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b4378aa1bb195375f79b5db785dca9d278baddf0340bd3d214a9b9d2f7a41dd5 | Text | 2,294 | 64 | # SSM: Bayesian learning and inference for state space models
[](https://travis-ci.org/lindermanlab/ssm)
**Note: We're working full time on a [JAX](https://github.com/google/jax) refactor of SSM that will take advantage of JIT compilation, GPU and... |
11449f9a1a650f0f3cba69b0ebac28582f268e98343ef794316859cadf737fe1 | Text | 2,306 | 16 | This repository holds the code and data for the following manuscript:
Minikel EV & Kuhn E (equal contribution), Cocco AR, Vallabh SM, Hartigan CR, Reidenbach AG, Safar JG, Raymond GJ, McCarthy MD, O’Keefe R, Llorens F, Zerr I, Capellari S, Parchi P, Schreiber SL, Carr SA. **Domain-specific quantification of prion prot... |
5a57900632e88f08a418b29e9852ad50aff0fe0736fb6fd6ccdb12415b6573be | Text | 2,314 | 15 | # NeuroConnectivity
Most neurological disorders share a phenotype of synaptic dysfunction. High-content microscopy is indispensable in the drug discovery process but the sensitivity relies on the accuracy of mature synapse detection. We present a workflow whereby synchronous calcium bursting is measured in GCaMP6f-tran... |
7e09f5a4de549f37c3feb91c36815765c89ebd20d0f287ac16399ca770ba51f0 | Text | 2,316 | 52 | PVBS: Prairie View Browsing Solution
Copyright (C) 2022-2024, Jaeyoung Yoon.
(jy.yoon@tch.harvard.edu)
- MATLAB-based general-purpose GUI for browsing and analyzing electrophysiology (patch clamp) and calcium imaging data
- Developed with Matlab R2023a on Windows
- Initially developed for interpreting d... |
8afff35a9633e1468e5e01ad8ef5d467a67ed73ed31a2cf460e131764615b0b4 | Text | 2,321 | 60 | # Longitudinal_ct_workflow
This repository contains the Python code used in the paper (submitted for publication) _"Longitudinal CT Scanning for Explainable Early Detection of Postharvest Disorders: The ‘Braeburn’ Browning Case"_. The paper presents two workflows for leveraging longitudinal computed tomography (CT) dat... |
bc8c94beedcedb83d2fb96540b1465af165a535c845cd26eac6647788b97fefe | Text | 2,323 | 43 | ## Neuromorphic hierarchical modular reservoirs
This repository contains code written in support of the work presented in
[Neuromorphic hierarchical modular reservoirs](https://www.biorxiv.org/content/10.1101/2025.06.20.660760v1),
as well as data necessary to reproduce the results.
We introduce a simple blockmodeli... |
9a379d041a949d4ab2bb188603a91b15b30b80592abe7b2e202ce2c7cadc8bd2 | Text | 2,324 | 57 | # MARCC: Mapping-Assisted Reaction Center and Classification
## 🔬 Overview
MARCC is a **cross-attentive multi-task graph neural network** for chemical reaction understanding.
It jointly predicts **atom mappings, reaction centers, and reaction classes** within a unified end-to-end framework.
Unlike existing appro... |
4d84bbbebbd4b78a72bfe05d9b310df229f34c745ad769e6037c1bd1f573c6aa | Text | 2,333 | 32 | This Code is for the paper titled 'Selective vulnerability of cerebral vasculature to NOTCH3 variants in small vessel disease and rescue by phosphodiesterase-5 inhibitor'. It is permanently open and free to read/download for the entire research community (no access code is needed).
1.Modify the directory in the BlueA... |
8c33f1207b02147dc1bfa8dbc9a4508bdad558b908370604c5d6718257dc80a0 | Text | 2,333 | 81 | # PETIMOT: Protein Motion Inference from Sparse Data
PETIMOT (Protein sEquence and sTructure-based Inference of MOTions) predicts protein conformational changes using SE(3)-equivariant graph neural networks and pre-trained protein language models.
## Installation
```bash
# Create and activate conda environment
conda... |
e9e6cde5c3824af2e636009c2e2a32a2f360499c7e2a3295e288e8bcbd79f3cc | Text | 2,336 | 12 | # CereBRLSIM
This repo corresponds to the manuscript: Physics-Informed Digital Twin Can Predict Cerebral Blood Flow and Cerebral Vascular Regulation in Neurocritical Care Patients by Briggs et al. Here, we construct and validate a digital twin of cerebral hemodynamics that can be used to estimate cerebral vascular regu... |
36affc69866a3af6af0bb14871a8e4124c08e28606828f252b1ec047943413d8 | Text | 2,337 | 56 | # RGAST
[](https://doi.org/10.5281/zenodo.18463983)
RGAST: Relational Graph Attention Network for Diverse Spatial Transcriptome Analysis [[paper]](https://doi.org/10.1093/bib/bbag298)
This document will help you easily go through the RGAST model.
