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a6868d044b4420b67982f4740d745573971f22bad1929d486c367a089591b875 | Text | 2,429 | 61 | # R2SN_construction
R2SNs provide a novel, reliable and biologically plausible method to understand human morphological covariance based on sMRI.
## Source
If you use R2SN_code, please cite this orignal paper: [Original Paper](https://dir... |
381336dd4edc6afac7cd9a002f15712723add228aea59995948523f5d2506129 | Text | 2,435 | 52 | # GNN-code
## Requirements
This project uses the Python packages listed in `requirements.txt`. Please install them before running experiments.
## Data Preparation (Skip if you already have the data)
1. **Generate MSN Dataset**
Create MSN data such that the variable name is `"connectivity"`, and save it as `cor... |
e066a345e9e4b1b6722f8cc4a734d7ac8c7cf4dd6e382f30af7f0308ded1640c | Text | 2,441 | 41 | # CARD
## Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
We developed a statistical method for spatially informed cell type deconvolution for spatial transcriptomics. Briefly,CARD is a reference-based deconvolution method that estimates cell type composition in... |
6c3ec80e0eb78f1da91889efd843a9339e1c218730e6d3394548e8a21919e4b6 | Text | 2,443 | 47 | ## Deep count autoencoder for denoising scRNA-seq data
A deep count autoencoder network to denoise scRNA-seq data and remove the dropout effect by taking the count structure, overdispersed nature and sparsity of the data into account using a deep autoencoder with zero-inflated negative binomial (ZINB) loss function.
... |
a319ffc356c5ac680aa0c5befff31d8628fc4e4c071ba0158bf39d8244fe917b | Text | 2,443 | 35 | # ToxMSRC
An innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection
# 1 Description
ToxMSRC is a deep learning model for peptide toxicity prediction that integrates multi-scale convolutional neural networks, bidirectional long short-term memory, a... |
d2d9fa13c6b3e5b02361f4cff8fb92ba5d1279a911352b9840ddef52d93f2f68 | Text | 2,457 | 41 | # abrWaveAnalyser
Marcotti's lab ABR wave analysis GUI. The software can be used to semi-automatically label thresholds and waves (wave I-IV supported) of auditory brainstem responses (ABRs).
## Updates
### 12/2024
- Added support for multiple-file analysis. This requires creating a csv file containing the following c... |
e5aa00650fd4a6f34bace564603688f4271ea91ea8e5b9a40a8c603492c9956e | Text | 2,457 | 41 | ## Table of contents
* [General info](#general-info)
## General info
This Git repository contains codes for the **'Importance of localized dilatation and distensibility in identifying thoracic aortic aneurysm contributors with neural operators'** paper which can be found here: [Link](link_url).
Authors: [Davi... |
bd249f33370c8d8f54243b30346301a7e1b69532a6660242f9e4b0704085f0f9 | Text | 2,461 | 15 | Author: Jingyi Wang
This pipeline calculate the rate of regional-whole brain resting functional connectivity pattern changes across time. To obtain the regional-whole brain resting state connectivity patterns for each session, we first averaged the time series across all voxels within each region of interest. To measu... |
e3f0b09288741617fc81a2ea5fa70b38b370e658c34b67b903b33c31082cc814 | Text | 2,467 | 63 | TOKI
===
deTOKI is a newly developed tool for identification of chromatin topologically associating domains (TAD) in single cells.
Although we use term "TAD" here, we refer to the TAD-like domains in single cells.
deTOKI decode TAD boundaries that keep chromatin interaction isolated with ultra-sparse Hi-C data (single... |
ffdaa486f163656aa51c5641563dff045eda80093e12871063477dcf1aeb239b | Text | 2,470 | 86 | # PCR-bias
This repository contains the code and data associated with the study:
> **Deep learning uncovers sequence-specific amplification bias in multi-template PCR**
It includes scripts for deep learning model validation and motif discovery, aiming to analysis sequence-specific biases that arise during PCR ... |
245cd8719ba35f226ccf0add07faa8ae1acc32c907404a3b750554bed515e6cd | Text | 2,477 | 35 | 
MATLAB toolbox for numerical modeling and image reconstruction in electrical tomography developed at Warsaw University of Technology
## Key Authors
- Dr. Damian Wanta
- Prof. Waldemar T. Smolik
- Dr. Jacek Kryszyn
### Additional Contributors
- Mateusz Szczęsny
... |
30321bf6672f5beaf1117c081130046eb13f0cedee9cfdf579aa67e7bdf141f1 | Text | 2,477 | 55 | # STAMapper
## Overview
STAMapper is a method that annotates cells from single-cell spatial transcriptomics (scST) data. It is a deep learning-based tool that uses a heterogeneous graph neural network to transfer the cell-type labels from single-cell RNA-seq (scRNA-seq) data to scST data.
