sha256 stringlengths 64 64 | language stringclasses 27
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|---|---|---|---|---|
4fda6b8f5e4d04d01ab75d112525bd01a21ef460d73df154f05c31f6874c92ba | Text | 1,917 | 19 | # Cheese3D Paper Figure Notebooks
The following notebooks can be used to generate the figures in our paper, provided that the required datasets are available (details in each notebook). See the descriptions below.
## Reproducing Cheese3D paper figures
The following notebooks contain the code required to reproduce th... |
e00a629f44ee99c82c61777a5a388300f545c5f8f4b83864cfae46476db57b38 | Text | 1,944 | 38 | [](https://openfree.energy/)
[](https://github.com/OpenFreeEnergy/cinnabar/actions/workflows/ci.yml)
[] [[Miniscope DAQ Software Wiki](https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software/wiki)] [[Miniscope DAQ Firmware Wiki](https://github.com/Aharoni-Lab/Miniscope-DAQ-Cypress-firmware/wiki)] [[Miniscope Wire-Free DAQ Wiki](https://github.com/... |
00ec4701d6ce5e4cd2c591eb3ec4afcf1f672242d7264ef36c8eda94135f4206 | Text | 1,974 | 64 | Introduction
============
This is a collection of handy small tools for analyzing neuroimaging data (esp.
high resolution fMRI), which can be used both as a Python package and
a set of command line tools. It is a useful augmentation to the ``AFNI`` tool chain.
Documentation
=============
The latest `mripy document... |
6f82c5b8585cb321b272a3def8632d9f87a313851d8c8c5ba19270b4120a20d7 | Text | 1,990 | 38 | # GSPcochlea
## GSP COCHLEA: A GRAPH SIGNAL PROCESSING APPROACH FOR STUDYING SOUND ENCODING
Melia E. Bonomo, Santiago Segarra, Robert M. Raphael, Rice University, 2026
This code is freely distributed under the GNU General Public License. http://www.gnu.org/licenses/gpl-3.0.html
### PATIENT GROUPS
- 32 patients spr... |
a448aca9152a2effbf2195b25f4497955fa797cd9b134c4b9c0922a13e620611 | Text | 1,997 | 35 | # XAI-Cancer-Survival
A Systematic Evaluation Framework for Explainable AI (XAI) in Deep Learning-based Cancer Survival Prediction
### 📖 Introduction
This project provides a systematic evaluation framework to assess the performance of various Explainable AI (XAI) methods within the context of cancer survival predicti... |
bb70910ff95ab92c15589610e71f08bc257ac106ad1da9e01e6aa26d8d366dc8 | Text | 1,999 | 70 | # Predictive Postural Control in Mice
This repository contains the codes accompanying:
**Doi et al.**
*A novel behavioral paradigm using mice to study predictive postural control.*
Frontiers in Neuroscience, in press.
---
# Overview
This system implements a predictive postural control task in freely-moving mi... |
3f3fee03019554c7d596bf1c79909df1769bb898132cc850967ef61bd1a728d3 | Text | 2,003 | 14 | # MT-and-permeability-effect-on-two-compartment-dMRI-WM-model
Repo for code that reproduces the results and analysis in the paper [Investigating the sensitivity of the diffusion MRI signal to magnetization transfer and permeability via Monte-Carlo simulations](https://www.biorxiv.org/content/10.1101/2025.07.16.664944v1... |
a126ccda8f2bc0af7659915cb26abfe81cda7bfb87a34b5c54807bca7f206275 | Text | 2,033 | 58 | # Beyond Brainscore
Code for "Illusions of Alignment Between Large Language Models and Brains
Emerge From Fragile Methods and Overlooked Confounds".
## Environment
Required packages can be installed using the requirements_updated.txt file.
We recommend first creating a conda environment: conda create -n "YOUR_ENV... |
1090c9cc1e5924c9f0f8217988ffc3ea207b3bced49f113371ba57e914b5ebb0 | Text | 2,074 | 40 | Latent Space Exploration of Generative Neural Networks
=====
Code and user instructions for usage in Python 3.6
Paper: Subham Choudhury, Ilias Toumpe, Oussama Gabouj, Jakob Sebastian Behler, Vassily Hatzimanikatis, and Ljubisa Miskovic. "Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via L... |
5e56a5e9cbec579eb8383b7b5fb8b7d3491c3a0ea08c10cd19d06422a30159c4 | Text | 2,083 | 58 | # MaskedFacePerception
This repository hosts the data and code supporting [our study](https://doi.org/10.48550/arXiv.2303.06031) on the neural correlates of masked face perception across levels of face familiarity.