## You can explore a live demo of the tool on Hugging Face Spaces:
https://huggingface.co/spaces/Ugo96/DiBiMa-EEGSR-Demo
## 🛠️ Third ... |
1fd3feafea942f48b305ddcd04108dcaa724c1869cb9259de604dbfc46689cd9 | Text | 2,355 | 96 | Louvain Community Detection
===========================
.. image:: https://travis-ci.org/taynaud/python-louvain.svg?branch=master
:target: https://travis-ci.org/taynaud/python-louvain
.. image:: https://readthedocs.org/projects/python-louvain/badge/?version=latest
:target: http://python-louvain.readthedocs.io... |
d5ad3c37f801cc0330383d25e87ed0416ccb968dd6095ba14f858c446a2347ed | Text | 2,365 | 51 | # critical_init
Code for [Pachitariu et al 2026](https://www.nature.com/articles/s41586-026-10528-1)
For Figures 2 and 3, the data is available on [figshare](https://janelia.figshare.com/articles/dataset/Data_from_A_critical_initialization_for_biological_neural_networks_/27854448), please cite this publication if you... |
268575aac96040d0ddf00cb928bbc5e1b03ba2227d3f262e9881dcb171f9d291 | Text | 2,366 | 51 | # VQ-Wave: Spatio-Temporal Inception Network for Analysis of Functional Lung MRI Data
This repository contains the official PyTorch implementation, **pre-trained model**, and inference framework for **VQ-Wave**, as described in the paper:
> **VQ-Wave: A Physics-Driven Spatiotemporal Deep Learning Approach for Noncont... |
295c62873e4578fc4aa2ddcc20774c50686ce659bf9cb09f0e8019a325d21a3c | Text | 2,374 | 95 | # Property-Guided CO₂ Carbanion Generation
A reproducible workflow for generating high-activity carbanion molecules for CO₂ activation using property-guided molecular generation.
## Overview
This codebase implements a complete pipeline:
1. **Chemprop Training**: Train a property predictor for Mayr nucleophili... |
74e989c03d2bd87280fc32c43217c55b776ce3627f905435d721a8acc5a79382 | Text | 2,375 | 60 | Code and Data for Figures 6–7
Description
This repository contains MATLAB code and processed data used to generate:
• Figure 6: Frequency tuning reflects fine-grained preferences, not strictly tied to dominant or least prevalent LFP frequencies
• Figure 7: Summary of frequency and phase tuning across neurons and re... |
8bdd7f4b5a7ccc363256a536708bc98e45a9b4180736cde1fe6343b563c9a688 | Text | 2,379 | 46 | # Inhibitory columnar feedback neurons are involved in motion processing in Drosophila
# Henning et al., 2025 elife
This repository contains code and data published in Henning et al., 2025 elife
All Matlab code, except for the code analyzing behavior data, was written by Miriam Henning. The code for behavior data analy... |
e983efc76d215bb5822e03d945ef6a8723c428423a8372439cb217b1a28c6b7d | Text | 2,383 | 55 | <img src="https://raw.githubusercontent.com/MolarVerse/PQAnalysis/main/docs/source/logo/PQAnalysis.png" width="250">
# PQAnalysis
[](https://github.com/MolarVerse/PQAnalysis/actions/workflows/ci.yml)
[ model introduced in our paper on cell viability assessment using deep learning. The NViR model is designed to non-invasively assess the viability of spheroids using br... |
d0d206a5ca8b40c1ea6e80c6f7a24bce383b62ed9508e3dca5c6e57db7ac4096 | Text | 2,405 | 53 | # MEDIC paper analysis scripts
[](https://www.biorxiv.org/content/10.1101/2023.11.28.568744)
The scripts in this repository perform analyses reported in the MEDIC paper.
MEDIC itself is implemented in the [Dosenbach and Greene Labs'... |
38608c296a8051144635f18a9c9adb9d9b2c114292ccfa48e1d331d8bc3b3236 | Text | 2,406 | 75 | <img src="notebooks/data/images/GPErks_logo.png" width=120 height=120 />
# GPErks
A Python library to (bene)fit Gaussian Process Emulators.
---
## Information
**Status**: `Actively developed`
**Type**: `Personal project`
**Development years**: `2020 - Present`
**Authors**: [stelong](https://github.com/stelong), ... |
5b3bddc3cba49c49b68bbb08a71fd9641f66e9c196eff68910a665d8715501fd | Text | 2,412 | 81 | # LLM-Generated-NN-Dataset
This repository hosts the dataset accompanying the paper **"On the Use of LLMs to Generate a Dataset of Neural Networks"**.
The dataset contains PyTorch-based neural network code automatically generated using GPT-5 according to specific requirements.