We also collected 81 scST d... |
4dd5f4a4b332162cebf7b547c93cec89a522bdc61f61bf6d3c42a8b0ab52d9f5 | Text | 2,480 | 35 | 
MATLAB toolbox for numerical modeling and image reconstruction in electrical tomography developed at Warsaw University of Technology
## Key Authors
- Dr. Damian Wanta
- Prof. Waldemar T. Smolik
- Dr. Jacek Kryszyn
### Additional Contributors
- Mateusz Stępniews... |
60af7799c31db26483dc51750b37259094535f2020106592da1df111b0dfbd48 | Text | 2,505 | 44 | # Analysis scripts for _seismic_
_seismic_ is a computationally efficient, powerful, and interpretable approach for
identifying associations between complex traits and cell type-specific expression
using GWAS summary statistics and single-cell RNA-seq data.
This repository contains all code and scripts required for re... |
adc8570cede57ca8a0e74bdde9173c3af4c4e4e45f18ee411486d011341b2a4f | Text | 2,505 | 41 | # One-shot learning for solution operators of partial differential equations
The data and code for the paper [One-shot learning for solution operators of partial differential equations](https://www.nature.com/articles/s41467-025-63076-z), *Nature Communications*, 16, 8386, 2025.
## Data
The datasets in the study are... |
d486169171a3080c88a961b76e61b576242437a9472594cb5c381a64ddd0d74f | Text | 2,507 | 23 | # scRNAseq-NN-LIME
This repository contains the code to train a neural network for classifying individual cells based on their treatment or disease status, using single-cell or single-nucleus RNA sequencing data (scnRNAseq). Additionally, it includes the code to decode the trained models using Local Interpretable Mode... |
096ff6e49ec78aedc1b520a95cfe942ffde032d88a5c923e98b286541ffb6be1 | Text | 2,510 | 72 | # EHR Yield Prediction
Code companion for the manuscript **“Predicting Annotation Yield in AI‑Ranked Electronic Health Record Cohorts: A Regression‑Based Screening‑Saturation Framework.”**
This repository contains Jupyter notebooks and minimal demo data illustrating how to:
1. **Pre‑process free‑text neurology notes... |
477d53c6d4d00e435e277f1680a6fdf207110a5fcc6b9f00888cdcc29b39156a | Text | 2,516 | 67 | ## Sample code for the paper *In vivo spontaneoous Ca2+ activity in the pre-hearing mammalian cochlea* by De Faveri et al..
This repository contains a pipeline for analyzing calcium imaging data for spontaneous activity in the developing cochlea.
## Project Structure
- **notebooks/**: Jupyter notebooks for movie reg... |
097d6f98e7549b029167021533e0be3c412ef4b19c8c1fe83b27db3884ce8376 | Text | 2,524 | 51 | README TO VERSION 2.0.1beta
CorticalSim - cortical microtubule simulator
If you use CorticalSim in publications, please include a citation to:
[for general use] http://dx.doi.org/10.3389/fphy.2014.00019
[for microtubule dependent nucleation] ] http://dx.doi.org/10.1371/journal.pcbi.1013282
[for microtubule dependen... |
cd59ab70744efc889e9b658a6bbf98962442cff8bf8b1a3a053037d88568b063 | Text | 2,527 | 74 | # 🛡️ Diamond: Error-Controlled Interaction Discovery
**Diamond** is a Python library for discovering feature interactions in machine learning models **with rigorous false discovery rate (FDR) control**. It is particularly useful for scientific and biomedical applications where interaction interpretability and statist... |
af43420e5e8aa0a5ce68869e509ac143b447fc4cbfd2457b369b751fd6fc698f | Text | 2,531 | 17 | # 📚 Publications
This repository collects code associated with some of my published works.
| Paper| Repository | Topic | Reference |
|:------|:-----------|:------|:----------|
| Morfini et al., (2025), *Imaging Neuroscience* | `CPM_ABCD_BANDA_predict future_depression_anxiety` | Baseline brain functional connect... |
d4437b587840180144f2d6797b655c60b2803efd50cc014fe01cd52f7b3a8d0e | Text | 2,536 | 82 | # IceQream (IQ) paper companion repository
Welcome to the companion repository for the **“IceQream: Quantitative chromosome accessibility analysis using physical TF models”** manuscript.
This repo contains everything required to:
1. Reproduce **figures** in the paper (R / Python notebooks).
2. Download the raw data ... |
ee5afabb527fcc151f29d311580f4a8c13a6b623f2c0cd31733b6fb3dc57f78c | Text | 2,541 | 49 | ## The best-performing algorithm in the WMH segmentation challenge at MICCAI
This repository provides codes, models, and containers for white matter hyperintensity segmentation in brain MR images with deep learning.
(The latest update was made on 03 November 2025 🔥)
### Use our pre-trained models for your MRI data (... |
f53310233fbed8b22569d95929339e9c0cd53a4547660f03006b650375b9e8eb | Text | 2,541 | 46 | # hippunfold-templateflow
Hippocampus & dentate gyrus surfaces and subfield segmentations, by running HippUnfold on templates in templateflow.
All surfaces have corresponding vertices, and come in three different densities (0p5mm, 1mm, 2mm) which relate to their approximate vertex spacing.