## Data Availability
The repository contains raw and processed behavioral and EEG data, experiment co... |
e825068ce7983838dba229624e71f4aa9305ffccee14d40ba633eaaab861d605 | Text | 2,086 | 52 |
[](https://travis-ci.com/ram-compbio/CANDO)
[](https://codecov.io/gh/ram-compbio/CANDO)
[** loading coefficients in new datasets, without the need to re-run the full ... |
e6ed6fb17cc7a00abf8d5716fd844d79596378e86531a461ca69637aaca992c1 | Text | 2,112 | 28 | # Rational Design of Single-Phase High Entropy Oxides via Large Language Model Data Mining and Explainable Machine Learning
## Summary
This study leverages the large language model **GPT-OSS-120B** to automatically extract high-entropy oxide (HEO) data from scientific literature with **96% accuracy**, enabling the ... |
b4b2b0276139308bb3fa49e5b89b8c24b58516ca25998b3c844d210b00bc18f8 | Text | 2,128 | 61 |
# Comparative single-nucleus and spatial transcriptomic profiling of opossum and mouse V1
Code for
**Gorzek & Trachtenberg (2025)**,
*Comparative transcriptomics reveals differences in cortical cell type organization between metatherian and eutherian mammals*.
**bioRxiv**. [https://doi.org/10.1101/2025.10.03.680397](... |
e8aad4a28b187ca76b0947bc07495e4730878ee6b1873bf502056e95373ed31f | Text | 2,180 | 52 | Minimal Implementation Package for Deep Feature Optimization using Fusion of Multiple Self-Supervised Learning Approaches and Filter-Based Feature Selection for Lung Cancer Histopathology Classification
Overview
This repository provides the minimal implementation package associated with the manuscript tit... |
0a2462dae7930171774117136df0d3497b70302f6f5c811b9689779b16608f8e | Text | 2,185 | 21 | # Chapman-et-al-iScience
Processing code written for "Experience and behavior modulate piriform cortex odor representation in freely moving mice" in iScience. This repository contains a small amount of sample data and scripts used to create clean response tables ("ProcessedData") and to generate the figures in the manu... |
da06a1470b4d3bf66df63ab6f8c288a8989171905f1e62300e83467c9cd10da7 | Text | 2,202 | 52 | [](https://openfree.energy/)
[](https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml)
[
This repository contains the analytical code used for the cost-effectiveness analysis presented in the manuscript:
"Cost-effectiveness of Esketamine versus Alternative Treatment Strategies for Treatment-resistant Depression in Hong Kong: A Mu... |
ca05a0a3b2326729916a0f82f5e925a252ba6999932c6b2e78ffe3bc0f853f4c | Text | 2,212 | 43 |
parallel-fastq-dump
===================
parallel ``fastq-dump`` wrapper
Why & How
---------
NCBI ``fastq-dump`` can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file (see the protip below). This tool speeds up the process by dividing th... |
529ad22f67dbbe1c16b05d4648a643e3b519d21b18b3f43d7b321e0519052483 | Text | 2,279 | 27 | # connectome_diffusion
Code to reproduce all analysis in Henderson et al. 2019 ("Spread of α-synuclein pathology through the brain connectome is modulated by selective vulnerability and predicted by network analysis", https://www.nature.com/articles/s41593-019-0457-5). In these analyses, we use a linear network diffus... |
35083366605e86a97fd656962670a4f96d34a0a655b9ce316d88653ec826e748 | Text | 2,333 | 95 | # Predicting Unconfined Compressive Strength of Geopolymer-Stabilized Clays Using SFF-ELM
This repository contains the dataset and runnable code used in the study:
"Predicting unconfined compressive strength of geopolymer-stabilized clays using a sector fruit fly–based extreme learning machine."
## Authors
Mo... |
2d77824e43356c0fba3a8c9be7fd1bd55d201e62cf3063daae28279ce5436f1b | Text | 2,347 | 55 | # Brainfound: A Foundation Model for Multi-modal Brain Medical Imaging
**Brainfound** is a large-scale, multi-modal foundation model for brain medical imaging. It is pre-trained on over **3 million brain CT images** and **7 million brain MRI images**, along with their corresponding radiology reports. By integrating ad... |
3ed1dc1e9a04618d18b9a1f16644525a0c08a7a69148cec3a0831cda29f8b10e | Text | 2,356 | 37 | # Ontology Based Application Starter Kit (OBASK)
Ontology Based Application Starter Kit (OBASK) is an innovative tool that empowers users to easily create search and knowledge exploration applications using their ontologies, without the need for any programming skills. With OBASK, users can quickly kickstart an ontolo... |
a94e0984b8ac4f8472e80ea3cc85ff94e69eeaa0409958c81ce3a4bd318bc6d4 | Text | 2,396 | 27 | # ConcatMiniscope
MATLAB algorithm for the concatenation of miniscope recorded sessions.
This pipeline is based on the [Miniscope Analysis Package](https://github.com/marcnormandin/MiniscopeAnalysis_CNMF_E) developped by Guillaume Etter - McGill University.
