. For questions or issues, contact: s.r.bergey@tilburguniversity.edu --- ## Table of Contents 1. [System Requirements](#...
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An HTTP backend for transforming coordinates (and, in the future, data) between the HBP core template spaces .. image:: https://github.com/HumanBrainProject/hbp-spatial-backend/actions/workflows/tox.yaml/badge.svg :target: https://github.com/HumanBrainProject/hbp-spatial-backend/actions/workflows/tox.yaml :alt: ...
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# Yeon-2025-pumping-analysis Scripts to quantify pharyngeal pumping frequency in *C. elegans* from video recordings, as described in **"An enteric neuron-expressed ionotropic receptor detects ingested salts to regulate salt stress resistance"**, *Yeon, ..., Sengupta 2025*. The analysis pipeline generates kymographs (...
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# SuperBigFLICA (SBF) [![Python 3.11+](https://img.shields.io/badge/Python-3.11%2B-blue.svg)](https://www.python.org/) [![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](LICENSE) [![Alzheimer's & Dementia](https://img.shields.io/badge/Alzheimer's%20%26%20Dementia-10.1002%2Fdad2.70360-blue)](http://d...
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# dlPFC in strategic trial aborting This is a project building models that exhibit trial-aborting beahvior. See [paper](https://doi.org/10.1101/2024.11.28.625897). All the codes have been tested on Windows machines with Anaconda and CUDA-capable GPUs. The following instructions allow users to run codes in this repo b...
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# 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...
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# SUMMER ## Single Unit activity during a Movie in the human Medial Temporal lobe via Electrophysiological Recordings [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20328875.svg)](https://doi.org/10.5281/zenodo.20328875) <a href="https://doi.org/10.48324/dandi.001616/0.260702.0824"><picture><source media="(prefer...
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# SpinalProjectome **SpinalProjectome** is a MATLAB-based framework designed to simulate the spinal cord circuitry of a mouse. It enables detailed modeling of neuronal populations with diverse cell types, spatial projection biases, and network connectivity, providing a powerful tool for studying spinal cord dynamics. ...
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This repository is a fork of [MouseLand/Kilosort2.5](https://github.com/MouseLand/Kilosort). It introduces specific enhancements to the preprocessing pipeline to improve flexibility in neural signal processing. ## 🛠 Key Modifications ### 1. Whitening Matrix Export (`Wrot.mat`) The original Kilosort 2.5 calculates a ...
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# Deep Learning-Based Desikan-Killiany Parcellation of the Brain Using Diffusion MRI [![arXiv](https://img.shields.io/badge/arXiv-2508.07815-b31b1b.svg)](https://arxiv.org/abs/2508.07815) This repository provides the official implementation of our hierarchical 3D deep learning framework for **Desikan–Killiany brain p...
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# MitoMutAccTimes-Part1 > Tools to analyze accumulation times of mitochondrial DNA deletion mutants from synthetic and scRNAseq data. This repository contains code and data for our study on the accumulation of mitochondrial DNA (mtDNA) deletion mutants, a hallmark of aging in post-mitotic cells (see [bioRxiv preprint...
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[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/polizzilab/NISE/blob/main/NISE_LASErMPNN.ipynb) # Neural Iterative Selection Expansion (NISE) using LASErMPNN/LigandMPNN with Boltz-1x/Boltz-2x ![A NISE Trajectory demonstraing optimization of P(bind)...
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# Neural Cell Knowledge Graph A hierarchical multimodal knowledge graph for neural cell-type-specific regulation integrating single-cell transcriptomics and literature evidence. ## Overview This repository contains the data and code for constructing and analyzing a neural-cell-centric knowledge graph that integrates...
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<h1> <picture> <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-cutandrun_logo_dark.png"> <img alt="nf-core/cutandrun" src="docs/images/nf-core-cutandrun_logo_light.png"> </picture> </h1> [![GitHub Actions CI Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20CI/badge.s...
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![Logo](https://github.com/ai4environment/WeatherBench/blob/master/figures/logo_text_left.png?raw=true) # WeatherBench: A benchmark dataset for data-driven weather forecasting **🚨🚨🚨 [WeatherBench 2](https://github.com/google-research/weatherbench2) has been released. It provides an updated and much improved benchma...