## Use cases:
1. Samplin... |
98da0fb45d2129643148aa9e8139663af8ca6e272ab21ded1235e002d0ad7b12 | Text | 2,545 | 49 | # SWD_AUTOSCORE REPOSITORY FOR SPIKE AND WAWE DISCHARGES (SWD) AUTODETECTION IN SYNGAP1 RATS BY CEPSTRUM ANALYSIS OF EEG SIGNAL
Contact for code: Dr. Alfredo Gonzalez-Sulser: agonzal2@ed.ac.uk
@Gonzalez-Sulser-Team
INCR - SIDB - University of Edinburgh
CODE WRITERN ON MATLAB R2018b
1. Create folder on C://SCRIP... |
6398e7c6439da189342d37c7382878df4add88a35e4d26bd2cca3e9f2b606235 | Text | 2,548 | 75 | # Meeko: interface for AutoDock
[](https://shields.io/)
[](https://pypi.python.org/pypi/meeko/)
[
# dartsort
## :warning: Work in progress code repository
We do not currently recommend DARTsort for production spike sorting purposes. We are in the process of implementing a robust and documented pipelin... |
28525d333e06d807f37a6f6eae487f9d9d61ebf5526f769ee081ea124a64c3e4 | Text | 2,584 | 64 | # GElib
GElib is a C++/CUDA library for building equivariant neural networks. The library can be used as a pure
C++ library or as a C++ extension for PyTorch.
GElib uses [`cnine`](https://github.com/risi-kondor/cnine) as its backend.
Documentation for the C++ API can be found in the 'doc' directory.
Documentation ... |
2aa932cbd57f84ea7019119a0917653e00ad1fdf7a0471a6d936b0611e744721 | Text | 2,584 | 102 | # PEC2 NetMed
**Population-scale single-cell network medicine for neuropsychiatric disorders**
Neuropsychiatric disorders lack effective treatments due to a limited understanding of underlying cellular and molecular mechanisms. To address this, we integrated population-scale single-cell genomics data and analyzed cel... |
7438fe40cc8b1b68ff3d7981e6c634c75ec2fe828d8943841f2651f414e0508b | Text | 2,597 | 34 | ## Application of a multimodal neural interface for monitoring and relapse prevention in alcohol use disorders
Conventional pharmacotherapies of mental disorders have just moderate effects; the probability of relapse remains high. This project, therefore, introduces bioelectronic devices as an alternative toolbox to t... |
c8f061f1b02694d4fdaaceadf4c9b16d62a6eb73402b4363b41c93553bd46970 | Text | 2,632 | 41 | # Gamified version for an Imagined Speech research protocol
Brain Computer Interfaces are a fast-growing technology that transform human thoughts into real-world actions. With this **gamified acquisition paradigm**, you will be able to register imagined speech of four different command words. Use these commands to gu... |
bf43ffc04ace744bf19d06d90d5f0805b9bb9dae64ee9826deb6b4fbaa48b2c5 | Text | 2,636 | 76 | [](https://doi.org/10.5281/zenodo.15733825)
# 🛡️ Diamond: Error-Controlled Interaction Discovery
**Diamond** is a Python library for discovering feature interactions in machine learning models **with rigorous false discovery rate (FDR) control**. It is ... |
47581b338e040284f585a7ee8f801169345409766b09d32bc4b08ccc5e2b64b3 | Text | 2,638 | 71 | ## MARLIN
**M**ethylation- and **A**I-guided **R**apid **L**eukemia Subtype **In**ference
MARLIN is a deep neural network model for DNA methylation-based Acute Leukemia classification from sparse DNA methylation profiles.
For more information please refer to our [paper](https://www.nature.com/articles/s41588-025-023... |
b8ac0fcb4e592c5f67e1a4dc6110794575e2a2b9ea1ba2bfffd9e12c9f65da33 | Text | 2,663 | 32 | # EFMouse: a toolbox to model electric fields in the mouse brain
[](https://doi.org/10.5281/zenodo.14777232) 
<img width="300" height="350" alt="EFMouse example image" align ="right" src="http... |
bf07cc9b9766a6ed264971702277024c668873acf4ca88c1d740ec47b536ce3d | Text | 2,666 | 38 | # Emotional Dysregulation and Adolescent Violent Crime Psychology: EEG Emotion Analysis & Digital Interventions
## Overview
This repository contains the research and implementation of a comprehensive approach to understanding and mitigating adolescent violent crime through the integration of psychological insights, e... |
b18b395cfd96f331ee8ec047b75c86954db79b57015be93f3e981cdb31ff86ea | Text | 2,676 | 62 | # snceg - Substantia Nigra Neuromelanin Segmentation with Attention U-Net.
Attention U-Net for the segmenting the NM hyperintensity of the substantia nigra from Magnetization Transfer Contrast MRI.
The model is used to derive SN masks from neuromelanin-sensitive MRI, but was trained on multiparametric MRI and is re... |
470fd0fb08a3ac8ef642947a4cd8973d0a8ef1bbfcffd7d751fe9bfdd523d054 | Text | 2,677 | 74 | <h1>ReaxNet</h1>
<p align="center">
<img src="./site/logo.gif" width="300">
</p>
**ReaxNet** package is a JAX implementation of polarizable long-rang interactions integrated equivariant neural network potential.
## Framework overview
## Installation
### Easy install
```bash
pip in... |
25b7712f07e59544ecc367ff17286521e80813dc15d37247c20a2417f2090db1 | Text | 2,684 | 48 | This project implements an attack knowledge inference model based on graph convolutional network (GCN) and convolutional embedding (ConvE) KGCoveE, which is built using PyTorch and SciPy. The model realizes attack knowledge inference by modeling the graph structure of CWE-related data.