Requirements:
1. Matlab 2016 or later
2. [NormCorre algorithm... |
ed402460fc0f94a9b63b00f3e2686398da054844f31e35113ff8bd95b2377d64 | Text | 2,430 | 29 | # ConcatMiniscope
**DOI: 10.5281/zenodo.5676164**
MATLAB algorithm for the concatenation of miniscope recorded sessions.
This pipeline is based on the [Miniscope Analysis Package](https://github.com/marcnormandin/MiniscopeAnalysis_CNMF_E) developped by Guillaume Etter - McGill University.
Requirements:
1. Matlab 201... |
0613fde9227ca4c8fb744618106d108588cee36b4a180144a65748002d9e8f84 | Text | 2,435 | 38 | # VDVAE hallucination code for the paper: "The oneirogen hypothesis: modeling the hallucinatory effects of classical psychedelics in terms of replay-dependent plasticity mechanisms"
By Colin Bredenberg, Fabrice Normandin, Blake Richards, and Guillaume Lajoie
This codebase is adapted from https://github.com/openai/vdva... |
ba7dbf798f64020bba460130a4b17f13902ddf9ccbc5d4f560d62a62be9e1c8c | Text | 2,474 | 83 | # KIMMDY
[](https://github.com/graeter-group/kimmdy/actions/workflows/tests.yml/?branch=release-please--branches--main)
Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamic... |
602f8ea3039e21d91e370251cd6cf6d30952a0b153e31f3937214d4c1482e16d | Text | 2,483 | 56 | [](https://industrybenchmarks2024.readthedocs.io/en/latest/?badge=latest)
[](https://doi.org/10.5281/zenodo.17245549)
# OpenFE 2024 Industry Benchmarking Project
Welcom... |
eb11c8f51aa4c2341546cf66ca7e8017821c1e6c52b1398e76ff39d3fe0621fb | Text | 2,639 | 57 | TAGNN
===============================================================================
Code for paper [**TAGNN: Topology-aware Graph Neural Network Framework for Link Prediction**](comming soon...)
This implementation of PairRE for [**Open Graph Benchmak**](https://arxiv.org/abs/2005.00687) datasets (ogbl-wikikg and ... |
b77d9a36814ee0e861556184860b7ab9c100378f0080c343347d0c204f79b39c | Text | 2,692 | 44 | [](https://zenodo.org/doi/10.5281/zenodo.10518989)
# OBASK: Ontology Based Application Starter Kit
Ontology Based Application Starter Kit (OBASK) is an innovative tool that empowers users to easily create search and knowledge exploration applications using their ontologie... |
af6c4c2aa0efe990a623d64dce93c0c42329dddbfe535b960fcba62ec2f01545 | Text | 2,725 | 67 | <img src="seege logo.png" width="600">
A Python-based framework for evaluating synthetic EEG signals along three dimensions: fidelity, diversity, and privacy.
## Contents
- Test EEG datasets (real and synthetic)
- Evaluation metrics & scores
- Metrics validation
- Usage examples
- Support material
## Installation
s... |
901c9469da767a6ea17a266dd24d1abb1e19f23a3e170e960b9917b69b6cf558 | Text | 2,731 | 56 | MetaNeighbor: a method to rapidly assess cell type identity using both functional and random gene sets
================
MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.
Please refer the [notebooks](./notebooks) for tutorials on how to use MetaNeighbor and consider ci... |
81c2e6795d46c9172ac15e2d83a3fa1841eaf6cded5025ee5301ea1696a2fbad | Text | 2,744 | 69 | # Gut Microbiota Comparative Analysis — Candrea et al.
## Comparative Analysis of Gut Microbiota Patterns in Irritable Bowel Syndrome, Anxiety, and Autoimmune Disorders
**Journal:** Biomedicines
**Authors:** Adelin-Rareș Candrea, Laura Ioana Gavrilaș, Andrei Mocan, Adriana Rusu, Gianina Crișan
---
## Repository C... |
d26847224806f1311094df4e5520e84c6eade90c55dee9dd3f736f5ccaba5115 | Text | 2,748 | 34 | # NeuroMiner 1.2 Feanor
NeuroMiner has been continuously developed by [Nikolaos Koutsouleris](https://www.imprs-tp.mpg.de/person/43420/2484), [Clara Vetter](https://cdn0.scrvt.com/4d3e519fe5939342b95c7312343779ef/d44b9dca07ed3899/0915c2a47419/Clara_Vetter_CV.pdf) and [Ariane Wiegand](https://www.psych.mpg.de/person/12... |
31174974ca9baddc6a2609222d1fa926e726e660ad4f7d35770a66d0f96d0997 | Text | 2,751 | 40 | # Diversity in emergent cell locomotion from the coupling cytosolic and cortical Marangoni flows with reaction–diffusion dynamics
## Authors
B. Ivšić, D. Vulić, I. Weber, P. Nowakowski, and A.-S. Smith
## Abstract
Cell migration is a fundamental process underlying the survival and function of both unicellul... |
d864ed8aa7c980eaac3c104170fb9bce2031828956b839a332f09d5e6fa52c9a | Text | 2,757 | 81 | # IRI2020 ionosphere model from Python and Matlab
[](https://doi.org/10.5281/zenodo.240895)
[](https://github.com/space-physics/iri2020/actions/workflows/ci.yml)
[](https://openfree.energy/)
[](https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml)
[](https://doi.org/10.5281/zenodo.15299996)
# Aurelian: Agentic Universal Research Engine for Literature, Integration, Annotation, and Navigation
| [Documentation](https://monarch-initiative.github.io/aurelian) |
```
aurelian --help
```
Most commands will start up a dif... |
cf3981ed7c87ce7ed3d54e975d54ec7777e8aaff2f11dfecbd36d9359bd6d6d9 | Text | 2,920 | 77 | # Code availability for manuscript figures
This folder contains the MATLAB scripts, helper functions, and all processed data files needed to reproduce the figures in the manuscript. Everything is self-contained in a single flat directory — no external data paths or folder rearrangement required.