## Overview
The dataset was generated... |
ad19a43950ad02837212c0b5bdb813b9f3d900b22ef3a2eb65f69e0a3c4bfb68 | Text | 2,412 | 42 | # TDLM-Python
This repository provides a Python implementation of [TDLM](https://github.com/YunzheLiu/TDLM).
\- Work-in-Progress -
Temporally Delayed Linear Modeling (TDLM) is a method used to quantify the "sequenceness" or sequential structure in time-series data. It's particularly useful for analyzing sequences... |
e41e918da9375e4fdd0f3e8978d55f4e88af79f46a73dceabc32495b91c40147 | Text | 2,425 | 82 | # TIGER
TIGER is an end-to-end deep learning framework for reconstructing aircraft trajectories from multi-station ADS-B signal observations.
## Environment Setup
Create a conda environment with Python 3.8:
```bash
conda create -n tiger python=3.8
conda activate tiger
```
Install the Python dependencies:
```bash
... |
550f5e41c293226e62f873c6ed38f9d8ee5db608012d48737144cbc8f949c0d8 | Text | 2,427 | 44 | # Acoustoelectric neuromodulation and its contribution to US stimulation
## Overview
The code contained in this repository, works in conjunction with the datasets uploaded to figshare at: DOI: https://doi.org/10.6084/m9.figshare.c.7909283
The purpose of this code and data is to recreate the figures in the article 'N... |
c5f4b21a0c1ef256c7796292f07c76cc9996f40838cf74eb1ffdf3c47414e1ac | Text | 2,433 | 18 | The code referenced in the Code Availability section consists of two MATLAB files: a main function named "modulation_scheme.m" and a supplementary script named "Takagi_factorization.m". These files provide the theoretical and methodological foundation for the numerical and experimental validations presented in the manu... |
cc9f37a139b48acac7168c131f53edacb8bfb025624ed3ad39820a9010383be4 | Text | 2,436 | 58 | # SSP-KAN: Small-scale photonic Kolmogorov-Arnold networks using standard telecom nonlinear modules
Code to reproduce all results from the Nature Communications manuscript (NCOMMS-26-022249).
A reproducible compute capsule is archived on Code Ocean (DOI: 10.24433/CO.0732940.v1).
## Reproducibility note
Results in t... |
09c8b622c77e52277239f3abaa509a3497b188bfacd446c3ebc3d35b3496d1a5 | Text | 2,451 | 44 | # Coral Larvae NE-ABM
A neuroevolution-driven **agent-based model of coral larval settlement**, built in
Unreal Engine 5.8 (C++). Each larva is an agent whose neural-network "brain" is evolved by
a genetic algorithm to settle in response to environmental cues: crustose coralline algae
(CCA), biofilm, depth, sound, and... |
b21755e68efe1bd54e9e61e5250e820ee18a23a20e104a0e5e2435b9827804cb | Text | 2,452 | 40 | This repository contains the scripts used to analyze grid cell properties associated with the published version of the preprint article entitled "Tiling of large-scaled environments by grid cells requires experience", available at https://www.biorxiv.org/content/10.1101/2025.02.16.638536v1.
The code was run and teste... |
231b2b972f64373f31acd5eb5dc8f58661f6bf207daeb4a6a3da6aca25301a14 | Text | 2,454 | 97 | # LSTM-Based Prediction of Big Toe Skin Temperature
[](https://doi.org/10.5281/zenodo.18851662)
## Safety-Oriented Modeling for Cold Exposure Assessment
This repository provides the full training and evaluation pipeline for an LSTM-based model designed to predict big ... |
a5a809e64648fbd7cef098a65d49f632856fcd545b59c1d6ec9eb70a72dada04 | Text | 2,460 | 33 | # X_maze
Build files and scripts for an automated delayed (non)match to direction task, with simultaneous video recording and TTL pulses to synchronize to additional data streams
This task is derived from the H maze, originally published in [(Seigle & Wilson, 2014)](https://elifesciences.org/articles/03061) with a det... |
7dd4e31b064ac43fec4c020ddde129fe0ded028116e5b7e5926588429f2e8b46 | Text | 2,477 | 90 | # Code and Data for "Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors"
This repository contains the MATLAB code and information about the processed data used to generate the figures and results in:
Mutlu et al., Topographically o... |
2599fdac6e1f6e8c05ced11ae5c1cad1b4c3c3d127c57090646a353ecf187d1a | Text | 2,496 | 45 | # LTFTNET - Documentation
Multiple Retinal Pathology Classification
Lightweight, Efficient, and High-Performance Deep Learning Model for Ocular Disease Detection
This repository provides the implementation of an efficient deep learning framework for **automated retinal disease classification** using fundus images.
T... |
96ee42a6da220e73f7165aa72019cdb7b479a79d888d6b648ea2dbd118cf22b6 | Text | 2,499 | 50 | # Metabolism Weighted Centrality
This repository contains the code to reproduce all results and figures related to the paper:
"Metabolism-weighted brain connectome reveals synaptic integration and vulnerability to neurodegeneration", by Mahnaz Ashrafi, Laura Fraticelli, Gabriel Castrillón, Valentin Riedl (2025).
