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23a0c79bcebefa9175261de7629f476e6ef44715317a8980763b62b964ab0d46 | Text | 3,456 | 68 | # Intro
GraphPPIS is a novel framework for structure-based protein-protein interaction site prediction using deep graph convolutional network, which is able to capture information from high-order spatially neighboring amino acids. The GraphPPIS source code is designed for high-throughput predictions, and does not hav... |
128664739b3fad3843c586969b1ff1886c15752e493f3f94d744bb7ca6ea2ba9 | Text | 3,461 | 69 | # HeartModelling
This repository contains scripts for defining **ventricular heart models**, including the **ventricular conduction system** and **engineered heart tissue (EHT)** + ventricular models.
The code supports common input and output formats used in [3D Slicer](https://www.slicer.org/), [MeshLab](https://w... |
d69201b2610209d1dc680da1e03cf8f844f455c945bf1431a62260834d6359e2 | Text | 3,463 | 65 | GENERAL INFORMATION
------------------
1. Dataset title: Dataset of "Neuron-like self-sustained oscillatory devices for unconventional computing applications"
2. Authorship:
Name: Gonzalo Rivera-Sierra
Institution: Instituto de Tecnología Química (ITQ), Universitat Politècnica de València- Consejo Superior d... |
dba1fffb49651e7dd516b6bb1b1e1b044a190c60572bab786de79d1a455e4f59 | Text | 3,475 | 56 | # Marmoset MIND
This repository contains code and data accompanying the article [Cortical myelination networks reflect neuronal gene expression and track adolescent age in marmosets](https://www.biorxiv.org/content/10.1101/2025.09.26.678906v1).
## Installation
```bash
# Clone the repository
git clone https://github.c... |
1ff212fdbeebcd00564b5b50fe2c5c98531b87da34478d30a660d6e4050b067c | Text | 3,494 | 227 | # EEG-ImageNet Source Localization and Feature-Based Classification
DOI: https://doi.org/10.5281/zenodo.20617271
This repository contains the analysis pipeline used for source-localized EEG decoding experiments on the EEG-ImageNet dataset.
The workflow includes:
1. Trial mapping recovery
2. Source-space ROI selectio... |
42d6c0898b1302531d9ce368f1a79acbf18332dc0fd22854c57bb5613293d2ed | Text | 3,499 | 56 | # Image-based Phenotypic Selection
## About
We describe a **Smart Microscopy pipeline** that automates imaging, detection of (synthetic) cells of interest, and photoactivation, marking cells for subsequent sorting purposes.
This work is part of the research project published _here_. It operates via protocols (called... |
123feeb37ed78fcf90e828fcd8c702dbac53c5cd6fa5e72e563864e6ab3c9991 | Text | 3,501 | 78 | # PQ
[](https://github.com/MolarVerse/PQ/actions/workflows/ci_build.yml)
[](https://codecov.io/gh/MolarVerse/PQ)
[![Docs](https://github.com/Mol... |
b618dbaab60ccc35eb0eb1d39e7460a551c213fbf887513b15c03fd3899ba167 | Text | 3,504 | 50 | # MeNet-AO
MeNet-AO is a Python package for fast optical aberration estimation from fluorescence images using Physics-informed multi-encoder trained on synthetic images or experimental acquired images.
This repository is developed based on the paper —"Physics-informed multi-encoder adaptive optics enables rapid aberr... |
2344e55d776810a7cff87564af5c0c8c026208ffb7f1b2bf017bec8e9da284b4 | Text | 3,512 | 72 | # seqNMF
This package is a Python port of the [SeqNMF MATLAB Toolbox](https://github.com/FeeLab/seqNMF). It provides a tool for performing unsupervised discovery of temporal sequences in high-dimensional data.
Credit for MATLAB toolbox: [Emily Mackevicius, Andrew Bahle, and the Fee Lab](http://web.mit.edu/feelab/).