## Quick start
1. Op... |
d362444a12cbcdea4c91335f7148bdde4223090a0795d6f712ba89df119f07a0 | Text | 2,944 | 44 | # Cellpose_pipeline-models
---
Supporting software for the research paper: *"Retinoic acid drives cell fate specification and maturation in human retinal organoids"*
---
## Research paper
- *Authors*: Benjamin Y.... |
6e98bb0d59bb0b46b92f93ef54ce411b57cd9290c0a9d4f5f3656640a6d3622b | Text | 2,975 | 57 | # rddm R package
The goal of rddm is to provide a user-friendly syntax in R to work with diffusion models of decision-making.
rddm is centered around two models: the drift diffusion model (DDM; e.g., Ratcliff et al., 1978, [Bogacz et al., 2006](https://pubmed.ncbi.nlm.nih.gov/17014301/))
and the pulse diffusion model... |
fe5072e5e196f8e7720d03f69b82960c27791b6c0b0ff12c3eb7907f34a5a03a | Text | 2,984 | 69 | # NeuroBED_ML
This repository accompanies the manuscript:
> **Multimodal Machine Learning Reveals Neurobiological Signatures of Binge-Type Eating Disorders**
> *Rommerskirchen, L., Skunde, M., Bendszus, M., Herzog, W., Friederich, H.-C., & Simon, J. J. (2026)*
---
## Overview
**NeuroBED_ML** provides the full ... |
ebe3226fae9d324d614c0cfc1369f268b8ef6ea96fa553e2965471f68ca21130 | Text | 2,996 | 86 | # Benchmarking metagenomic binners
This repository accompanies the manuscript:
> **Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery**
>
It provides simulation and real datasets, binning outputs, benchmarking metrics, and all scripts used to perform and reprodu... |
f9d99a341a758f49aac1c7f38a699d7caa025cfa8cb965e09da0134d90bae8cd | Text | 3,005 | 86 | This Zenodo repository contains the data and code associated with the
paper:
"A sensorimotor instability drives a locomotor transition during fish development"
The repository is organized in a modular way, reflecting the different
experimental and computational components of the study. Each module is
self-contained a... |
57745566c3a8d0618844236db7b2e93dffce4b0d6ac109c2bb56b53ab55fd5e6 | Text | 3,053 | 78 | # Early Stopping for PyTorch
Early stopping is a form of regularization used to avoid overfitting on the training dataset. Early stopping keeps track of the validation loss, if the loss stops decreasing for several epochs in a row the training stops. The ```EarlyStopping``` class in ```early_stopping_pytorch/early_stop... |
62beb87d4875e69c1b029f33c25e52a4253fb87be3c73c3fbfe0544d5b60d690 | Text | 3,088 | 43 | # srinivasan-speech-modes
This repository houses codes related to analyzing intracortical neural activity of speech modes and loudness.
