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ee068bb88b1aed3337c784667c3ef7e295bc80657d4471a851b36c49aac0eb83 | Text | 6,960 | 60 | # PetaKit5D
Tools for efficient and scalable processing of petabyte-scale 5D live images or large specimen images from lattice light-sheet microscopy (LLSM) and other light sheet microscopies, as well as other imaging modalities. It is featured by fast image readers and writers (for Tiff and Zarr), combined image desk... |
5380627e85c0f29aa30e7575a4a4c7179eabce7dbd76b339f5550739d73d28ff | Text | 6,964 | 163 | .. Following contents should be from LONG_DESCRIPTION in abagen/info.py
abagen: A toolbox for the Allen Brain Atlas genetics data
=========================================================
This package provides a Python interface for fetching and working with the
`Allen Human Brain Atlas`_ (AHBA) microarray expressio... |
2b1d0a11427803d2e4aaedd35dd74deea49a38bceb82b1590a8e9d5d8b75cf62 | Text | 6,969 | 124 | # pyls
This package provides a Python interface for partial least squares (PLS) analysis, a multivariate statistical technique used to relate two sets of variables.
[](https://travis-ci.org/rmarkello/pyls)
[![CircleCI](https://circleci.com/gh/rmar... |
66d8afad1c6682a665f6f3f587b80e8f453f5651752e9cd0216e3255d7d7c446 | Text | 6,987 | 150 | ## GenLouvain Version 2.2
### released July 2019
Please cite this code as
Lucas G. S. Jeub, Marya Bazzi, Inderjit S. Jutla, and Peter J. Mucha,
*"A generalized Louvain method for community detection implemented
in MATLAB,"* https://github.com/GenLouvain/GenLouvain (2011-2019).
## Contents:
This pa... |
919a2128a412e20add90c24818275e2a46f8502b14e79e4ccade1d9e7847404d | Text | 6,991 | 194 | # pisces2
Sleep classification from wrist-worn accelerometer data.
## What is pisces2?
Pisces2 is a Python library for multi-class sleep staging from wrist-worn accelerometry and derived features. It provides a suite of model architectures (LSTM, Transformer, Random Forest, Logistic Regression, and more), a configur... |
52f1567b0fa7a0d30016de7fe45b3be34526567d6603d883ec5c150231f772e1 | Text | 6,992 | 134 | # Physiological Workload ML Pipeline
Analysis repository for the OpenNeuro study [`ds007262` version `1.0.6`](https://openneuro.org/datasets/ds007262/versions/1.0.6), titled `Cognitive Workload 8-level arithmetic` (DOI `10.18112/openneuro.ds007262.v1.0.6`). The codebase covers dataset acquisition, trial-table construc... |
7c05f4ef2332fadee5e8933d8754442f98200f1b905f3edf331e227ff85afe64 | Text | 6,995 | 119 | # Neural similarity between choice options predicts group-level context effects
Code and data for the manuscript *"Neural similarity between choice options predicts group-level context effects"* by **Asaf Madar, Tom Zemer, Ido Tavor\*, and Dino J. Levy\***.
---
## Overview
The study includes **two tasks**:
| # | T... |
0b4c6c1b92bf3b40ec6ec5676c56b519eee7b9ce8653ada63b0710a6d4139d98 | Text | 7,002 | 182 | # Alternating Neural Integrators (ANI)
## System Requirements
The codebase has been tested in a standard Linux environment and is intended for research use on workstation- or server-level hardware. This repository has been tested on Ubuntu 22.04 LTS with Python 3.11 and MATLAB R2024a.
### Operating system
The reposi... |
af51d462384dfd995dbf61cc29fbd265c29a6d521e55a72187fca231c514dd93 | Text | 7,033 | 126 | <p align="center">
<a href="https://www.biorxiv.org/content/10.64898/2025.12.06.692728v1">
<img src="assets/githubRepo.png" width="100%" alt="Calarco et al. 2025 — Multiscale characterisation of the human claustrum from histology to MRI"/>
</a>
<br/>
<em>Click to read the preprint →</em> <a href="https://ww... |
257bb3c1cc6fff041b66a9ecb9392ae42b916884e278efbb7a1208c57014a0b0 | Text | 7,035 | 154 | # C4TUNE - C<sub>4</sub> TUNing Engine
## General description
A detailed description can be found in the associated publication:
Preprint:
**Kinetic parameter prediction using neural networks identifies limitations to C4 photosynthesis**<br>
Philipp Wendering, John Ferguson, Rudan Xu, Johannes Kromdijk, Zoran Nikolos... |
42af29c3a188a5c304b7e9d08fca45011ac22d8d2a6d2c5c75c55aed182263b7 | Text | 7,039 | 73 | # UnitMatch
Ephys toolbox to match single units (electrophysiology) either within the same recording (oversplits) or across recordings, by using spatial position and waveform-based parameters - both standard and unstandard metrics to the field.