(1) CWE data source
--Data from t... |
dfcd4779057226f59b976565dc8a00f62783c6cb61a31f26f38b4510705edb07 | Text | 2,686 | 68 | .. -*- mode: rst -*-
.. image:: https://travis-ci.org/LABSN/expyfun.png
:target: https://travis-ci.org/LABSN/expyfun/
.. image:: https://coveralls.io/repos/LABSN/expyfun/badge.png
:target: https://coveralls.io/r/LABSN/expyfun
`expyfun`_
=========
This package is designed for audio-visual experiments with precise... |
0fdb519209ef2bc813a6e53ebd87222cabf7d3af82cd2c0f73d545aaefcb4d2c | Text | 2,693 | 24 | # Geometry Reduced Order Modeling (GROM)
Code for the paper **"Geometry Reduced Order Modeling (GROM) with application to modeling of glymphatic function"**
Preprint available from: http://arxiv.org/abs/2506.09442 <br>
Work pending review
**Abstract**:
> Computational modeling of the brain has become a key part o... |
5935ff370f3d3c0c14dbd1a49274fd0a97c22a58abee70ed41c29d682cd03f17 | Text | 2,693 | 98 | # Tissue
## Features
tissue is a model repository in a single python package for the manuscript Fischer, D. S., Ali, M., Richter, S., Etrürk, A. and Theis, F. "Graph neural networks learn emergent tissue properties from spatial molecular profiles."
![Screenshot 2023-07-31 at 18 49 03](https://github.com/theislab/t... |
93132e272703132c8f16f8646be32114517f1a9faaa063b0fab1596a2679e165 | Text | 2,699 | 39 | # DBS Outcome Prediction Using Resting-State fMRI Connectivity
This repository includes anonymized data and code for doing feature extraction on resting-state fMRI ROI-ROI Pearson's correlations and predicting Parkinson's medication change with DBS. The code is written in Python. The repository is part of ongoing rese... |
1c4da30ca73e0cfe04bd039f82cd57fa3580e9123233c0c57c1592e269931442 | Text | 2,714 | 66 | # neuron-to-SCLC-synapses
This repository contains the scripts used in the manuscript, "Functional synapses between small cell lung cancer and glutamatergic neurons". It includes two analysis pipelines:
1. **Orthology mapping pipeline**: For generating orthology mappings between human and mouse genes.
2. **PiggyBac... |
d54d8358fed9817bbd9f7fe34cdb398b2075bb7d85d1e056fa6cc8d667aa11c9 | Text | 2,717 | 89 | **Overview**
This repository contains analysis and plotting scripts to replicate Figures 4 and 5 from our eLife paper.
Here is a link to the paper: https://doi.org/10.7554/eLife.92088.2
Data source: Available from Dryad: https://datadryad.org/dataset/doi:10.5061/dryad.qz612jmsh
There are three experiments, ea... |
0d48c1fc2077f68e5257bda388832849ccb044a28d68a4a721171849d197f5d0 | Text | 2,725 | 53 | # OpenFF Recharge
[](https://github.com/openforcefield/openff-recharge/actions/workflows/ci.yaml)
[ is a biologically-driven
multi-resolution mapping strategy to assess the transcriptional fidelity of
midbrain cultures via scRNA-seq. In the first tier, query datasets are projected
onto the fetal whole brain atlas to assess the brain region specificity of ... |
6ce24f5f319fdf20ca672cf7b545e75d47a6b57d2aa69775043d6f521d701f29 | Text | 2,736 | 50 | # Robust-Uncertainty-Estimation-Framework-in-Deep-Reinforcement-Learning-for-Active-SLAM
This repository contains work on deep reinforcement learning for a TurtleBot robot using a custom-built architecture called Bayesian A2C. The project used the Gazebo simulator and an open-source OpenAI gym extension named [gym-gaze... |
90f6a0a2158e745b6cfc64178f5e2d22468abf56eee00af0e3a285c9605bdb76 | Text | 2,749 | 63 | # Enhancing Human Activity Recognition with Machine Learning
This repository contains the reproducible workflows and setup instructions for the study:
> **Enhancing Human Activity Recognition with Machine Learning: Insights from Smartphone Accelerometer and Magnetometer Data**
> Luis Augusto Silva, Paulo Jorge Coel... |
a2692fbae7793a145f3b6592c2af247379fe2ef79a13146b485c30dfb7831d32 | Text | 2,757 | 50 | # Critical Slowing Down in Free Recall
This repository contains relevant code, data and documentation associated with the study "Adaptive proximity to criticality underlies amplification of ultra-slow fluctuations during free recall". The study explores how the phenomenon of "critical slowing down" (CSD) may be relate... |
78ec852d521c07518a8457cc7b4a36da3680fcf24eda62299dcf9502d773ba78 | Text | 2,763 | 68 | # Bio-Formats
[](https://github.com/ome/bioformats/actions)
[](https://github.com/ome/bioformats/actions)
[. The details of the dataset can be found here https://elifes... |
b1733204dfbb5da3f7bd47f75a02e4c00dae2d0a914078f770e8ad5ace15ea9f | Text | 2,773 | 23 | # Phase coherence Kmeans
## Github repository for the following publications:
#### [Castro, Luppi, Tagliazucchi et al, Nature Communication Biology (2024)](https://www.nature.com/articles/s42003-024-06858-3)
#### [Hoffner, Castro et al, eLife (2024)](https://doi.org/10.7554/eLife.101688.2)
## Overview
To analyze brai... |
4493d95b2686cf8202b4fa35c9bebcd63ff644c786b7eb98315160be43048578 | Text | 2,775 | 103 | # Nextflow Workflow for Meteor2
## Overview
This repository provides a [Nextflow](https://www.nextflow.io/) workflow to run **[Meteor2](https://github.com/metagenopolis/Meteor)** on short-read, single-end metagenomic sequencing data.