## Installation
**Requirements:** Code has been tested in Python 3.9. Clone the repository and install required libraries.
You can create a conda environment to run the ```plotting_s... |
42b90ac2319ef3ea2433396e05e238b6ca6f413fe349453c0d74f80a28ea6952 | Text | 3,115 | 91 | #==================#
#| ForceBalance |#
#==================#
If you're reading this, you are probably looking for help. :D
The ForceBalance project website is located at
https://simtk.org/home/forcebalance
There is documentation available online in html at:
http://leeping.github.io/forcebalance/doc/html/index.html... |
9195712ab0493af1fcb09fbe33300c72366eeeb9962d7cbf2659396271c0944d | Text | 3,129 | 25 | # Sex- and site-specific reference data for size-invariant properties using multi-stack HR-pQCT
Simone Poncioni<sup>a,b</sup>, Dominique Luscher<sup>a</sup>, Michael Indermaur<sup>a</sup>, Daniela Angelika Frauchiger<sup>a,b</sup>, Christian Meier<sup>c</sup>, Philippe Zysset<sup>a</sup>, Kurt Lippuner<sup>a,b</sup>
... |
4d2efa6ab551dc681bfcb825dade3655060d1d9afceb493c2e74468f14f8fec4 | Text | 3,146 | 56 | # SAHLSIS mRS Prediction
**Author**: Jesper Olsson, [jesper.olsson@gu.se](mailto:jesper.olsson@gu.se)
**Date**: 2026-04-15
**Principal investigator**: Christina Jern
## General Information
This repository contains code necessary to reproduce the results for the manuscript [*Predicting Post-Stroke Functional Outc... |
bb4e14ff4a495313195b386075f3efc0723ef57e7d8a84f5d854f091e97de41b | Text | 3,170 | 68 | # Animal-Behabiour-Apps
These are a set of Python-based GUI applications for the analysis of various rat behavioral tests performed for rehabilitation after spinal cord injury.
The programs were written by [Abel Torres Espín](https://github.com/ATEspin) for analysis at [The Fouad Lab](http://www.rehabresearch.ualbert... |
16fab7435177794df1de8022fbdfffcf43ab87f63298e87b634dbe5f7d799213 | Text | 3,189 | 85 | # Codebase for the paper: "The oneirogen hypothesis: modeling the hallucinatory effects of classical psychedelics in terms of replay-dependent plasticity mechanisms"
By Colin Bredenberg, Fabrice Normandin, Blake Richards, and Guillaume Lajoie
This code repository was produced by simplifying and adapting the Mila IDT ... |
07783482ce115cd31fd8db9b7994dd1ddd2e041f48dbbfbadae2d0a10a458044 | Text | 3,221 | 27 | # Sex- and site-specific reference data for size-invariant properties using multi-stack HR-pQCT
Simone Poncioni<sup>a,b</sup>, Dominique Luscher<sup>a</sup>, Michael Indermaur<sup>a</sup>, Daniela Angelika Frauchiger<sup>a,b</sup>, Christian Meier<sup>c</sup>, Philippe Zysset<sup>a</sup>, Kurt Lippuner<sup>a,b</sup>
... |
fcc763cddf0d1f6f21ae2e4089d33773892613632b6326065194b3f74f203b18 | Text | 3,236 | 99 | SAKE-PP: Spatial Attention Kinetic GNN for Protein–Protein Interactions (JACS Au, 2026)
==============================================
[](LICENSE)
[](https://www.python.org/downloads/)... |
e377b6b9a86500892021f7245a04d895f084360b8deb3f153bcd18bcfe25e6d8 | Text | 3,262 | 38 | # CNN Models for Predicting Minimum Inhibitory Concentrations (MICs) in <i>Mycobacterium tuberculosis</i>
This repository contains code for the manuscript title "Convolutional neural networks quantify antibiotic resistance in Mycobacterium tuberculosis with diagnostic grade accuracy and predict treatment response"
Th... |
fee6fa707424129422283905cf3a2eedf6f2460a281d7df9502ff50ab6c11cc0 | Text | 3,262 | 43 | # VR-RW
Under VR and real-world environments, the differences of neuronal spatial and task representations in non-human primate's hippocampus and orbitofrontal cortex
猕猴海马及眶额皮层，在VR和RW两种环境中，空间与任务的神经表征差异
# Participant
Wenxin Yan; Dun Mao
ION, Shanghai, China
# Code description
1. **Behavior**
- duration_fit.m: Nu... |
098252e534e204a7f80fbb3e79e25aa9afdbcee17e9a526719609a5c0c550482 | Text | 3,283 | 21 | # Capacitive Port Interface for Bpod State Machine
<img align="right" src="PortBreakoutCapacitive.png" width=200>A drop-in replacement for the [regular port interface](https://www.sanworks.io/shop/viewproduct?productID=1004) enabling for capacitive sensing of lick events. Connect a metal lickspout with a short piece o... |
aa07db53c886aea620cc3e1ece42b722cd1a8b5fe9e61befcdf31e5b79911329 | Text | 3,347 | 100 | # Functional Network Connectivity Interpolation
Code for the paper: [Brain functional network connectivity interpolation characterizes neuropsychiatric continuum and heterogeneity](https://direct.mit.edu/imag/article/doi/10.1162/IMAG.a.1220/136217/Brain-functional-network-connectivity)
... |
57abcf7bc6f89210f53652fb8207e31e5544f7d6a8e72e18ba1564e515397010 | Text | 3,368 | 63 | ## kinematics3d
Pipeline for calibration, triangulation, and data processing using DeepLabCut and Anipose.