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# bbbp-overrepresentation-bias [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) This repository contains the official code and data to reproduce the findings of the paper **"Overrepresentation bias leads to performance overestimation in blood-brain bar...
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<picture> <source media="(prefers-color-scheme: dark)" srcset="logo-layerbn-2.png"> <img src="logo-layerbn.png" alt="layerbn" width="380"> </picture> > [!NOTE] > **About `layerbn`** > > Many research questions involve multiple outcomes and a range of interrelated factors, > which influence one another and the ou...
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<p align="center"> <img src="assets/scAgeClock_GraphicAbstract.jpg" alt="scAgeClock graphical abstract" width="100%"> </p> # scAgeClock scAgeClock: a single-cell transcriptome based human aging clock model using gated multi-head attention neural networks ## Quick Start ### making age prediction by scAgeClock (comman...
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# Drosophila Neurotransmitters This repository contains curated data on neurotransmitters used by different cell types (Bates et al. 2019) in *Drosophila melanogaster*. The data is stored in a version-controlled .csv file named `gt_data.csv`, with changes managed through GitHub Pull Requests. For a complete list of r...
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BronchiNet ============================== Airway segmentation from chest CTs using deep Convolutional Neural Networks Contact: Antonio Garcia-Uceda Juarez (antonio.garciauceda89@gmail.com) Introduction ------------ This software provides functionality to segment airways from CT scans, using deep CNN models, and in ...
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# Code for "Serotonergic modulation of motor subspace dynamics drives a sleep-independent quiescent state" MATLAB code used for the analyses and figure panels in the paper **"Serotonergic modulation of motor subspace dynamics drives a sleep-independent quiescent state"**. This project combines two-photon calcium imag...
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# DRIL Classification Benchmark [![Hugging Face Spaces](https://img.shields.io/badge/%F0%9F%A4%97%20Hugging%20Face-Spaces-blue)](https://huggingface.co/spaces/AI-RESEARCHER-2024/DRIL-Classification-Benchmark) A comprehensive deep learning benchmark for **Diabetic Retinopathy-related Inner Layer (DRIL)** detection on ...
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# CLoPy Closed-loop feedback training system (CLoPy) for neurofeedback and specified movement feedback in mice This work accompanies the research paper - https://www.biorxiv.org/content/10.1101/2024.11.02.619716v1 For more documentation please see the Docs: https://clopy-docs.readthedocs.io/ ## Folder structure ```...
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# HypEReg-TransMorph &mdash; IXI evaluation and manuscript assets [![DOI](https://zenodo.org/badge/1224333340.svg)](https://doi.org/10.5281/zenodo.19888526) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) **Maintainers:** Mohan Xu, Shiyi Xu. This repository...
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# PARK: Multimodal Feature Extraction, Unimodal and Fusion Modeling, and Evaluation Pipeline End-to-end repo for extracting features from **smile videos**, **finger-tapping videos**, and **speech (quick brown fox)**; training **unimodal** and **uncertainty‑aware fusion** models; and running paper-ready **analyses** an...
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# UniSynapse **Unified Synaptic Puncta Analysis Pipeline** A comprehensive Python toolkit for neurite segmentation, puncta detection, synaptic pairing, tracking, and codistribution analysis in fluorescence microscopy timeseries and z-stacks. > **Drift correction** can be found in the standalone **[ConsensusDrift](Co...
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--- language: en tags: - exbert license: apache-2.0 datasets: - bookcorpus - wikipedia --- # BERT base model (uncased) Pretrained model on English language using a masked language modeling (MLM) objective. It was introduced in [this paper](https://arxiv.org/abs/1810.04805) and first released in [this repository](http...
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#### **Important Notice:** This site and algorithm is ${\textsf{\color{red}for research users only, not commercial use.}}$ Commercial users should contact exclusive DunedinPACE licensee [TruDiagnostic<sup>TM</sup>](https://trudiagnostic.com/). --- # News ### DunedinPACE now works on EPICv2! Follow instructions an...
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# Wearable EEG Attention Tracking across Dynamic Listening Scenarios <p align="center"> <img src="article/figures/visualAbstract.png" width="700"> </p> Everyday communication is dynamic and multisensory — involving shifting attention, overlapping speech and visual cues. Yet most neural attention tracking studies ar...