... |
01268cbd2467a4c2e3d85a99a8b5adab1d499c6cf1989690a6e0c290280fb1ca | Text | 3,517 | 67 | [](https://zenodo.org/badge/latestdoi/59303623)
# Segmentator
<img src="visuals/logo.png" width=420 align="right" />
Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed a... |
c4b09149ad5838ea15d8144890ed533f3b45db8077c571caa4ecfef5606ebd45 | Text | 3,520 | 79 | # HEPPy — Heartbeat-Evoked Potential (HEP) extraction for EEG
HEPPy is a simple, user friendly pipeline for extracting heartbeat-evoked potentials (HEPs) from EEG recordings that include an ECG channel. It provides a **thin GUI** to:
1. run **ecg analysis** to detect R-peaks and generate per-file QRS plots;
2. *... |
73334f187e59427a4843fcaaa945a4dd98e0fee33bf846a440f4652c485cc97c | Text | 3,536 | 58 | # AutoCurationKilosort: Automated Curation for Kilosort Output
[](https://github.com/jiumao2/AutoCurationKilosort)
**AutoCurationKilosort** is a MATLAB-based pipeline designed to streamline and automate the curati... |
26fa8b00807e5b1157cc43c11ab04da8a1f99f90ca558c9b301fa7b48ada48bf | Text | 3,540 | 78 | <div align="center">
<h2 class="papername"> Incorporating brain-inspired mechanisms for multimodal learning in artificial intelligence </h2>
<div>
<div>
<a href="https://scholar.google.com/citations?user=Em5FqXYAAAAJ" target="_blank">Xiang He*</a>,
<a href="https://scholar.google.com/citations?user=2E9Drq8AAAAJ... |
c54b448679c3215acf1fb00c7c519dae54ef0e3dc738f78fb525a0598b1371f3 | Text | 3,567 | 91 | ** IMPORTANT: This repository is in archive mode meaning that it is read only and will not undergo further changes. All further development will be done on REINVENT 4. **
REINVENT 3.2
=================================================================================================================
Installation
------... |
3422f76aeb0ef43db8b63983d0394c5d310340ed2c6a1abe4b7561cc748ab964 | Text | 3,574 | 55 | # Cell registration across multiple sessions in large-scale calcium imaging data
This package is an implementation of a probabilistic approach for tracking the same neurons (cell registration) across multiple sessions
in Ca2+ imaging data. The package includes a GUI that supports the entire registration procedure.
F... |
f46acf62adba27cf55c292b0442d69080b2fd34438f040fde4c205e1f344add4 | Text | 3,580 | 44 | PsPM-FR dataset
================
Repository Version: 2018.08.29
This dataset includes skin conductance response (SCR), electrocardiogram (ECG), electromyogram (EMG, only relevant for extinction phase) and respiration measurements. Also included are CS and US information, keypress responses and keypress response ... |
ee0960e52b9c79fd0ce79f6019e90a51c461c6866dab507971531f9542e45c85 | Text | 3,581 | 103 | # Habenula Segmentation
---
Automated Human Habenula Segmentation Program
---
## Requirements
* Python: version 2.7
* Python libraries: numpy, scipy, nibabel
* FSL
---
## Input Files
* nifti1 is the only supported file format.
* AC-PC aligned T1w image
* T2w image that is registered to T1w image
* Habenula center pos... |
b66fc083cea44ea832aff83eb241c9642e802b1c5cfb9b40744f230e08533cb4 | Text | 3,586 | 70 | # Neuropixels Data Analysis
An example recording can be found under: https://upenn.box.com/s/hiivvfe3rc07ft60rdv563018n0nfmc4
Note that all data can be downloaded fairely quickly (in a few minutes with normal internet connection, except for the file `1k_train.npz`, which however is not required for most basic analyse... |
88070cc4b3ae064c03e82943b624eb401a4122abc95f21e54fffebe872bcc0ff | Text | 3,589 | 66 | # FireNet
FireNet is an artificial intelligence project for real-time fire detection.