## Installation
Download the repository on your local machine by running the following line in the terminal:
```bash
$ git clone https://github.com/NeLy-EPFL/kinematics3d.git
```
After the download is complete, ... |
3c9b4d6301566c0b5d1f7a1ae571c77b8501f81c0639ba0f6eb3b42bdc3cdffb | Text | 3,378 | 111 | # PCB Exposure and Gene Expression in Mouse Brain: snRNA-seq Analysis
## Overview
Single-nuclei RNA-sequencing (snRNA-seq 5') analysis investigating polychlorinated biphenyl (PCB) effects on gene expression in the RTT mouse and human prefrontal cortex.
### Associated Publication
**Female cortical cellular mosaicism... |
9a0e63515349210ead00a52988928785a3b7f565d637672ec7649103014f5aa7 | Text | 3,393 | 49 | [](https://github.com/choderalab/openmmtools/actions?query=branch%3Amain)
[](https://anaconda.org/omnia/openmmtools)
[![Downloads Badge](https://anaconda.org/... |
686b28d2c856e3bddb2a25d57fef058b98b5e5ae8aa2565eb11a24da56ee3a29 | Text | 3,399 | 68 | # Neuromuscular-Inspired Control in Pong
<p align="center">
<img src="NeuromorphicPongControl/Visualization/pong.gif" alt="Adapted Pong game GIF" width="400" />
</p>
This repository contains code where you can train a neuromuscular-inspired system to play the game of pong. To download the required packages, run:
``... |
62e7429b1bce032dff37ca0474ae2a19eabfa6206a479bfd2cc558c20e2c6e92 | Text | 3,413 | 97 |
# TEGNet: Thermoelectric Generator Modeling and Simulation
This repository provides Python-based tools for training and using the **TEGNet** neural network model to predict the performance of thermoelectric generators (TEGs). Once models for different materials are obtained, users can flexibly combine them to design ... |
c2bae8d89f342f91746c05853ab0f5fb894842f7647e9d51c294ee66f39bdcdc | Text | 3,483 | 108 | # ethopy_plugins
The `Ethopy plugin` system provides a flexible way to extend the functionality by adding custom modules, behaviors, experiments, interfaces, and stimuli. The system supports both core modules and user plugins with intelligent conflict resolution.
## Plugin Categories
Ethopy supports two types of plu... |
72bd73c480ca3ae1957676153fee340ad1ea219ca83248ef67a6650829f692a4 | Text | 3,524 | 70 | HierarchBayesParcel: A Hierarchical Bayesian Brain Parcellation Framework for fusion of functional imaging datasets
====
Diedrichsen Lab, Western University
This repository implements the hierarchical Bayesian framework for learning brain parcellations across task-based and resting-state fMRI datasets.
The technical ... |
f2e388ae97c4be6c2c71b14466a329cff064a1c56b0d7e5478a201bacc1d1a84 | Text | 3,574 | 141 | # WGBS methylation analysis during aging
## Overview
This repository contains R scripts for analyzing whole-genome bisulfite sequencing (WGBS) data across three age groups (8, 44, and 74 months). The analyses include principal component analysis (PCA), identification of differentially methylated regions (DMRs), and ge... |
d2020758c3351dd461429f1be167aa48cbc40c34e6d03e0bc9499925560c5995 | Text | 3,614 | 28 | NAGL
==============================
[//]: # (Badges)
| **Latest release** | [](https://github.com/openforcefield/openff-nagl/releases) . Each dataset has its own folder with subfolders for:
- count matrix
- locations
- giotto R-script with secondary analyis (when available)
- raw data (optional)
These datasets can be downloaded directly f... |
83f2f2b52f27682e5ac88a2f8b3f5c450b929baed45dfdf83661e2f987f628d1 | Text | 3,731 | 86 | RENAISSANCE: Generation of kinetic models using Evolutionary Strategies
==========================================
RENAISSANCE is a workflow to generate valid kinetic models of metabolism using evolutionary strategies on Neural Networks.
Here are the instructions for installing and using the Python implementation of R... |
855ff6f30e3618146eaab361cedc29bcbcdd4c3aece8e2c056346a05fc9522af | Text | 3,737 | 112 | # BRISC 2025 — Brain Tumor MRI Dataset
> **BRISC** (BRain tumor Image Segmentation & Classification) — a curated, expert-annotated T1 MRI dataset for multi-class brain tumor classification and pixel-wise segmentation.
[ArXiv preprint (Fateh et al., 2025)](https://arxiv.org/abs/2506.14318)
---
## 🚀 Overview
BRISC ... |
0e899146fd7616e19e952e909f425dcbea9619f041a92086047126c45d87db1c | Text | 3,741 | 74 | # NetBID 2.0
NetBID (**Net**work-based **B**ayesian **I**nference of **D**rivers) is a data-driven system biology pipeline and toolkit for finding drivers from transcriptomics, proteomics and phosphoproteomics data, where the drivers can be either transcription factors (**TF**) or signaling factors (**SIG**).