If you have questions about UnitMatch, please use the 'Q&A' in the Discus... |
f03fc08bc82af59aef77923313f561f0ba80f3f88eb865eb71bbcde004d886bc | Text | 7,046 | 190 | [](https://gist.github.com/cheerfulstoic/d107229326a01ff0f333a1d3476e068d)
](https://doi.org/10.5281/zenodo.19011503)
This repository contains computational models and analyses for studying proton diffusion in the TBC1D5-Rab7-NHE6 protein complex. The project investigates how protons ... |
6ce4ad8b9c622ae6bd87621d5656c782687c8d2c3904e8050bf5d0573ccf3e52 | Text | 7,061 | 184 | # Prediction of Clinical Features Using Graph Neural Networks
Discovery of functional motifs by association to clinical features using Graph Neural Networks.
## Installation
### Using Conda (Recommended)
The project includes conda environment files. To set up the environment:
```bash
# Create environment from the... |
e805a0bb5e5b3287c439e1f3d82ea85e0868e008128626a6a889905df6384576 | Text | 7,102 | 80 | # DNA methylation signature of cognitive reserve moderates CSF tau pathology in prodromal Alzheimer’s disease
David Lukacsovich, Juan I. Young, Lissette Gomez, Brian W. Kunkle, Zhixin Mao, Wei Zhang, X. Steven Chen, Deirdre M. O’Shea, Tatjana Rundek, Eden R. Martin, Lily Wang
### Description
This GitHub repository in... |
96a8cc92f78fcfe16d6a9836b6f3170c2e2737e3e6597b847490fff7a79c594e | Text | 7,105 | 138 | # Multimodal gait, brain, and muscle dataset accompanying: "Central and Peripheral Neuromuscular Mechanisms Underlying Functional Recovery Heterogeneity in Tibial Plateau Fractures"
[](https://doi.org/10.5281/zenodo.20339370)
[](https://multilayer-notchdelta.readthedocs.io/en/latest/?badge=latest)
We present a computational toolkit for simulating and analysing Notch-Delta signalling in three-d... |
ad4c92f658b5e9939ebbcb3e4076b57f3199d00cde55e38575bbd4dcdaef6b8d | Text | 7,186 | 109 | # mGluRIII
Latest release: v1.0 (use Latest Release tag on the right side of this page!)
**Overview**
This is a NEURON compartmental model designed to validate experimental data showing that mGluRIII activation reduces proximal and distal inhibition onto CA1 pyramidal cells (PCs) from parvalbumin and somatostatin int... |
5d54cd8d0fafb16ddd458cb4c146228e866da09e74b2b81c447104b5c526a237 | Text | 7,205 | 175 | # Semantic Distance Signature
This repository contains the code, demonstration data, word-pair stimuli, ROI
definitions, and group-level neural signature maps for the manuscript:
> Zhuang, K., Liang, X., Smallwood, J., Jefferies, E., & Vatansever, D.
> Model-based semantic distance reveals adaptive coordination of di... |
4ca92d2e67d844aa6d9ce9d5a16b435613fb08106f5f4b06ab3cee32c18ac595 | Text | 7,211 | 97 | <img src="https://github.com/dsilvestro/PyRate/blob/master/pyrate_lib/PyRate_logo1024.png" align="left" width="80">
### PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
[](https://zenod... |
c222cc7712645c84b15bc3d13973bd728a54333bd159b1325f0ea6a7e9aada73 | Text | 7,218 | 141 | # Deep learning-based automatic field of view planning for prostate MRI in oblique coronal and oblique axial planes
This repository contains the official code for:
Quinsten et al. 'Deep learning-based automatic field of view planning for prostate MRI in oblique coronal and oblique axial planes', Scientific Reports, 20... |
68698db4b9d48f1e6ffc360912f36467dde46e739c704648896dcfa256f31cb2 | Text | 7,241 | 185 | # phy: interactive visualization and manual spike sorting of large-scale ephys data
[](https://github.com/cortex-lab/phy/actions/workflows/python-test.yml)
[](https://www.medrxiv.org/content/10.1101/2024.11.14.24317328)
License: CC BY-NC 4.0
📢 [SSL Pretrained and Finetuned Models](https://huggingface.co/Edoardo-Coppola) on... |
9dbef9146412924b993ad692af1c4888c5b4ec87f7461eee6b5e2707214cee0b | Text | 7,274 | 86 | PsPM-SPRM dataset
=================
Repository Version: 2021.06.21
This dataset includes (1) skin conductance (SCR), electrocardiogram (ECG), respiration measurements recorded with Biopac Acknowledge, (2) combined skin conductance, skin potential and skin susceptance response measurements recorded with labview, and (... |
049a83e894b9091df7a8ab514e1776d807c2851ef6ee03096d4fea39b67827b1 | Text | 7,281 | 108 | # Membrane Kymograph Generator
<p align="center">
<img src="https://raw.githubusercontent.com/tatsatb/membrane-kymograph-generator/233f5c6074246d4c9a667ca47ee3ee1140c5786c/icons/ICON.svg" width="280" alt="Membrane Kymograph Generator Icon">
<br/><br/>
</p>
---
# ✅ 📚 Please visit the [Wiki](https://github.com/tats... |
10c554b9df770419feee5efe61987c3c4a31500e31b359033fff651ebeef25e9 | Text | 7,284 | 128 | |banner|
-----------------
BluePyEfe: Blue Brain Python E-feature extraction
=================================================
+----------------+------------+
| Latest Release | |pypi| |
+----------------+------------+
| Documentation | |docs| |
+----------------+------------+
| License | |license| ... |
09781ecd69619e391ab3d29b241b512d1af37f9a581d31e98305de92f61362ee | Text | 7,320 | 100 | # GACELLE (GPU-AcCELerated toolbox for high-throughput multi-dimensionaL quantitative parameter Estimation)