## R... |
31102942ecc95da649d2230235d372f494b920a11e6e5c070bf7e19fbf202748 | Text | 2,503 | 39 | # PyTorch Examples
https://pytorch.org/examples/
`pytorch/examples` is a repository showcasing examples of using [PyTorch](https://github.com/pytorch/pytorch). The goal is to have curated, short, few/no dependencies _high quality_ examples that are substantially different from each other that can be emulated in your ... |
4f18dccdacc537f9bb8ee810f62be795f0850c7cc12d60d8d165fc1d8a6e1bbb | Text | 2,510 | 73 | # pLM-SAV
## Important notes
- Some scripts contain hard-coded paths that reflect our internal directory structure (e.g., paths to Eff10k data, which we cannot distribute). Example input and output files are provided in the `examples` directory.
- Neural network definitions are in the `mynn.py` file.
- Suppleme... |
118def47411f32bbbb63181683772361e6391c50a32fa2f009636bfdb7d308e4 | Text | 2,514 | 76 | # Local graph estimation – paper repository
This repository accompanies the paper:
**Local graph estimation with pathwise false discovery control** • [[arXiv]](https://doi.org/10.48550/arXiv.2507.17172)
It contains the code, included datasets, stored outputs, and setup instructions needed to reproduce the analyses, ... |
101eb8c71981094158748764be8b12f3dcab402fee234c40df4f8141e3240d60 | Text | 2,515 | 35 | # Semantic Mnemonic Similarity Task (sMST)
The experimental files and preprocessing scripts of the sMST to create analysis-ready tables of the behavioural data.
Preprocessed data is uploaded to OpenNeuro, at: https://openneuro.org/datasets/ds007275
Behavioural and fMRI analysis scripts available at: https://github.co... |
0ff6c90db7c443bb48af6c8143eefa4e1f77b794ac6c76fc93fce89e782a9cbc | Text | 2,521 | 89 | # DA_Salience_NAc_2025
## Project Overview
This repository contains data and analysis code for the project:
**"Dopamine in the Nucleus Accumbens Signals Salience of Auditory Deviance"**
---
## File Structure and Contents
All files are located in the project root directory. The main file groups are as ... |
3dec7a25f2fcfeda29b83fb396285034603926b2fa765a2904104e08dd635f04 | Text | 2,525 | 40 | # Cogitate Experiment Code Repository
Welcome to the Cogitate Experiment Code Repository! This repository is dedicated to hosting the code used for acquiring data from the Cogitate Consortium split by modality. Our experiments are designed to explore various aspects of cognitive science through different modalities in... |
2ce141d70f09ba37ef1f18159d33b7d088da2d84306698627193ff3b29d5773a | Text | 2,528 | 63 | # Selective perturbation of mirror and non-mirror neurons in an in silico model of the Action Observation Network
**Guglielmi et al.**
This repository contains the TensorFlow 2 implementation of the recurrent rate-based neural network model described in
*Selective perturbation of mirror and non-mirror neurons in an i... |
be9e53dba5da9c21790d4b7c4359e1fbce0e292bf62238c723375a228adf6565 | Text | 2,537 | 27 | # Shared latent representations of speech production for cross-patient speech decoding
## Overview
This repository contains code used in analyses and creation of figures for the paper "Shared latent representations of speech production for cross-patient speech decoding".
We use an app... |
f0c568cd3a9263194f8470d3c3b510e1cad7aa9c44fb889366c765f31278bf8f | Text | 2,547 | 59 | ## Hippocampo-neocortical interaction as compressive retrieval-augmented generation
Code for the paper "Hippocampo-neocortical
interaction as compressive retrieval-augmented generation".
The repository contains four main simulation pipelines:
- `full_model/`: narrative encoding, consolidation, forgetting, semantic m... |
55f42527eb1a5232158fe93004bdfbc546553d54a149e558098ba929060b4537 | Text | 2,548 | 39 | # lrrk2_photometry_analysis
Project Overview
This repository includes all custom code used to analyze data in our manuscript. We analyzed fiber photometry recordings from head-fixed LRRK2 mice running on a treadmill while receiving optogenetic stimulation in the striatonigral dopamine neurons. Custom code necessary f... |
3c49aa7ad8c39909e5780689d78d4ada3711a00e8555564e04c35b9195be6b9a | Text | 2,553 | 91 | # Connectome Analysis
#### General functions to analyze connectomes from a topological perspective.
---
## Documentation
See our [**documentation**](https://openbraininstitute.github.io/connectome-analysis/) for detailed explanations including examples and tutorials.