<br><br>
<img src="images/fire_net.jpg" />
<hr>
<b>FireNet</b> is a real-time fire detection project containing an annotated dataset, pre-trained models and inference codes, all created to ensure that machine learning systems can be t... |
621067bdd306f053c88ccf44a8ecfc8197a10780b4bd55dd13228780c0bf4d6b | Text | 3,591 | 106 | # **Allele Specific Expression in Alzheimer's Disease\**
<br /><br />
## **Introduction**
If you use or adapt our code in your study, please cite our paper [Under submission].
If you run into issues, you can contact authors: zishan.wang{at}mssm.edu or kuan-lin.huang{at}mssm.edu.
Seven folders listed here, with each... |
1a1749337bdb954b8a9c5db5ec010749a0f67375359d5b8d9b510c477a46c457 | Text | 3,595 | 68 | ## Aim
Bulk RNA-seq, Ambra Villani's in-house microglia iPSC-derived cultures (and engineered Slc37a2 and TREM2) plus public bulk RNA-seq data.
## Methods
Inhouse RNA-seq and McQuade's TREM (PMID 31088905) raw reads were processed with ARMOR (PMC6643886). Reads were aligned and counted using the human genome GRCh38 ... |
111c3161c4d01b68056adba3779bce647c939465eb16a4a05fe3f9466ac3e59e | Text | 3,604 | 85 | # ReconST: Optimal Gene Panel Selection for Targeted Spatial Transcriptomics Experiments
## 1. Introduction
ReconST is a data-driven framework for designing optimal gene panels for targeted spatial transcriptomics experiments. Modern spatial transcriptomics platforms ... |
071fc7ab07f1f6f1da08068b8284e7ea6d21e5ea98edd8f6e748e05f508c038e | Text | 3,611 | 44 | # Code and data repository for Srinath et al., 2024
## Coordinated Response Modulations Enable Flexible Use of Visual Information
### Abstract
We use sensory information in remarkably flexible ways. We can generalize by ignoring task-irrelevant features, report different features of a stimulus, and use different acti... |
f2ea85dd99730c9774f9fe26db0274c5070ee33bc1dead97a8c416cd2ba0c804 | Text | 3,618 | 115 | # Pharmacophore Pooling Graph Neural Networks for Molecular Property Prediction
This repository contains the code used for pharmacophore-based graph reduction and hierarchical pooling graph neural networks (GNNs) for molecular property prediction.
The project includes pipelines for:
- Converting SMILES datasets into ... |
fbb62db8de18c3686e1e43b01ccfbd202555f5997089832d93135d281e00d922 | Text | 3,624 | 85 | # Memristor-Model
SPICE models and testbenches for **Diffusive Memristor** and **Drift Memristor**.
## Overview
This repository provides reusable core model netlists and ready-to-run test circuits:
- Diffusive memristor core model with optional cycle-to-cycle stochastic variation
- Drift memristor core model based ... |
785f9ecfbce77825b7552d9878a6c1ec0e4cfc2d6bf1bffca29ece782be8303f | Text | 3,630 | 40 | # Deciphering spatial domains from spatial multi-omics with SpatialGlue
This repository contains SpatialGlue script and jupyter notebooks essential for reproducing the benchmarking outcomes shown in the paper. We provide experimental data in each case with details available within the notebook. All experiment data is ... |
d093b5ce0bb4c3eb28ab991501569b4f60d269b41c10753d9a87434de5c01792 | Text | 3,638 | 82 | # DeorphaNN
DeorphaNN is a graph neural network that prioritizes peptide agonists for G protein-coupled receptors (GPCRs) by integrating active-state GPCR-peptide predicted structures, interatomic interactions, and deep learning protein representations.