Among other outputs, it generates gene and species abundance tables.
> ⚠️ **Note:**... |
9604d1ee1f9d356d631e801a60da1fb9d15be5922b93cd84072215c80d732d90 | Text | 2,789 | 68 | <div align="center">
<img src=./docs/_static/_images/isf-logo-white.png#gh-dark-mode-only width='350'>
<img src=./docs/_static/_images/isf-logo-black.png#gh-light-mode-only width='350'>
# The In Silico Framework (ISF) - hotzone
[![Linux](https://github.com/mpinb/in_silico_framework/actions/workflows/test-isf-py38-pix... |
856618b1fc9fbb97a39424d7cdb228ca90e293a71a81a34a2b5b9f616738586e | Text | 2,800 | 84 | # Discovering Sensorimotor Agency in Cellular Automata using Diversity Search
Code to reproduce the experiments from the paper : Discovering Sensorimotor Agency in Cellular Automata using Diversity Search
Gautier Hamon¹, Mayalen Etcheverry¹, Bert Wang-Chak Chan², Clément Moulin-Frier¹, and Pierre-Yves Oudeyer¹
1. I... |
24d73ac5317254057fd90b98f02cc96690f8cd322bdb0d2a815de591aa045b26 | Text | 2,803 | 100 | # Tissue
## Features
tissue is a model repository in a single python package for the manuscript Ali, M., Richter, S., Etrürk, A. , Fischer, D. S. and Theis, F. "Graph neural networks learn emergent tissue properties from spatial molecular profiles."
[... |
dbeef18743340ae0c697268ff76e826bbd30eb7c740c0a91ee2e0cde728a05d2 | Text | 2,822 | 74 | # Mixture of von Mises disttributions
This module contains an EM algorithm aiming at fitting a mixture of [von-Mises distributions](https://en.wikipedia.org/wiki/Von_Mises_distribution).
- Official repository is on [https://framagit.org/fraschelle/mixture-of-von-mises-distributions](https://framagit.org/fraschelle/m... |
12dfaa5d89c9c77e85c82c900e238b6424faf1c8d7c2e527ef14813fdb3b510c | Text | 2,826 | 59 | # MC_MMD
---
Modality Contribution in Multimodal Medical Datasets (MC_MMD)
---
"What are You looking at? Modality Contribution in Multimodal Medical Deep Learning Methods"
## method
The modality contribution is a measure for the importance of one modality in a multimodal dataset.
*(Details in paper)*.
We applied o... |
99f5fef700f065e9bc7493623cc9be1cf66c021c66d877467307efd28f8df5ee | Text | 2,826 | 54 | [](https://doi.org/xxx)
# Ripple LFP Classifier
The code in this directory demonstrates how to infer the CSD laminar profile of individual hippocampal ripples from the local field potential (LFP) signal recorded along the somato-dendritic axis of CA1. This work is highlight... |
7fed19d3789a67b1815cc987592e1d7e47c9f48d18fcc0823b98101be37eb94b | Text | 2,835 | 85 | # VentriclesCNN
[](https://doi.org/10.17605/OSF.IO/HPU5B)
[](https://osf.io/hpu5b/)
[](https://openso... |
1337ff2d5d3271e82c3542be72e1dc9bcc43ea4754ae167f0414faec06509550 | Text | 2,836 | 75 | <h1>ReaxNet</h1>
<a href='https://arxiv.org/abs/2410.13820'><img src='https://img.shields.io/badge/arXiv-2403.13820-blue'></a>
<p align="center">
<img src="./site/logo.gif" width="300">
</p>
**ReaxNet** package is a JAX impl... |
c1f3e077f993c93446a07245e0998439b797daa94e64ea59e61aacc0b1fc8617 | Text | 2,841 | 59 | This is the LAMMPS software package.
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed unde... |
c96d148185c9555f77621dd84b60c762f788e24fc449af94d685ddd51092d753 | Text | 2,846 | 17 | # ChangeDetectionPANN
This repository contains the offical code used in the Training-free AI for Earth Observation Change Detection using Physics Aware Neuromorphic Networks as publised in [Nature Scientific Reports Paper](https://www.nature.com/articles/s41598-025-19057-9).