NetBI... |
11b37afb80e4b068d029c0251cbc25543eacbd51f792b40d17a6e78a4546be32 | Text | 3,743 | 74 | Shield: [![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa]
This work is licensed under a [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].
[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]
[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/
[cc-by-nc-s... |
dbf9b6449b7226396cfcd125035bef595ad911d1f7d1709ed3e435a37fbfc1f6 | Text | 3,877 | 154 | <p align="center">
<img width="500" alt="zonesig_logo_NEW" src="https://github.com/user-attachments/assets/2a55c828-69e7-410b-a427-a89f3fef6f25" />
</p>
# 🧠ZoneSig (Neuron Zone Segmentation & Quantification)
✨ A lightweight toolbox for **3D confocal neuron image analysis**, built for:
- 🧩 **Soma segmentation** (Cel... |
43a1c6005ea0cbfbbdd76724ac1a246d04d48ed08bb8acda8f928adb340573af | Text | 3,919 | 78 | # A large-scale vision-language fMRI dataset for multi-modal semantic association
---
## Updates
🔄 **May 14, 2026:** The main CSD dataset was updated, with the `pp_eyetrack` and `freesurfer_results` directory restored and revised.
🔄 **May 23, 2026:** [The CSD extended derivatives dataset](https://www.scidb.cn/en/... |
fd846500d8328a3ac3f894a5e54254a68ee82b2033de262f178dd6d88dc0fe20 | Text | 4,029 | 64 | ## Code supplement to the publication "Predicting human aluminium exposure from vaccinations using a physiologically-based toxicokinetic model" by Weisser et al. (2026)
The R Markdown script provided here allows to reproduce all results reported in the above article. To do so, follow these steps (more detail is provid... |
0b831f61f0b0695e6e6d221d0bfa236aad4cfc90a288ce9cc3a9b3041e8c8e9c | Text | 4,144 | 71 | # Cortico_Cereb_Connectivity
This repository includes the code to train and test cortico-cerebellar-connectivity models, as described in King et al. (2023).
The original code underlying that paper is maintained in a different repository (https://github.com/maedbhk/cerebellum_connectivity).
This repository is a cleaned-... |
fc77231111b2f52dd7e72e5359b9d8842a9bf94a28916568798881c04498e8a7 | Text | 4,189 | 102 | This repository contains information necessary to reproduce the figures in the paper **Single-nucleus brain transcriptomics reveals microglia dysfunction in Multiple System Atrophy brains** by Rydbirk *et al*.
We provide objects necessary to produce all figures presented in the manuscript, except for QC which we provi... |
78350e9afbd264ca88e901c0bdadf413671eec5e9fe95b9f5731860d043bef0a | Text | 4,202 | 79 | # RNVT
Empirical Validation
# RNV-T empirical validation code
This package provides a **reference implementation** of the RNV-T pipeline described in the manuscript, covering all five phases:
1. **Local Vascular Extraction (LVE)**
2. **Global Transformer-based Encoding (GTE)**
3. **Graph-based Convolutional Attention... |
155f32615d54db9bd21147e2bcdb6effbbe79816de92c25ae1b21104fbbfb274 | Text | 4,216 | 133 | # multimodal_decoding
## Data
The fMRI data can be downloaded from openneuro:
https://openneuro.org/datasets/ds007272.
## Decoding analysis
```
python analyses/decoding/ridge_regression_decoding.py
```
## Searchlight analysis
Modality-agnostic decoder:
```
python analyses/searchlight/searchlight.py --model imageb... |
e9dcbe4ffde00883c6daa5e762bc10057da90bf26482297fd83d58446dabe5ee | Text | 4,258 | 127 | # KULeuven Neuro Imaging Suite (KUL_NIS)
KUL_NIS provides tools:
- for conversion of dicom data to BIDS format of
- T1w (with and without Gd)
- T2w
- FLAIR
- PDw
- FGATIR
- DIR (double inversion recovery, in development)
- ASL (not fully BIDS compatible yet)
- MTR
- fMRI
- dMRI
- QSM (in development)
- f... |
c92706f97255064a50b048d2edb71af3c9c0e7c240a5d738c33114af1f2342b5 | Text | 4,302 | 55 | # Convergent transcriptomic signature in iPSC-dopaminergic neurons of hereditary Parkinson’s disease
   ![Quarto](https://img.shi... |
d29d13640d8603a85dec577c0d245d6b1c806b0170aec5548919a47232c3df0e | Text | 4,340 | 74 | # Machine Learning-driven Alignment Architecture of Heterogeneous Data with Transient Varying Semantics
## Instructions
The software and code involved in paper "Machine Learning-driven Alignment Architecture of Heterogeneous Data with the Transient Varying Semantics", including the synchronize triggering software and ... |
685da815e2d3642f6b58624000cb17ca0cf6b49d76b497c13b62a116a9d93490 | Text | 4,350 | 118 | Code used in "Nonergodicity and Simpson's paradox in neurocognitive dynamics of cognitive control" (Mistry*, Branigan*, Gao, Cai, Menon).