See our... |
edb621ef138e21b5600a6d7dac924e8136e3c995014d769e60041b1dc58eff88 | Text | 2,559 | 24 | # Model Network Simulations
## Dependencies
The code was developed and tested in MATLABR2025B and requires MathWorks Toolboxes:
'Signal Processing Toolbox',
'Statistics and Machine Learning Toolbox'
## DeNovoBase
The script file **DeNovoBase.m** instantiates a 1D network object, samples external and intrinsi... |
3522c6247d5962de25a749c09f9773dae510f5234c7d84745edcf56a83653b1f | Text | 2,567 | 36 | This repository contains the datasets and code used in the manuscript “3D epithelial cell topology tunes signalling range to promote precise patterning” by Paci et al
Subfolders content is as follows:
- Figure 1:
• Raw image for SOP overview in panel C
• Raw images for SOP spacing in panel D (folder “Images_SOP_spa... |
f9d2273127e0a3046fb9424542b1bafd1155abbd96db814880ae8ee25d82b265 | Text | 2,569 | 41 | # EASELAN: An Open-Source Framework for Multimodal Biosignal Annotation and Data Management
Contributing Authors: Moritz Meier, Rathi Adarshi Rammohan, Dennis Küster, Tanja Schultz
## Overview
EASELAN is a comprehensive human-in-the-loop framework for high-dimensional sensor data annotation aligning multiple modaliti... |
e79f0ba057d7d6593332668f356ac32a8196f4133e9255d3601039aa1fd5f7c3 | Text | 2,580 | 62 | # MANTIS post processing pipeline
<p align="center">
<a href="images/github_figure.png">
<img src="images/github_figure.png" width="600">
</a>
</p>
Reference github repository for the paper “Multispectral Extended Depth-of-Field Fluorescence Microscopy with Co-designed Meta-Optics and Neural Reconstruction” b... |
a900a9eec9334d6b1735ab785504a21f06d5f73484d4072a3965ae720906e8ab | Text | 2,582 | 69 | ## LFP-LOC
Code associated to the method presented in the paper: "LFP-LOC: an LFP power–based method for the anatomical localization of high-density neural probes" ([link](https://doi.org/10.3389/fnins.2026.1816533)).
Estimate a probe's anatomical location using the power spectral features present in canonical LFP ba... |
2bfcc8ee0832d0ae0722f48bb898184ddc16606c3f1effa8bc89c005400689fe | Text | 2,586 | 79 | # Atac Mapper
[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/quadbio/atac_mapper/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/atac_mapper
Map query scATAC-seq data to a single-cell chromatin a... |
48caee9a764f52caa32de5f04f19df8c370c537f2ff59c5e2f1e2af0fbdd26b3 | Text | 2,593 | 42 | # Scrublet
**S**ingle-**C**ell **R**emover of Do**ublet**s
Python code for identifying doublets in single-cell RNA-seq data. For details and validation of the method, see our paper in [Cell Systems](https://www.sciencedirect.com/science/article/pii/S2405471218304745) or the preprint on [bioRxiv](https://www.biorxi... |
cd580ef3b652ceca5c8e703e3dd12dc77180e63b3adbb27ddb041817f39b9053 | Text | 2,605 | 81 | 1. Overview
This dataset contains fluorescence imaging data acquired during wide-field calcium imaging experiments, together with synchronized TTL and auditory stimulus information.
Raw data were originally recorded in TDMS format using a LabVIEW-based acquisition system.
To ensure accessibility and reproducibil... |
b42d9ce7245639377dc641186a5bb6493cc5d02054ecb4a0e0a416300adf8bf9 | Text | 2,613 | 43 | # pCCA-FA
## (a combination of probabilistic canonical correlation analysis and factor analysis)
pCCA-FA is a dimensionality reduction framework that combines probabilistic canonical correlation analysis (pCCA) and factor analysis (FA) to model across- and within- dataset interactions. This project contains a Python ... |
44a214158cdb8060465a2948817eee8acbea464dd2ef7749d63a0faad4240c9f | Text | 2,616 | 74 | # sleuth
__sleuth__ is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via [kallisto](https://github.com/pimentel/kallisto) for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and ... |
4ccf42121ccc29a1959fb61f70b0dbd9e7a89357a6028970218481c8534d3522 | Text | 2,625 | 45 | # Deep Learning-Based Air Permeability Classification of Knitted Fabrics
This repository contains the official implementation, datasets, and explainability scripts for the classification of air permeability in knitted fabrics. The study utilizes ISO 9237 standards and extends the classification into 12 distinct leve... |
fdc2aa630e28ad511495d7e2754c8fbc00f94d27ae2e7bad36889b41fa21f311 | Text | 2,631 | 47 | 