## Training-free AI for Earth Observation ... |
d0e2c0b30c1270c02b3eed4ea4e9504e57b4396f7f0cc99cfe915f85160782b0 | Text | 2,848 | 16 | ### Note: This repository describes how to build FED3 devices, and is mostly here for historical purposes. If you purchased a FED3 device and want to know how to program and use it, please visit the [FED3_library wiki](https://github.com/KravitzLabDevices/FED3_library/wiki).
---
FED3 is an open-source battery-powered... |
5b03ebe8957a6dcd53769eb3cfa24b732af710e6140ce094cb1986be509f686a | Text | 2,851 | 55 | GROMACS v. 2020.4 MD simulation protocol
The directory where the calculations run must include CHARMM36 directory downloadable from
https://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
We used charmm36-jul2021.ff version for our simulations.
gmx pdb2gmx -f initial_*.pdb -o prot.gro -ignh
gmx editconf -f prot.gro... |
aab07d6f3907cee17ebcf3de86a825d70137da544fc43d50136a29708554ad70 | Text | 2,853 | 54 | # Figure 8 Code
Reproduces Figure 8 from Wisser, Blackwood et al., 2025 (iScience)
## Python (Motion correction/source extraction using CaImAn and session alignment/cell matching)
### Installation
Required data: Figure8.zip from https://zenodo.org/records/17117612. Download and unzip, preferably to the same folder ... |
151e5aadd1a73f56ec6519061f2b5900fa164b11b5a2d47c546b68401b43d51b | Text | 2,865 | 41 | # Brain-metabolism-and-connectivity-dynamics
## Description
This repository contains the scripts used for the study _"Multiscale excitation-inhibition balance dynamics: integrating metabolite kinetics with time-varying executive networks"_.
It implements the analysis of novel interleaved dynamic functional MRI and fun... |
a8a11b6dff24cc5b159d29e426bccc44e1b6b0ef9ab2ebd8f031916bec312d0a | Text | 2,870 | 43 | # STARmap
Reference: Xiao Wang1^, William E. Allen1,2^, Matthew A. Wright1,3, Emily L. Sylwestrak1, Nikolay Samusik4, Sam Vesuna1, Kathryn Evans1, Cindy Liu1, Charu Ramakrishnan1, Jia Liu5, Garry P. Nolan4,†, Felice-Alessio Bava4,†, Karl Deisseroth1,3,6,†, "Three-dimensional intact-tissue sequencing of single-cell tra... |
79ad2d0e82e4d27c3ef8963f317c6dc1d04919d40cc1f46195e3bf4e99f55f43 | Text | 2,881 | 27 | # Mass_Univariate_ERP_Toolbox
### MATLAB functions for analyzing and visualizing large numbers of *t*-tests performed on event-related potential data.
The Mass Univariate ERP Toolbox is a freely available set of MATLAB functions for performing mass univariate analyses of event-related potentials (ERPs), a noninvasive... |
f30b8920c4701704764c6d214dd8e60abc0c1acf4036bf3a82b18b8eb7683fe2 | Text | 2,905 | 34 | # Elucidating Reaction Dynamics in a Model of Human Brain Energy Metabolism
*This software is used for producing the results included in the following paper:*
**Patsatzis, D. G., Tingas, Ef.-Al., Sarathy, S. M., Goussis, D. A. & Jolivet, R. B. (2025). Elucidating Reaction Dynamics in a Model of Human Brain Energy Met... |
d9810d3caa31c6cba46933a8a0d5c922d93ca3cd6ce73641da19055e4bb7234a | Text | 2,912 | 62 | GRE_vessel_seg computes a vein (or arteries) segmentation (output=vein_seg) from multi-echo or single-echo
gradient echo data in Matlab. As the algorithm is implemented in a modular way, it
is possible to replace the functions for background suppression, calculation of the
vesselness function, the scale-wise represent... |
7cd1819fb6f10570bde697d75fb6be701180e0edc9b18466652e7f89167f0e49 | Text | 2,914 | 46 | # [TransMarker: Unveiling dynamic network biomarkers in cancer progression through cross-state graph alignment and optimal transport](https://github.com/zpliulab/TransMarker)
**TransMarker** is a computational framework for detecting dynamic biomarkers in cancer progres... |
f05c3546d8d44bc5ea9e8cd8e1b55d0c0d78ed9e60a30e7c9357f39969231d8d | Text | 2,915 | 18 | These scripts allow to run the physical and mental effort tasks that we used. The tasks consist in a physical and a mental effort task spread into 4 blocks, alternating between physical and mental effort with the order between physical and mental effort being counterbalanced across participants. Each task was performed... |
f360e1ecc8bc254e023593b0e2624e6d5ee337b93627bf6cbfccace6076a025d | Text | 2,922 | 87 | <h1 align='center'>Scipion flexutils plugin</h1>
<p align="center">
<img alt="Supported Python versions" src="https://img.shields.io/badge/Supported_Python_Versions-3.8_%7C_3.9_%7C_3.10_%7C_3.11_%7C_3.12-blue">
<img alt="GitHub Downloads (all assets, all releases)" src="https://img.shields.io/github/downloads... |
39ab76985b469e7b4014a9a249df4ca68d55419b201aabc85c77fb83e49ae845 | Text | 2,926 | 95 | # HEMF
This repository provides the supplementary code and data to the paper entitled "***HEMF: An Adaptive Hierarchical Enhanced Multi-attention Feature Fusion Framework for Cross-scale Medical Image Classification***".