# Brain-behavior relationships
To reproduce the findings:
0. Set up your Conda environment.
* `environment.yml` in the root directory
* This environment was used to run a... |
0704dccc4716824040e429d38ffab4a0d84f4ac3f406ec22111cd0a007ea9ce2 | Text | 4,359 | 105 |
# CellNiche
## Overview ✨
**CellNiche** is a lightweight and scalable representation learning framework for **atlas-scale spatial omics** that **identifies and characterizes cellular microenvironments**. It flexibly accommodates multiple forms of cellular identity representations, including **expression matrices, pre... |
2939d8268af85634daab96be1ce9ec9eb7515620aa06785bb93ef15b8fbccb1c | Text | 4,387 | 68 | # Information about this fork
Modified source code to remove dependencies on Qt6. Needs an appropriate
[cvutil](https://github.com/sotlampr/cvutil).
TODO:
- Better replace Q* clases with std equivalents
- Use RoiManager (uses QtGraphicsRectItem for calculations)
## ![RhiZoVision Explorer Logo](./RVElogoclearback-80.... |
4b3513954e39e4d5229fcefa1342e52740f3942c595d5e6aaf4707bf4e0ce08d | Text | 4,465 | 95 |
Omics Playground: Explore Omics Data Freely
================================================================================
Omics Playground is a comprehensive *self-service analytics platform* for
the visualization, analytics and exploration of Big Omics Data. It allows
biologists to apply a multitude of state-of-t... |
559422b1658ea98a7181cd753bcefdfe3a7e36d6c8d927b336190fc38fd54893 | Text | 4,465 | 152 | # HDFNet Skin Lesion Classification —
This project implements the pipeline: preprocessing, class-aware selective augmentation, ALC-VGG16, DFE-ResNet50, dynamic-patching ViT, feature fusion, HDFNet classification, ROC/confusion-matrix evaluation, and Grad-CAM.
The uploaded CODE USES four-class dermoscopic classifier f... |
61449c89519ba054be767000c89e0b735aad2b1048d2d6c911293b6bb9e048ff | Text | 4,559 | 116 | # TimeFlies
A single-nucleus RNA-seq aging clock for the *Drosophila melanogaster* head, built on a 1D convolutional neural network.
**Paper:** Tennant, Pavuluri, Singh, Cortez, O'Connor-Giles, Larschan & Singh. "An snRNA-seq aging clock for the fruit fly head sheds light on sex-biased aging." *Scientific Reports* (2... |
4d16f9bd4350fa2a5de5ef6af0b742d232bb87c560fea2d0dfc9bcf6788e64c9 | Text | 4,571 | 113 | # GWAS_locus_browser
* updated 5/6/2021
## Contributors
* Main Developers: Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious
* Design and Concept: Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious, Cornelis Blauwendraat, Andrew B. Singleton
## File Overview
* ui.R - code for user interface layout.
* server.R - ... |
c5070401ef92120e228f928c0b6bea6fb2e186276dec373bb7ce3a3735ee74e6 | Text | 4,573 | 104 | Repli-Seq pipeline package (Wei, Pei-Chi group; DKFZ)
====================================================
Global Run-On Sequencing (GRO-Seq) pipeline for analyzing transcription activity of genes from engaged RNA polymerase.
Table of Contents
=================
* Using Repli-seq docker image
* [Singularity](... |
76e9065822a2b06f8abfc9c1c588de3728d189f67d9764a9c854c27c0bf9ef67 | Text | 4,591 | 109 | # ProtoCloud
[](https://doi.org/10.5281/zenodo.18882740)
[](https://doi.org/10.1016/j.xgen.2026.101217)
[](https://www.b... |
9981c80027f51a8c17ee8c7d3d77ef8978a77bcb7a915a762252ecf1605726ae | Text | 4,634 | 145 | <p align="center">
<img src="documentation/public/docs/image/logo_v2.png" />
</p>
[](https://pypi.org/project/ydf/)
[](https://opensource.org/licenses/Apache-2.0)
[
This repository contains a spatio-temporal fetal MRI atlas of the Ganglionic Eminence (GE) from 19 to 36 gestational weeks (GWs) at 0.5-mm isotropic resolution. The atlas... |
43934ed9449ea2378b4c6a863d1064ea15051366dfe5f875ac116ac215fdd921 | Text | 4,722 | 96 | # <img src="docs/assets/EthoPy_logo.png" alt="EthoPy Logo" width="200" style="vertical-align: middle;">
[](https://pypi.python.org/pypi/ethopy)
[](https://pypi.org/project/ethopy/)
[![Documenta... |
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