## About
### What is Spatial Omics Toolkit (SOTK)?
* The Spatial Omics Toolkit (SOTK) is an R package that offers a comprehensive suite of functions for identifying biologically meaningful modules from spatial transcriptomics data. It enables integrative analysis across multiple cohor... |
0bd1c93447f4c0d4a48d7d8ef97b801c3a5ac83d9d21b8eaccfcc49d14e596c7 | Text | 2,640 | 35 | # IceNODE
## Overview
This github repo provides the analysis and code for a scientific machine learning analysis of depositional ice growth models. We provide a PyTorch implementation of the code for the paper "Discovering How Ice Crystals Grow Using Neural Ordinary D... |
d4830d91605aa91950f36684def48873ccaad5f09ab79752863616cb1e4bfc8e | Text | 2,659 | 29 | # Shared latent representations of speech production for cross-patient speech decoding
## Overview
[](https://doi.org/10.5281/zenodo.20531684)
This repository contains code used in analyses and creation of fig... |
1da6fb5c7c3b03fbb0f2d7c96561056a9d38f3215e9e560b9d8f1fb04316405c | Text | 2,665 | 64 | # snATACutils
## The utilities for single nucleus ATAC-seq analysis.
* Please find useful scirpts and codes in folder `bin`.
* We dissect the analysis into multiple steps, detailed description can be find in corresponding folders.
* This package is still under active development.
## Table of Contents
#### - 00.data p... |
015eb22b3e3bb0ad177fdacfbb393f1cc4ceae3eb9268345bf932dc9bff74c4a | Text | 2,674 | 36 | [](https://stare.readthedocs.io/en/latest/?badge=latest)
[](https://doi.org/10.5281/zenodo.5841991)
[ and offline MATLAB reconstruction, under BSD 3-Clause License. The data is available in zenodo: 10.5281/zenodo.20533698
We propose a group-patch joint compression technique to reduce the com... |
e58557da90e619c07bd82c2e2b530817a8e6a718a8a6784957a60c39f20ed2cd | Text | 2,674 | 80 | # Replay of Procedural Experience is Independent of the Hippocampus
This repository contains the code and data necessary to reproduce the figures from our publication: [Replay of Procedural Experience is Independent of the Hippocampus](https://www.biorxiv.org/content/10.1101/2024.06.05.597547v1.full.pdf).
----------... |
d0cd6192e379e4864376b6f75d6bb7fb08d509c320957ec40c8648115685668d | Text | 2,675 | 48 | # Analysis Scripts: Plasma GFAP, Externalizing, and Resting Brain Connectivity
Analysis code for the manuscript:
**Plasma Glial Fibrillary Acidic Protein (GFAP) Shows Age-Dependent Associations with Externalizing Psychopathology and Atypical Brain Connectivity**
---
## Pipeline overview
| Step | Script | Descripti... |
8b15fdaaef516f3b23fc8fad217eb410d01279a63d35be8f3eab26c988a1604a | Text | 2,676 | 87 | # Accurate brain tumor segmentation from incomplete MRI data
This repository provides a **minimal-yet-complete PyTorch implementation** of a **Mixture‑of‑Experts (MoE)** encoder with a **Holistically Guided Decoder (HGD)** for robust brain tumor segmentation under **missing MRI modalities**.
> Educational reference i... |
e7853bccf8dffc20e7f10def12aa6adfe23358ee351a285a4ccb776db7456abd | Text | 2,687 | 39 | # PlantDoc: A Dataset for Visual Plant Disease Detection
This repository contains the Cropped-PlantDoc dataset used for benchmarking classification models in the paper titled "PlantDoc: A Dataset for Visual Plant Disease Detection" which was accepted in the Research Track at ACM India Joint International Conference on... |
8e6f501287d570e7273413b875b6a568173e859512aea4610ff566338d7282a7 | Text | 2,690 | 43 | _Note: the pipeline implemented in this code has been incorporated into the PhysioData Toolbox, which is a free compiled application aimed at creating an easy-to-use graphical environment for visualizing, segmenting and analyzing physiological data. See https://physiodatatoolbox.leidenuniv.nl/ for more information._
#... |
2469ff6665c055b2fb9034711e3aef614d9def2132c1bd5b5eed8750854c5552 | Text | 2,691 | 44 |
# Cyber-Physical Dataset for UAVs Under Normal Operations and Cyberattacks
Unmanned aerial vehicles (UAVs) are being used for various applications, but the associated cyber risks are also increasing. Machine learning techniques have been successfully adopted to develop intrusion detection systems (IDSs). However, non... |
cf3b4b1ce3d706da543270d13f10bfa8bfbd4bf762d147b890dcbdf2ab45cfdf | Text | 2,695 | 49 | 
[](https://github.com/siegert-lab/MorphOMICs/blob/master/license.txt)
[ in Torch by the authors, which is very useful.
[](https://doi.org/10.5281/zenodo.18913386)
pCCA-FA is a dimensionality reduction framework that combines probabilistic canonical correlation analysis (pCCA... |
fb2f0047b47b49ce087be52bd9b3a0571862b846d0a3b25a4bd7d7718bbbb151 | Text | 2,726 | 74 | # Particle Classification
Python scripts for particle classification
Used by particle trieur to perform model training.