## Introduction
**GACELLE** is a MATLAB parameter estimation tool optimised for high-throughput data processing.
GACELLE prov... |
d18d161584f3b6c9d667907d7ea31dd91f412e3f56ad8a656a49b02acf73ce67 | Text | 7,328 | 135 |
# Overview
NeNe-Top - <ins>Ne</ins>ural <ins>Ne</ins>twork for <ins>T</ins>emperature <ins>O</ins>ptimum <ins>P</ins>rediction
## ✨ Project goals
Microorganisms live and grow across a wide range of temperatures, and this project provides a way to predict the temperature at which they grow best. Measuring optimal gro... |
0bd892a30299329b728de7c12532a7b6b21d828cc02452c4e3de34918c60e6c8 | Text | 7,329 | 145 | # Cell2Map
Cell2Map is an unsupervised deep learning method that integrates single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) to map individual cells to spatial locations within tissue sections. While scRNA-seq provides genome-wide expression profiles at single-cell resolution but l... |
f5350b091153706c80d64c538550df2ded1bac3b16fcd34fc6f77c3a65069996 | Text | 7,349 | 192 | # Bayesian Hyperbolic MDS
Python implementation of **Bayesian Hyperbolic Multidimensional Scaling (HMDS)** — a method for embedding pairwise distance matrices into hyperbolic space via Stan-based optimization.
Based on: [Bayesian Hyperbolic Multidimensional Scaling (bioRxiv 2022)](https://www.biorxiv.org/content/10.1... |
cf753d41330011effc4ce57790db81f9bd78615659906e602690c562efb6f43a | Text | 7,358 | 133 | pySuStaIn
============
**Su**btype and **St**age **In**ference, or SuStaIn, is an algorithm for discovery of data-driven groups or "subtypes" in chronic disorders. This repository is the Python implementation of SuStaIn, with the option to describe the subtype progression patterns using either the event-based model, t... |
51dbab07527980d33abc5d3aa1ebbf598d9b93fcc411a7d7a677aa9fa59e99b4 | Text | 7,361 | 191 | # SDAN (Supervised Deep Learning with Gene Annotation for Cell Classification)
## Overview
SDAN is a supervised deep learning framework for cell classification that incorporates gene-annotation structure into representation learning. This repository contains the core SDAN implementation, dataset-specific training pip... |
b103b7bee3add3db8603773af3ff67da667c800f68251bc4e016ff5631ee5518 | Text | 7,401 | 181 | # *R*efining *O*penfold predictions with *C*rystallographic/*C*ryo-EM Li*KE*lihood *T*argets (ROCKET)
[](https://github.com/alisiafadini/ROCKET/actions/workflows/test.yml)
[
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel ... |
b6c96c66f4de06f45492c98a87862c6492e20250f0e73a631121a07f950f5a3c | Text | 7,451 | 140 | # HarMNqEEG
[](http://hits.dwyl.com/LMNonlinear/HarMNqEEG)
[](https://doi.org/10.1016/j.neuroimage.2022.119190)
**HarMNqEEG: ... |
5e0d96c8aa03915b3013a43e82fa683c7c4f1c5ba1e288f31f8c033bacd30d5f | Text | 7,458 | 198 | # ecSeg: Semantic Segmentation of Metaphase Images containing Extrachromosomal DNA
This repository is the official version of ecSeg, a tool used to quantify ecDNA in DAPI-stained images. It also has an extension to analyze FISH probes. Please cite (Bibtex at the bottom) the following reference if using ecSeg in your w... |
dbba5f0f7ae9238e8e4cf3d4dfc9f9c2fb04d2127b6e77c0b92554365a32d167 | Text | 7,481 | 177 | # README #
# Description
ELECTRA is a command-line software and library for solving PDEs for cardiac electrophysiology simulation using Finite Element and meshless methods.