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## Free Waveform (FWF) encoding pulse sequence resources ### Overview This repository contains materials and tools to support the implementation and use of the "Free Waveform" (FWF) MRI pulse sequence. The sequence is a diffusion-weighted spin-echo that facilitates the execution of user-defined gradient waveforms for ...
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# TransMorph: Transformer for Unsupervised Medical Image Registration <a href="https://opensource.org/licenses/MIT"><img src="https://img.shields.io/badge/License-MIT-yellow.svg"></a> [![arXiv](https://img.shields.io/badge/arXiv-2111.10480-b31b1b.svg)](https://arxiv.org/abs/2111.10480) keywords: Vision Transformer, Sw...
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Drug_induced_spectral changes is a pipeline designed to work with the TUH EEG Corpus: https://isip.piconepress.com/projects/tuh_eeg/ It can be used to mine for data from the Corpus, process and clean the data, calculate the powerspectrum and compare "normal" data to data from patients that used certain drugs. A list ...
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# TENET: Two-Photon Microscopy Image Enhancement NETwork **TENET** is a fully unsupervised deep-learning framework for simultaneous deblurring, super-resolution (up to 12×), and semantic segmentation of two-photon microscopy (TPM) volumes in a single pass. > Morita H\*, Hayashi S, Tsuji T, Kato D, Wake H, Shimamura T...
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# KG-Bench: Benchmarking Graph Neural Networks for Drug Repurposing This repository accompanies the paper "KG-Bench: Benchmarking Graph Neural Network Algorithms for Drug Repurposing". It provides a FAIR-compliant benchmarking framework for evaluating GNN architectures on drug–disease association prediction tasks, usi...
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# IUPAC Digitized pKa Dataset **Important note: This is the first release of this dataset. The detailed process of digitization and curation of this dataset can be found in the *IUPAC pKa Data Digitization Report* attached in this repository. Our validation process is ongoing and will continue. Please be advised that...
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# BrainInterface3D BrainInterface3D is a modular pipeline incorporating multiple imaging modalites, 3D modelling, and making use of 3Dslicer to integrate magnetic resonance imaging (MRI), functional MRI (fMRI), computed tomography (CT), 3D electrode models, vasculature, and any relevant and useful information to be use...
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<p align="center"> <img src="src/resources/assets/MDH_Logo_Credit_DALL-E.png" alt="MedicalDataHandler_Logo" width="200"> </p> <h1 align="center">MedicalDataHandler</h1> <p align="center"><em>A Research-Oriented GUI for DICOM Data Management</em></p> <p align="center"><em><a href="https://github.com/AustenMan/Medic...
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# Microbiome Comparative Analysis — R Pipeline A complete R analysis pipeline for comparing microbial communities between two or more groups using shotgun metagenomic feature tables. The repository covers diversity analysis (alpha and beta), differential abundance, community assembly mechanisms, enterotype clustering,...
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# ELA/GAopt This repository contains the code for our paper: **Energy Landscape Analysis with Automated Region-of-Interest Selection via Genetic Algorithms** **ELA/GAopt** is a framework for data-driven ROI (Region of interest) optimization in Energy Landscape Analysis(ELA). This repository contains code for select...
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# Replicability of FC in the Seven Resting-State Brain Networks Project Repository This repository contains all of the information and code required to download the data, run the analysis, and reproduce the results from our study on the effects of pipeline, band-pass filtering, and brain parcellation on the replicabi...
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# SKINET <b>S</b>upport vector <b>K</b>ernel for <b>I</b>nferring <b>N</b>atural selection and <b>E</b>volutionary <b>T</b>arget detection <i>SKINET</i> is a framework to distinguish signs of selective sweep from genomic data. We use a custom kernel using Support Vector Machine (SVM) framework to facilitate classifica...
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# Volume tracking from slices into CCFv3 ABA space Toolbox to track volumes (such as injections, stroke area, region of interest etc...) and translate the location into CCFv3 ABA Space using FIJI and MATLAB. This pipeline is fully based on the amazing AP_histology (https://github.com/petersaj/AP_histology) for alignme...
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# nf-ViralMutations ## Pipeline intent This pipeline is intended to be used to align Illumina or MinION reads to a reference and call the mutations and consensus. The mutations called include non-consensus mutations, which is useful when looking at the dynamics of the viral population over time. The pipeline is desig...