## Installation
```
conda create -n miso python=3.9
conda activate miso
conda install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0
pip install tensorflow==2.10.1
pip install miso
```
## Updating
`... |
1157e019fd4025d47f1e8be754112abba008ed92aa94a2ecb80794da5f10c102 | Text | 2,727 | 75 | # OmniConnectModel
This repository is an **umbrella project** for computational neuroscience tools and models.
It integrates multiple approaches to studying brain networks across scales, from **cross-species atlases** to **directed connectomes** and **network modeling**.
---
## Structure
All projects live under t... |
2a711ecbdf17b64a6bd0833167df0c9b93b5cccf6364e8b4c973ede355663a9a | Text | 2,728 | 55 | # README
[](https://doi.org/10.5281/zenodo.20085437)
This directory contains the code and data used for the analyses in our paper. Below is a brief overview of the folder structure and key scripts:
## Folder Structure
- `Simulations_discrete.m`: MATLAB script for genera... |
37b19f5f6fd56264084afe5639a771b3a4cd64dfd1a2a30dddcfa03af5f4911c | Text | 2,735 | 70 | # Identification of Bacterial Essential Genes Based on Fusion of Four Types of Heterogeneous Data
This project identifies essential bacterial genes using a fusion of sequence, PPI, subcellular localization, and GO data. It includes scripts for feature extraction, data fusion, and prediction using machine learning mo... |
3ab7c98f6e8353e531dcce496e58c3d87fc438c2c17b1d7f19d08d1cba19daf8 | Text | 2,742 | 39 | Welcome to the Silverbush Lab Github page containing code for data exploration and figure reproduction from our manuscript "The critical role of the host endogenous immune compartment after intracerebroventricular CAR T cell therapy in recurrent GBM".
Data availability
Raw data are protected to preserve patient priv... |
5b50d7edba110f3b05838e5594251cd4280963b3671661cc41e59a61a7c3e67b | Text | 2,744 | 64 | # **Bech & Dard Figure panels reproduction**
This repository allows the reproduction of figure panels in [Bech & Dard, eLife 2026](https://elifesciences.org/reviewed-preprints/109717), starting from intermediate dataset.
Intermediate dataset can be downloaded from [Zenodo](https://doi.org/10.5281/zenodo.17424306) or g... |
d4b2b9413c20a2ff8545924cf01a569702394e9353d84039aa353b30259afa34 | Text | 2,744 | 64 |
## Requirements
The scripts were tested on window. Before running, a established python environment should be prepared as follow:
--Python = 3.8
--Numpy
--pandas
--statsmodels
--matplotlib
--Networkx
--scipy
--jupyter
The version of package was not assigned, so that you can adjust the version of package... |
2ea2a82d25d74f5fa7a69d076c23d6f3143dd090337cc42df0c7900f0c81557e | Text | 2,768 | 42 | # Myelin-Birefringence-measurement
This repository contains the analysis scripts and processed data for the manuscript:
**"Measurement of the absolute value of the optical birefringence of myelin in primate brain tissue"** (Submitted to *Neurophotonics*).
## Overview
This project provides tools to calculate the abso... |
e592f10532b599eac7ed7a0707dc54304b91908bb6cbe7364f119ce16791392f | Text | 2,773 | 17 | Associated publication: Srr2-dependent SOX2 levels govern the chromatin and transcriptional landscape of adult neural stem cell fate decisions in mouse.
Authors: Sara Cruces-Salguero, Antonio Jordán-Pla, Ana Domingo-Muelas, Jose Manuel Morante-Redolat, Karine Rizzoti, Ander Matheu, Isabel Fariñas, Robin Lovell-Bad... |
1868938637e364083a780efe9c8f0d1519718dde69b137dfacbcfa44fcde5659 | Text | 2,784 | 19 | # Repeated selection across landlocked alewife populations
Repository for the code used to process the sequencing reads from Corcoran et al. *in preparation*
All scripts in this repository start blank, and are automatically filled in with user-specific names, paths, etc. Blank scripts are located in `scripts/blank_scr... |
a1c86402800ffb1814c69b8e5aa954e12c63abb7b8b5b39963e1fd64b0fbac31 | Text | 2,788 | 72 | # fancr
<!-- badges: start -->
[](https://natverse.github.io)
[](https://flyconnectome.github.io/fancr/reference/)
[.
The scripts in this repository test positional encoding, model capacity, discretization effects, explicit versus implicit regularization, ensemble variability, noise sensitivity, and related inversion settings ... |
5932320e3814cbf34528571b07712b6e013d3e6e5128e1d9b26beca17c35de69 | Text | 2,821 | 30 | # Synthetic super-enhancers enable precision viral immunotherapy
This repository contains steps taken to analyse single cell RNA-seq and SOX2 and SOX9 ChIP-seq data in GBM stem-like cells (GSCs), as used in Koeber and Matjusaitis et al, Nature 2026.