## Features
- Cardiac Electrophysiology Simulator
- Finite Element Method
- Meshless Methods
- Non-distributed memory
- Ensight binary results
... |
55f3496c4e46528b54b4bc5feac625645a362377c92b1dae7b01598250ad201a | Text | 7,498 | 89 | [](https://github.com/prody/ProDy/actions/workflows/main.yml)
[](https://anaconda.org/conda-forge/prody)
[![ProDy pypi page](https://img... |
809e55c2f21b1e1c53a026aba03028c5bb5efc89740894eb6beaf07edeac18d7 | Text | 7,498 | 248 | Companion repository to "Combining Machine Learning and Iterative Experiments to Keep Pace with Emerging Viral Variants of Concern"
Thomas Sheffield, Ryan C. Bruneau, Stephen Won, Kenneth L. Sale, Brooke Harmon, Le Thanh Mai Pham. PLOS Computational Biology (2026)
R Packages used:
Matrix 1.7-2
data.table 1.17.0 ... |
c8cbb307104a7fffb3ba8556deb995203e48d787ba8bab746e7d26d1b4eb9a10 | Text | 7,504 | 76 | # SSMTool 2.4: Computation of invariant manifolds in high-dimensional mechanics problems
[](https://doi.org/10.5281/zenodo.4614201)
What's new in SSMTool 2.4
- Computation of higher-order approximations to non-autonomous invariant manifolds,
- Applications... |
8043998357304a256b62d337619b495d79f18dd823c5e4c0c27657c9ca7b54d2 | Text | 7,507 | 188 | # Welcome to DYNAMAX!
[](https://pypi.org/project/gget)
[](https://pepy.tech/project/gget)
[![Conda](https://img.shields.i... |
150289fd399acadfc910512c1c521fc41c0894851b82709817633c04d2014f3f | Text | 7,531 | 76 | <img src="docs/images/SSMLearnLogo.png" width="350" align="right">
<h1 style="font-family:Helvetica;" align="left">
SSMLearn
</h1>
### Data-driven Reduced Order Models for Nonlinear Dynamical Systems
This package identifies reduced-order models on spectral submanifolds (SSMs) from data. The required input consis... |
fddcd7b1f99cbcf26b8b8e0716589f30453feabcfd7133b88b4a19e920f47b63 | Text | 7,558 | 134 | .. warning::
The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
Future development will take place at: https://github.com/openbraininstitute/BluePyEfe
|banner|
-----------------
BluePyEfe: Blue Brain Python E-feature extraction
================... |
7f07ef38b8202fc7ca3cc6860c61cd6896f2b6bfa0ca9d42ad95eafd72226668 | Text | 7,570 | 79 | # SSD-DIS: A Semi-Synthetic Dataset for Document Image Shadow Removal
SSD-DIS (Semi-Synthetic Dataset for Document Image Shadow Removal) is a large-scale, high-quality dataset specifically designed for the task of document image shadow removal. With the proliferation of remote work and learning, shadows captured by mo... |
67725301a5794f1b79bbdd6e5981d85c2c94d2017c91210b9d40dd5391371580 | Text | 7,574 | 142 | # SpikeInterface: a unified framework for spike sorting
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/spikeinterface/">
<img src="https://img.shields.io/pypi/v/spikeinterface.svg" alt="latest release" />
</a>
</td>
</tr>
<tr>
<td>Documentation</td>
<td>
<a href="... |
8316ff3aacd24abdd3abcb0cc6f2743622b3c91be7be226b024c8c27b6b36864 | Text | 7,586 | 212 | # HVG–Autoencoder–SINDy: Chaotic Dynamics of Cultural Attention
[](https://www.python.org/downloads/)
[](https://pytorch.org/)
[](https://qupath-to-lmd-mdcberlin.streamlit.app/)
# Introduction
QuPath-to-LMD is the easiest way to go from QuPath annotations to LMD collection!
With more than 60 unique users, we try to help everyone co... |
ef860b34d34810c259cda346a52343c5bdfb3a24d142390dd2717c680f0c80d3 | Text | 7,586 | 106 | # Batch balanced KNN
BBKNN is a fast and intuitive batch effect removal tool that can be directly used in the [scanpy](https://scanpy.readthedocs.io/en/latest/) workflow. It serves as an alternative to `scanpy.pp.neighbors()`, with both functions creating a neighbour graph for subsequent use in clustering, pseudotime ... |
2af7a5c7f5f9fa4e5922a903024047c1929a564ccf09f4a5dffc1ad852e75dce | Text | 7,591 | 224 | # Attention-Guided CNN-Transformer Hybrid Model for Emotion Classification in Traditional Chinese Paintings
Official implementation of the paper "An Improved Attention Guided Convolutional Neural Network and Transformer Hybrid Model for Emotion Classification in Traditional Chinese Paintings".
## Abstract
Traditiona... |
0d7d3e4ebafede121f50c9232e5935aad5b70f9a98a58d1b8b2ae924ce423aa7 | Text | 7,593 | 101 | This repository contains scripts and guidelines to analyze the bulk RNA-seq with UMIs and scRNA-seq datasets after infection with Zika viruses from Malaysia, Puerto Rico, and Uganda agaisnt a mock condition.