 [![DOI](https://zenodo.org/bad... |
28fe9f46d0312ba3d98abb767d10828e737b570bef27d6b520049c63ae845cdd | Text | 2,929 | 72 |
# Higashi: Multiscale and integrative scHi-C analysis
<img src="https://github.com/ma-compbio/Higashi/blob/main/figs/logo2.png" align="right"
alt="logo" width="290">
https://doi.org/10.1038/s41587-021-01034-y
As a computational framework for scHi-C analysis, Higashi has the following features:
- Higashi repre... |
53b1e98e31845d3fbe52fff2c9be3ea532ef9f404f17e4333798e6bcc4f30b7b | Text | 2,932 | 75 | # Dual contrastive learning-based reconstruction for anomaly detection in attributed networks (DCOR)
Official implementation of **DCOR**, which uses dual autoencoders with reconstruction-level contrast (RLC) for anomaly detection in attributed graphs.
## Overview
<p align="center">
<img src="docs/dcor_augmentation... |
e9cb312aedc71a3caee3cdae32c704e628dd4b5bf15a781223fd35524e1950f8 | Text | 2,939 | 35 | <h1 align="center">SARS-CoV-2_TissueDiversity: SARS-CoV-2 spike protein functional adaptation across 27 tissues in a fatal case of COVID-19</h1>
<h2 align="center">Manuscript information</h2>
<h3 align = "center">SARS-CoV-2 spike protein functional adaptation across 27 tissues in a fatal case of COVID-19</h3>
<p... |
812c961d1b8f0f497016944a1e86e7e52b369e2455fe3554e5dbb971b80f1ef4 | Text | 2,951 | 51 | # Exploring the Role of Language in Public Perception of Environmental Health and Exposure Risks Using EEG
Understanding public perception of environmental health and exposure risks is critical for developing effective public health strategies. Traditional methods, such as surveys and retrospective analyses, often fai... |
51be76a5393181c5a21d10a12a2dbc308fc1a3e6ed39efa5d1a72cb17403676c | Text | 2,970 | 81 | [](https://github.com/amueller/word_cloud/blob/master/LICENSE)
[](https://zenodo.org/badge/latestdoi/21369/amueller/word_cloud)
word_cloud
==========
A little word cloud generator in P... |
474c5e2bab2bca94b32f18fba3e10568e56e83f61b94995d314b3bf59f02a3cc | Text | 2,988 | 56 | # Structure-Aware Image Generation
## Introduction
This is a project about Plants & AI, featuring multiple functionalities.
Title: [LeafGen: Structure-aware Leaf Image Generation for Annotation-free Leaf Instance Segmentation](https://www.sciencedirect.com/science/article/pii/S2643651525000986)
Based on this paper, ... |
f28598f594815b5d58c4e2a7347b3870095a22041a92643c315846338e3b7bf2 | Text | 3,003 | 41 | # COVID-19-APP
COVID-19 Pneumonia Diagnosis Using Medical Images: Deep Learning–Based Transfer Learning Approach
Abstract
Abstract
Background:
SARS-CoV-2, the causative agent of COVID-19, remains a global health concern due to its high transmissibility and evolving variants. Although vaccination efforts and therapeuti... |
35464c6f8aa45f6a7ee378681f946f896978a962d279fcd5b39fe39a5f259f2c | Text | 3,007 | 86 |
# Install
**Install conda to control environments**
**To access complete project data and code click on Zenodo button**
[](https://doi.org/10.5281/zenodo.13647157)
**Linux**
Download installer:
```
wget https://r... |
cd7e831cb277651e95891a796ec097f3e605f930f8115125e14e1728aab44dc4 | Text | 3,048 | 63 | <h1 align='center'>FINDR</h1>
<h2 align='center'>Flow-field inference from neural data using deep recurrent networks</h2>
Neurons work together in large groups to solve tasks — like deciding whether to buy a laptop or not based on online reviews. A central premise in neuroscience is that the brain's algorithm for doin... |
fe2ee3c1ead8c8df6f28980dab0f5d17a56eddff87c5af419b31e06cd2cce9a0 | Text | 3,048 | 29 | About
-----
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the ultrafast [STAR aligner](https://github.com/alexdobin/STAR), and ... |
cf37de6373b9f6c750f2559e58d22a77f1e83e200764f93f51d470dabe4d0692 | Text | 3,079 | 36 | <h1 align="center">SARS-CoV-2_TissueDiversity: SARS-CoV-2 spike protein functional adaptation across 27 tissues in a fatal case of COVID-19</h1>
<h2 align="center">Manuscript information</h2>
<h3 align = "center">SARS-CoV-2 spike protein functional adaptation across 27 tissues in a fatal case of COVID-19</h3>
<p... |
91e44bbf8e3b4ae971eccbae497ff769ebc31a7b7c7dfa3d205eab8023e13ecc | Text | 3,082 | 27 | # Route-Centric Ant-Inspired Memories Enable Panoramic Route-Following in a Car-like Robot
Code (and dataset) for our submitted paper "Route-Centric Ant-Inspired Memories Enable Panoramic Route-Following in a Car-like Robot" in *Nature Communications*.