## scRNA-seq
Steps:
8 human GSC lines (E17, E20, E21, E28, E31, E34,... |
6136fe381119407952493b9c61271d50b843c3edc0d9ea912ddf122161cf50ba | Text | 2,838 | 24 | # LAVI
Toolbox to compute the rhythmicity profile and automatic band detection (both sustained and transient bands) of electrophysiological data, introduced in [Universal rhythmic architecture uncovers distinct modes of neural dynamics](https://www.biorxiv.org/content/10.1101/2024.12.05.627113v1) (Karvat et al 2024).
... |
7cdae9d90d888e81e887928323b452aa9c5ed6bbd93f5d48ebc2269cfdcc9c3e | Text | 2,841 | 51 | # scCross
A Deep Learning-Based Model for the integration, cross-dataset cross-modality generation, self augmentation and matched multi-omics simulation of single-cell multi-omics data. Our model excels at maintaining in-silico perturbations during cross-modality generation and harnessing these perturbations to identif... |
60dadb0e8ea664062f4abfadd507986a4f5cd1ede42d3b010244abe77840a8a4 | Text | 2,845 | 46 | # PhotoBatch
PhotoBatch is a specialized Python script for processing several pairs of behavioural data and fiber photometry data.
Currently, this is Legacy Code that supports ABET II raw output and Doric Lenses Fiber Photometry Data in csv format.
Example templates are presented for file and event sheets.
# Confi... |
bf023aa7abe8ac16e46f934fef0ff1105f0aa3a78ba83d12f079fb5ea728e631 | Text | 2,849 | 116 | # gencode_regions
Extract 3'UTR, 5'UTR, CDS, Promoter, Genes from GTF files.
# Data
If you only care about the final output, they are hosted build and GTF version wise on [riboraptor](https://github.com/saketkc/riboraptor/tree/master/riboraptor/annotation).
# Using Python
## Dependencies
We recommend setting u... |
d593318d37a854f35be63bc47bf2559d36eae452ded72422add77611da8932a2 | Text | 2,850 | 67 | # CDVMBG_BRM_CNNOculomotorAnalysis
This repository contains the scripts for a CNN-based analysis of time-course oculomotor data, as described in Crotty, Doyle, Volkova, Massa, Benson, & Grubb (2026). The associated manuscript is linked [here](https://doi.org/10.3758/s13428-026-03057-2).
**NOTE:** All associated da... |
a4a8b3e7f846baa168ac4afd1bc20fcdee094949c176835d0ad83eddeebf1681 | Text | 2,851 | 55 | # Efficient robot navigation inspired by honeybee learning flights
This repository contains all code for the paper:
> **Efficient robot navigation inspired by honeybee learning flights**
> D. Ou¹, J. J. Hagenaars¹, M. Jankowski¹, M. V. M. Firlefyn¹, C. De Wagter¹, F. T. Muijres², J. Degen³, G. C. H. E. de Croon¹
> *N... |
7f7fc799e68d1e5a67da87057c07bc96a72bb98927a72682f4a20591a996e0b9 | Text | 2,853 | 105 | # Deflex: Deep Formula Discovery for Complex Systems
A symbolic regression system that combines neural networks (Deflexformer) and symbolic regression (LambdaRegression) to discover mathematical formulas in complex dynamical systems.
## Overview
Deflex is designed to work with 3D tensor data representing temporal dy... |
fc56cfcdb854a13f4f76598bb17dcf59f4ab594e5995a023aac0a5e17e3f86e6 | Text | 2,855 | 100 | # CAHA-Net
本仓库提供脑肿瘤 MRI 图像多分类研究的代码、实验脚本和论文材料。研究以 DenseNet121 为基础网络，引入坐标注意力机制、CLAHE 图像增强与 FMix 混合增强策略，用于提升小样本医学图像场景下的特征表达能力和分类鲁棒性。
## 代码结构
- `train_*.py`: 各模型的训练入口，包括 CAHA-Net 主模型、CNN/ViT/Swin/DINO 系列基线、部分微调实验和文献对照方法。
- `run_train_suite.py`, `run_kaggle_all.py`: 批量训练与 Kaggle 数据集实验入口。
- `model_utils.py`, `*_classifier... |
6f41b397b6fb6ecade9606a6c80eee73b909e7bfd3711cc7a380629a5c1cf8a2 | Text | 2,859 | 60 |
<div align="center">
# 🚀 ROCKET
#### *<ins>R</ins>efining <ins>O</ins>penfold predictions with <ins>C</ins>rystallographic / Cryo-EM Li<ins>KE</ins>lihood <ins>T</ins>argets*
</div>
<p align="center">
<img alt="PyPI - Version" src="https://img.shields.io/pypi/v/rs-rocket">
<a href="https://github.com/alisiafa... |
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