# Zika Virus Infections of Human Stem Cell-Derived Cerebral Organoids Reveal Viral Lineage-Specific Pathogenesi... |
ba39c96d86c0a9528a3ceb4b8ad631e2f3ccb33a3ef68e876d12ffd237e1f705 | Text | 7,613 | 189 | # LFP choice probability source data and code
This repository contains source data and custom code for the manuscript:
**Distinct sources of decision-related signals in visual cortex are represented in different local field potential bands**
The most efficient workflow is to use the one-command runner in `Code/figur... |
c9b3667e47e109283cd9f449140708a0576b89749010ada8d9c7e32a50b08e2c | Text | 7,626 | 234 | # dHCP Structural Pipeline
The dHCP structural pipeline performs structural analysis of neonatal brain
MRI images (T1 and T2) and consists of:
* cortical and sub-cortical volume segmentation
* cortical surface extraction (white matter and pial surface)
* cortical surface i... |
d3bb59d640e71dec227f74048b727d17b380539045557fd69bb37c593a5b4c9f | Text | 7,630 | 163 | # ALDH1A1-PD Meta-Analysis
**ALDH1A1-Dopaminergic Gene Co-expression in Human Substantia Nigra: Meta-Analysis of Disease-Associated Correlation Changes Across Seven Independent Parkinson's Disease Datasets**
Drake Harbert — Inner Architecture LLC
---
## Overview
This repository contains the complete analysis code ... |
1ad928fd57412c5efcae4605f3ccee26f50cba206b5e43ae63c2afffe22a332a | Text | 7,638 | 142 | # GNN Attribution Alignment with AOP-40 Reactive Centers
Code and data for the manuscript "Systematic Validation of Graph Neural
Network Explanations Against Adverse Outcome Pathway Reactive Centers for
Skin Sensitization" (Journal of Cheminformatics).
## Quick start
```bash
conda env create -f environment.yml
conda... |
807fcf4dd6a636becb25e9ac6d5844fabeaf1563e9d062f52ebb184e4612dac8 | Text | 7,638 | 239 | # StabLyzeGraph
<div align="center">
<img src="src/logo.png" alt="StablyzeGraph Logo" width="300"/>
**StabLyzeGraph: High-Throughput Screening of Combinatorial Mutations Using Graph Neural Networks**
[](https://python.org)
[![PyTorch](https://im... |
00801f3b42de18b594e3ef17afc77bebd9c7105ec268f4c780f5f8db6bedc213 | Text | 7,677 | 204 | # Multimodal Patient-Specific Identification of Atrial Flutter Circuits From ECG Time Series Using Explainable Machine Learning
S. Ruipérez-Campillo et al., "Multimodal Patient-Specific Identification of Atrial Flutter Circuits from ECG Time Series Using Explainable Machine Learning," in IEEE Journal of Translational ... |
08d883d520bcbd6ac813831d3ea6e39c001a25e3a95a846ee0ea3a1d74168d5e | Text | 7,701 | 141 | # plotSurfaceROIBoundary
<img src="./figures/SurfaceBoundaryPlotsExample.png" width="100%">
These MATLAB scripts will plot the boundaries of a ROI on a surface. Additionally code is provided so that certain regions can be excluded from the colourmap.
There are five ways of defining a boundary here (I know right? Ove... |
22803fa4c157e635c8128c17fe022e1f47852997884aa57787d33ae44baac73b | Text | 7,743 | 160 | # MPSUR: Predicting Causes of Unplanned Reoperations with an AI-based Multi‑Modal System
## Abstract
Unplanned reoperations are commonly regarded as key indicators of surgical quality and patient safety, yet the process of determining their underlying causes is often time‑consuming and non‑standardized. In real‑world ... |
2ee7ad9dfdb5d7f28c468bfa62e2cf7ff171f27924687ae03056e3384f324e4c | Text | 7,748 | 151 | # precon_all
precon_all surface pipline
precon_all is an animal surface generation pipeline that can be easily adapted to work with multiple species.
The curent example we'l use is the pig as it's what the pipeline has been used for the most.
For comments and questions email **r.austinbenn@gmail.com**
First clone ... |
7853c8582f511930f43cfc231c46bcd9932777dd4bc284ada4fffe14ee47b9b1 | Text | 7,749 | 270 | # SPN/CNV EEG preprocessing and analysis pipeline
This repository contains the analysis code only.