You can download the paper via: **Upon Publication** <!-- [[... |
e07687f8f49600bf8a9b8780346d187de77e17548e6bdc06b6f6cfec78075759 | Text | 3,102 | 38 | [](https://doi.org/10.5281/zenodo.14960397)
# COX_TDP43-fingerprinting
This repository contains the analysis code associated with the MND<sub>TDP</sub> single-molecul pulldown project, led by Dr Dezerae Cox. This manuscript has been submitted for publica... |
33ceda5e606fb3fb9135e49fc692b46981cab468b78832add96c44495cd94344 | Text | 3,118 | 73 | <p align="center">
<!-- Hero image (replace with your actual path/filename) -->
<p align="center">
<!-- 3-panel gallery of sample frames -->
<img src="images/imagen_real_1.jpg" width="30%">
<img src="images/pointcloud_filtrada_1.png" width="30%">
<img src="images/pointcloud_original_1.png" width="30%">
</p>
... |
5575de4c4a669018be17bbec2fa197aad4c71f5de92ccf0673f6ef4991d3ec0e | Text | 3,123 | 83 | # DIMS
Pipeline that processes raw Direct Infusion Mass Spectrometry data.
### Folder Structure
```
.
|───CustomModules/ (GitHub repo with pipeline scripts)
|───assets/ (extra Nextflow files)
|───db/ (Human Metabolome Database files)
```
## Docker image
```
docker build -t ghcr.io/umcugenetics/[NAME]:[tag] .
docker ... |
02d96aef8c44b36d1977264cdef7a7de80482c2ed58daa0d45ef669dc73b24e5 | Text | 3,141 | 58 | # Kv7.1 Ion Channel Modeling and Pharmacological Analysis
This repository contains the code and data associated with the manuscript:
**"Electrophysiological characterization of the state-dependent inhibition of Kv7.1 and IKs by UCL2077"**
Authors: Daniel Sastre, Efthimios Kyriakis, Julia Schauer, Magnus Chan, Ying... |
9b1f14a7ba5815635f8bb137350de283d801a55c03d6d7b28e9ef3e9252c972a | Text | 3,174 | 89 | # AD and PD Brain Organoid Comparison
This repository provides all scripts and data required to reproduce the results from:
**Single-cell analysis reveals shared and distinct molecular signatures in brain organoid models of Alzheimer's and Parkinson's disease**
**Authors:** Sophie Le Bars, Mohamed Soudy, Sarah Lou... |
1b25a313ddaa63767fd559b5667ccd571fc7686e6816fa3ef7214594d87a0278 | Text | 3,183 | 72 | # HeatmapGenerator
This is a script to create heatmaps for publications.
This is an example for how it can look generated from the date in "data/example.csv".
In the current version (v2.0.6), the following has be... |
1f01233c93c659fb299332bfe7ea718dc7f19de0d1192d193e39f63d36d4dede | Text | 3,191 | 63 | [](https://hippomaps.readthedocs.io/en/latest/?badge=latest)
<img align="right" width="200" src="https://github.com/MICA-MNI/hippomaps/blob/mast... |
69845e9c6e40fcebec6809686b27b9667b38870cc89643b650a5066a9c6e2448 | Text | 3,196 | 52 | # Cortical gradient analysis
Author: A Zarkali
Date last updated/checked: 16/09/2025
# Content
This repository contains code and group-level data presented in this paper: https://www.biorxiv.org/content/10.1101/2025.06.25.661456v1
It provides details on the pipelines used to generate the data and results presented in... |
036a61706c903d5ff1865cc9f5049a59bb956fd86f7991bf1e55ef891e27efb9 | Text | 3,211 | 40 | [](https://doi.org/10.5281/zenodo.14960397)
[](https://doi.org/10.5281/zenodo.14965410)
# COX_TDP43-fingerprinting
This repository contains the analysis code associated with the MND<sub>TDP... |
1f6b7d34072939b69ef92c3053631408b840fc47c618d91dbaef894d56a27553 | Text | 3,229 | 79 | # bullseye pipeline
Pipeline for creating a _bullseye parcellation_ of the cerebral whiter matter using part of the FreeSurfer output and commands.
It provides an (anatomy-independent) spatial localization based on an radial component (ie, lobes) and a depth component.
It can be used to obtain region-specific quantific... |
2388dca45d1afd33ec839f09f89e5fa05ef396594cec0df7f51798247d3a829d | Text | 3,233 | 29 | # bids-pipelines
This is a matlab script for using BIDS (Brain Imaging Data Structure) apps to process BOLD functional MRI (fMRI) using offline recon such as those with amri_epi, where no dicoms are available.
More info on BIDS can be found at https://bids.neuroimaging.io. Overall, this pipeline uses sMRIPrep and fMRI... |
53260662494c8b50653d698ce2e50aeec2bddfb0f64bf9262c1537266902e48c | Text | 3,243 | 86 | # Fiber Photometry Analysis - Vestring et al. (2025)
Code and data for the fiber photometry analysis featured in **Figure 3** of the publication:
**Vestring et al.**, *Nature Communications*, 2025.
---
## Repository Structure
├── 1-Raw/
│ ├── Recordings/ # Raw .lvm files
│ └── V... |
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