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# DeepFrag DeepFrag is a machine learning model for fragment-based lead optimization. In this repository, you will find code to train the model and code to run inference using a pre-trained model. ## Citation If you use DeepFrag in your research, please cite as: Green, H., Koes, D. R., & Durrant, J. D. (2021). Deep...
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# Improving protein-ligand complex generation with force field guidance Codebase for the paper [Improving protein-ligand complex generation with force field guidance](https://doi.org/10.1186/s13321-026-01198-2), published in Journal of Cheminformatics. In this work, we propose a novel method to apply energy guidance ...
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# <b>iMOSS</b>: Immobility/Mobility Optimized Scoring System <p align="center"> <img src="Image/iMOSS_logo.png" width="600" alt="iMOSS Logo"> </p> <p align="center"> <a href="https://www.frontiersin.org/journals/behavioral-neuroscience/articles/10.3389/fnbeh.2026.1819512/full"> <img src="https://img.shields...
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[![Test](https://github.com/raqueladaia/AxoDen/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/raqueladaia/AxoDen/actions/workflows/test.yml) [![Lint](https://github.com/raqueladaia/AxoDen/actions/workflows/lint.yml/badge.svg?branch=main)](https://github.com/raqueladaia/AxoDen/actions/workflows/li...
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# Architecture-Data Matching for EEG–EMG Decoding > Compact deep models match classical spectral decoders during grasp-and-lift on the WAY-EEG-GAL dataset. This repository contains the code, derived results, and figures supporting the manuscript: > **Pinto Neto, O.** (2026). *Architecture-Data Matching for EEG-EMG D...
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# SCORM Agents > AI-powered SCORM 1.2 course generator — transform corporate documents into interactive e-learning packages. ![Python 3.12+](https://img.shields.io/badge/python-3.12%2B-blue) ## Overview SCORM Agents converts corporate documents (PDF, DOCX, PPTX) into complete SCORM 1.2 course packages using an AI-d...
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# Architecture-Data Matching for EEG–EMG Decoding > Compact deep models match classical spectral decoders during grasp-and-lift on the WAY-EEG-GAL dataset. This repository contains the code, derived results, and figures supporting the manuscript: > **Pinto Neto, O.** (2026). *Architecture-Data Matching for EEG-EMG D...
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# Xsembles2P **_Xsembles2P_** is a faster<sup>†</sup> tool to analyze two-photon calcium imaging videos to extract neuronal activity and identify xsembles (ensembles and offsembles). The MATLAB function to use it is `Xsembles_2P.m`. The algorithm performs the following computations: 1. Read raw video(s). 2. Read ext...
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# CellLoop:Identifying single-cell 3D genome chromatin loops # ---------- ### Latest updates: October 30, 2025,version 0.0.2 ## Contents: 1. [Overview](#Overviewn) 2. [Installation](#Installation) 3. [Usage](#Usage) 4. [Update Log](#UpdateLog) 5. [Maintainers](#Maintainers) 6. [Citation](#Citation) ## 1. Overview ![]...
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# Xsembles2P **_Xsembles2P_** is a faster<sup>†</sup> tool to analyze two-photon calcium imaging videos to extract neuronal activity and identify ensembles (onsembles and offsembles). The MATLAB function to use it is `Xsembles_2P.m`. The algorithm performs the following computations: 1. Read raw video(s). 2. Read ex...
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<p float="left"> <img width="50%" style="max-width:450px" alt="Helios-Web" src="https://github.com/filipinascimento/helios-web/raw/main/media/helios-web-logo.svg"> <img width="25%" alt="Helios Web demo" src="https://github.com/filipinascimento/helios-web/raw/main/media/WS_very_low.gif"> </p> <!-- Create a table cente...
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# Welcome to ROICaT <div> <img src="docs/media/logo1.png" alt="ROICaT" width="200" align="right" style="margin-left: 20px"/> </div> [![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/RichieHakim/ROICaT) [![build](https://github.com/RichieHakim/ROICaT/actions/workflows/.github/workflows/build...
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# Early Adversity Imprints Multisystem Biological Aging **Paper:** "Early Adversity Imprints Multisystem Biological Aging: A Longitudinal Study of Dimensions of Stress and Biomarkers of Aging Across Adolescence" **Status:** Under review at *Biological Psychiatry: Global Open Science* (Manuscript ID: BPSGOS-D-26-0010...