The dataset is available on Zenodo: [https://doi.org/10.5281/zenodo.19344047](https://doi.org/10.5281/zenodo.19344047)
This repository contains a MATLAB/EEGLAB preprocessing pipeline and a Python-based analysis workflo... |
c32d85de4cc1b8b9ae1f546fbefb2a85d05279271a2073aac843b0de209dd493 | Text | 7,760 | 206 | # Electrostatic Interaction Determines the Docking Specificity and the Formation of Functional Cx36 Gap Junction Channels
[](https://www.python.org/downloads/)
## Abstract
Connexin36 (Cx36) is broadly expressed in neurons and serves as the principal pr... |
6290b163de65b2dd0ddc24fce68087b425f478e4646f202fdeffd7ec23a20cba | Text | 7,771 | 119 | # Spike2Pop: Bridging Experimental Neuroscience and Computational Modeling
## Introduction
The human brain remains one of the most enigmatic and complex systems in nature. Understanding its mechanisms is fundamental to unraveling cognition, advancing treatments for neurological disorders, and driving innovation in ar... |
e1aaca71459d6cc2d2dd88c873f3fbc5d14912e3aff61c4adbc13b5c506ae00a | Text | 7,791 | 137 | |banner|
BluePyEModel: Blue Brain Python Electrical Modeling Pipeline
============================================================
+----------------+------------+
| Latest Release | |pypi| |
+----------------+------------+
| Documentation | |docs| |
+----------------+------------+
| License | |license... |
b3eb78097181dbb06ffd5431f1a6e7f7cbd419aece556e96ff95adfcaed4e18e | Text | 7,810 | 124 | <!-- START doctoc generated TOC please keep comment here to allow auto update -->
<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
## Table of Contents
- [MODA](#moda)
- [Purpose](#purpose)
- [Getting started](#getting-started)
- [References](#references)
- [Example applications](#example-applicat... |
923eb6b6a0a9c7bd3479e5e4c728a2d30dc2ffdfbc1c0d07d3b22acfff0d2287 | Text | 7,813 | 57 | # Recursively embedded atom neural network
## Introduction
Recursively embedded atom neural network (REANN) is a PyTorch-based end-to-end multi-functional Deep Neural Network Package for Molecular, Reactive and Periodic Systems. Currently, REANN can be used to train interatomic potentials, dipole moments, transition d... |
46c6163b546d1d48b6f866c5bbb6ad709b1de0234d79385c26f71e20efb617de | Text | 7,848 | 122 | # Spatial dependency-aware deep generative models
SpaVAE, spaPeakVAE, spaMultiVAE, spaLDVAE and spaPeakLDVAE are dependency-aware deep generative models for multitasking analysis of spatial genomics data. Different models are designed for different analytical tasks of spatial genomics data.<br/>
**spaVAE** is a negati... |
3f3fe493b36ff6bb481402f5f44dab2a64f7b96b12fe44b0cacaa9d5d006a254 | Text | 7,862 | 160 |
[](https://travis-ci.org/ReddyLab/DP_GP_cluster)
## DP_GP_cluster
DP_GP_cluster clusters genes by expression over a time course using a Dirichlet process Gaussian process model.
## Motivation
Genes that follow similar expression tra... |
c0af532a34030bbca4527c00127e1573847a21ce8f2c3eb8f72ec5d4facbc3d3 | Text | 7,864 | 191 | # Computational mechanisms for temporal integration in the anterior claustrum
This repository contains cleaned reproduction code for the recurrent neural network (RNN) simulations and downstream population analyses associated with the eLife reviewed preprint:
**Kuenbae Sohn, Donghyeon Yoon, Junghwa Lee, and Sukwoo Ch... |
a6a05f7e8f5fb4613953bebd575f3cdf33705390de58181ed58078b455898e53 | Text | 7,877 | 168 | # Diffusion Convolutional Recurrent Neural Network: Data-Driven Traffic Forecasting
This is a TensorFlow implementation of Diffusion Convolutional Recurrent Neural Network in the following paper: \
Yaguang Li, Ros... |
351a0201dfc89d96b8fe10b562343d28ec8e59ca2b73d13acfcea7ce73387ed3 | Text | 7,932 | 154 | TableOne
=========
.. image:: https://travis-ci.org/tompollard/tableone.svg?branch=master
:target: https://travis-ci.org/tompollard/tableone
tableone is a package for researchers who need to create Table 1, summary
statistics for a patient population. It was inspired by the R package of the
same name by Yoshida a... |
a81da4f73e080646cf2588b951bd46bcde88c85919c306f9cc6c0cef2ceb022b | Text | 7,936 | 329 | # 🌀 EKF Oscillator Tracking (EKFOT)
MATLAB implementation of an **Extended Kalman Filter (EKF)** for tracking
time-varying **frequency**, **damping**, and **amplitude** of narrowband oscillations
using a reparametrized AR(2) resonator model.
The repository includes:
- ✅ EKF-based oscillator tracking
- ✅ Genet... |
68eb9f0c6999a3677861d7d0ab553e39ebe226eef987c5cbbff88510a0929563 | Text | 7,987 | 143 |
# TRAILMAP
This is a software package to extract axonal data from cleared brains as demonstrated in [Mapping Mesoscale Axonal Projections in the Mouse Brain Using A 3D Convolutional Network](... |
e4215b0bd1017f181a3f1ed9b02aa864a3d5b6c48adc38e95f1f825d134f2838 | Text | 8,003 | 253 | # MBBN: Multi-Band Brain Network
Official PyTorch implementation of **Multi-Band Brain Network (MBBN)**, published in *Communications Biology*. \[paper link will be added soon\]
> MBBN is a self-supervised, pre-trainable transformer for functional MRI (fMRI) that decomposes BOLD signals into three frequency bands and... |
7d72625e33c636c6f3a47e153b1e7542dbb25edc7ea638d418c7fffebd0dbcb6 | Text | 8,012 | 64 | # GCpaper2026
Matlab and R code used for data analysis in Krause et al. 2026.
## Fluorescent image analysis
### PURPOSE and FUNCTIONAL DESCRIPTION of the program:
The program runs in a batch mode, by first mapping the presence of all the NL360 .xml files contained inside an umbrella folder organized in a specific... |
cba69bbd55440c79de35f53417c33438dd27ec763294118563f7079c074602d7 | Text | 8,019 | 141 | .. warning::
The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
Future development will take place at: https://github.com/openbraininstitute/BluePyEModel
|banner|
BluePyEModel: Blue Brain Python Electrical Modeling Pipeline
=====================... |
ba0f617cd79eaf8ff85187eb1c98326090b9c5a3cfde39289aeaa54855e1930b | Text | 8,020 | 106 | # 📊 Table Analyzer v1.10
Table Analyzer is a modular R/Shiny application for analysing tabular datasets with modern statistical methods and generating publication-ready visualizations. It can process multiple variables in parallel, apply optional stratification, and produce fully auto-arranged plots without any manua... |
1652bc220a41ed036124b83346f43cfb23801fbc4ab5317e26b490a43c1214a2 | Text | 8,035 | 294 | # tf-explain
[](https://pypi.org/project/tf-explain/)
[](https://zenodo.org/badge/latestdoi/196956879)
[](https://github.com... |
1908088251181748ce961a7e76922361ea723d0a8108ccd26540168e883454f3 | Text | 8,053 | 153 | # Autoencoder-Enabled Localized Regression (AEnabledLoReg)
## Abstract
This repository contains the source code for the paper, "Contrasting Global and Patient-Specific Regression Models via a Neural Network Representation". We introduce a novel methodology to contrast global and local modeling strategies by enabling... |
a6e5a2574724be50c0856ddbfbca4c0ba7ff5d9328a44626ef7fc83d17a78046 | Text | 8,141 | 155 | |License| |PyPI version| |doi| |Python versions| |Documentation Status|
==============================================================
siibra - Software interface for interacting with brain atlases
==============================================================
Copyright 2018-2026, Forschungszentrum Jülich GmbH
*Auth... |
6e007b110d309a829edbba2f2f03e9b0ef4a5d00267d51a64a3532edbb79da4a | Text | 8,184 | 131 | # FlowMol3: Flow Matching for 3D De Novo Small-Molecule Generation
[](https://arxiv.org/abs/2508.12629)
This is the offical implementation of FlowMol, a flow matching model for unconditional 3D de novo molecule gene... |
63bd2029e1d58c8754b62b59dde1e51d547df9dc02db32f464bbdda8e1c5ff54 | Text | 8,238 | 269 | # STED: Single-cell Topic Modeling & Epigenetic Deconvolution
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
**STED** is a Python package designed for the... |
bacf968f2bd29072bb61e573ef8a8ba6a79df679212ef4e688ec61a5d39418e1 | Text | 8,247 | 190 | # LIOM Toolkit
[](https://badge.fury.io/py/liom-toolkit) [](https://github.com/LIOMLab/liom-toolkit/actions/workflows/ci.yml) [ used in the paper ([link](https://doi.org/10.1038/s41467-026-73865-9)) by Colwell _et al._ concerning the influence of H3R inverse agonism on the neural dynamics of learning.
The code reproduces behavioural and com... |
83007ff0cebcc239c77b52353a159b5eedc81510b4be819eff53bae2c89954f6 | Text | 8,344 | 149 | <image src="https://github.com/evarol/dredge/blob/main/assets/logo.png" width="200px"></image>
Published in *Nature Methods*: https://www.nature.com/articles/s41592-025-02614-5
Free PDF link: https://rdcu.be/ecqZf
# DREDge: Decentralized Registration of Electrophysiology Data
DREDge is an algorithm for estimating t... |
6081da47e5b5100ef423a093cfc753a600c9cf54a9a97eb3235678292f85b4dd | Text | 8,376 | 182 |
# <span style="font-family: sans-serif;">HARPA</span>: High-Rate Phase Association with Travel Time Neural Fields
## About
This is the source code for paper _High-Rate Phase Association with Travel Time Neural Fields_.
## Installation
Simply run:
```python
pip install -q git+https://github.com/DaDaCheng/phase_as... |
fb86345d7129b25875b503967cbc860c6fee76a5339990ce82bb43e0ee46f21d | Text | 8,416 | 76 | # README: Raw patch-clamp recordings — subchronic PAH effects on navaga cod ventricular cardiomyocytes
## Overview
This dataset contains the original, unprocessed electrophysiological recordings underlying the study *"Beyond Acute Toxicity: Subchronic PAH Effects on Navaga Cod Ventricular Cardiomyocytes"* (Dzhumaniia... |
36c4df3ccf4a773968895243c9acba8448f2cc49ac4748b6ca51c727b29a6284 | Text | 8,430 | 188 | # An ECG Biomarker for Sudden Cardiac Death
This repository contains the code accompanying our paper:
> **An ECG biomarker for sudden cardiac death discovered via deep learning**
> Ziad Obermeyer, Alexander Schubert, James Ross, Sendhil Mullainathan, Markus Lingman
The codebase implements three interconnected compon... |
7cb1aa7393198428ac673c393d53c1bc685194b7bc21082172a6d1f748968953 | Text | 8,433 | 100 | # Description
This repository contains source data and scripts (preprocessing, modelling and analyses) used in pre-print ([link](https://www.biorxiv.org/content/10.1101/2025.10.05.680501v1)) by Colwell _et al._ concerning the influence of histamine autoreceptor blockade on human learning.
The code reproduces behaviou... |
1202081e4bc14f5e3c3961013538696600f3b2588e730ab5c5f82a63465043c7 | Text | 8,434 | 184 |
# <span style="font-family: sans-serif;">HARPA</span>: High-Rate Phase Association with Travel Time Neural Fields
## About
This is the source code for paper _High-Rate Phase Association with Travel Time Neural Fields_.
## Installation
Simply run:
```python
pip install -q git+https://github.com/DaDaCheng/phase_as... |
5849f1090763d03cd7f9c44bead8df6d94596da87f1899d024b34df7540bb76e | Text | 8,439 | 100 | # Neural Synchrony for Figure Ground Segregation
Analysis and simulation code accompanying the article:
Karimian, A., Roberts, M.J., De Weerd, P., & Senden, M. (2025). **Principles of Gamma Synchrony Predict Figure–Ground Perception in Texture Stimuli**. *eLife* **14**:RP105482. [https://doi.org/10.7554/eLife.105482.... |
ea3d82f768234905275aeecf75c5712edc1014e41a6cc21ab2a54f309935a854 | Text | 8,440 | 162 | # Joint Variational Autoencoders for Multimodal Imputation and Embedding (JAMIE)
Single-cell multi-modal datasets have emerged to measure various characteristics of individual cells, enabling a deep understanding of cellular and molecular mechanisms. However, generating multi-modal data for many cells remains costly a... |
17013af76ad705e513483fbf52c2709c298ff45cbbfb3682d6c0354d2c12a9ea | Text | 8,469 | 72 | # From aging to Alzheimer’s disease: brain DNA methylation changes in late life
David Lukacsovich, Juan I. Young, Lissette Gomez, Michael A. Schmidt, Wei Zhang, Brian W. Kunkle, Xi Chen, Eden R. Martin, Lily Wang
### Description
This GitHub repository includes scripts used for the analyses in the above manuscript.
... |
fed8c9fcb5cce0d85eb1fd7a15927f5f477d97ad7b1dadd27fc9274f05b6125d | Text | 8,478 | 185 | # SaAki_Sofa_benchmark
Open-source SOFA-2 SQL implementation on **MIMIC-IV v3.1**.
> To our knowledge, this is the **first publicly available SOFA-2 SQL implementation on MIMIC-IV**.
---
## Background
SOFA-2 is the second-generation Sequential Organ Failure Assessment score,
introduced in 2025 as an update to the ... |
3b7175886d856007ddcb33e8a5326babe931080d47c50071a6a1e56f7d8aebe6 | Text | 8,481 | 244 | # 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... |
f7389c8a47956417156e43c6011c4c944a3b5c0b130ce01e50d0eb5abf93ca7d | Text | 8,496 | 340 | # Age–Mutation Spline Toolkit
This mini-toolkit provides reusable functions to test and visualize binary mutation status (0/1) as a function of age, using logistic regression with natural splines via `splines::ns()`.
## What this supports
- Mutation columns that are binary: `0/1` (also accepts `TRUE/FALSE` and coer... |
1f466e468b2db9a744069f40d0ba83017b8791c7da14ed291fee886921520b42 | Text | 8,503 | 176 | pySCENIC
========
|buildstatus|_ |pypipackage|_ |docstatus|_
pySCENIC is a lightning-fast python implementation of the SCENIC_ pipeline (Single-Cell rEgulatory Network Inference and
Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from
single-cell RNA-seq d... |
5eb808f0cca16fcec7d19895e3e9b1acd0f776d0fefe43d369c3972d4780549a | Text | 8,517 | 73 | # Open-Access Derived Data for White Matter Micro and Macrostructure Brain Charts
## Dataset Overview
* This dataset provides quantitative scalar data, derived from diffusion MRI (dMRI) and T1-weighted scans, that were used to create comprehensive normative reference charts that document changes in white matter (WM) m... |
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