## Associated paper
DeorphaNN: Virtual screening of GPCR peptide... |
dab9ccfa1d5401cf72c7ce7a750635b8e365442c1ed6b9f88fcd8f34dc7d9d6c | Text | 3,642 | 108 | # SHIELD: **S**patially-en**H**anced Immun**E** **L**andscape **D**ecoding
*Weakly supervised graph attention networks for interpretable cell-cell interaction analysis*
<img width="1575" height="1487" alt="only_Colobar_Shield" src="https://github.com/user-attachments/assets/77e42ea4-3756-4a01-b539-ec203d9c9984" />
... |
bc18ca1ebf5c4d77ae402407861087095b6e2e62d52fa4b1841425236667e353 | Text | 3,649 | 104 | # Neural rhythms as priors of speech computations
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://www.doi.org/)
## Introduction
This repository con... |
e7f4177abfd637650dbc3aad6d81a204a95cfa666366a9fdb57a5c38cc4f27c3 | Text | 3,655 | 86 | # MPM_QSM
QSM pipeline for Multi Parametric Mapping acquisitions
# MPM_SWI
CLEAR-SWI pipeline for Multi Parametric Mapping acquisitions
# MPM_QSM main computational steps:
1) phase unwrapping and B0 map calculation using ROMEO
2) masking based on ROMEO quality map
3) rotation to scanner space for oblique acqui... |
8fb7ff687306c59ee32d278691ee52f59385f55085f24709b280ee64b76a310c | Text | 3,679 | 90 | # pyDANT: A Python toolbox for Density-based Across-day Neuron Tracking
[](https://github.com/jiumao2/pyDANT)
[](https://dant.readthedocs.io/en/latest/)
[](https://github.com/ampl-psych/EMC2/actions/workflows/R-CMD-check.yaml)
[](https://CRAN.R-project.org/p... |
85a666eab937f26a1a37c0392dc8b8ee67faa5faeee0a64b5fd81aee92a39251 | Text | 3,693 | 51 | # spDDB
A Comprehensive Benchmarking of Spatial Deconvolution and Domain Detection Methods across Diverse Tissues and Spatial Transcriptomic Technologies [https://doi.org/10.64898/2026.05.11.724248](https://doi.org/10.64898/2026.05.11.724248).The Github provides installation instructions, set up and runnable files used... |
63e72c9a2a28c6d80eb4c3e9660036b912d81a286dd97b2070aea8741bb79aae | Text | 3,698 | 59 | # Marmoset MIND
This repository contains code and data accompanying the article [Cortical myelination networks reflect neuronal gene expression and track adolescent age in marmosets](https://www.biorxiv.org/content/10.1101/2025.09.26.678906v1).
## Installation
```bash
# Clone the repository
git clone https://github.c... |
d9510192e2329368504acc52e7203aaa588700df4bd0a8a0282f0a47776a6690 | Text | 3,707 | 91 | # Chinese Brain PET Template
<h2 id="english">English</h2>
[简体中文](#zh-cn)
This repository provides a PET brain template specific to the Chinese population, and also includes programs for the building and applying of the template. This project was developed by [Medical Imaging Research Group](https://biomedimg-dlut-... |
01d84490979a412829f515df7f675fd3aa17a60175964c3c455a6b9751011eae | Text | 3,708 | 69 | # dev-ctx-meta-atlas
## System Requirements
### Dependencies
R version 4 or later and Seurat version 4 or later.
Packages required for each step are indicated in each script, and include:
*Seurat, tidyverse, WGCNA, factoextra, dynamicTreeCut, data.table, ggplot2, stringr, dplyr, readxl*
### Versions tested on:
... |
9564ef29fa0bf7b5dc7605913a9f939124eaf8038cd4996dd1c96951db801c84 | Text | 3,708 | 121 | # Q-CHIPP
Q-CHIPP (Quantum Convolutional HLA Immunogenic Peptide Prediction) is a combinatorial framework integrating MHC binding and T-cell recognition to more accurately identify immunogenic peptides, improving the prognostic impact of predicted neoantigen load.
## Citation
Please cite the following article if you... |
4dc7dba85943ae8cf69faf2add65e8ae410ad1ac21c067fd8be45150ec1241ac | Text | 3,714 | 50 | PsPM-VC7B dataset
==================
Repository Version: 2018.10.03
This dataset includes pupil size response (PSR) and skin conductance response (SCR) measurements. Also included are CS and US information, keypress responses, keypress response times, key correctness and shock ratings for each of 21 healthy unme... |
82e0b180a89625cd2f3f72b2da80a273134625c628843e7fdbe825b0187a35d4 | Text | 3,714 | 50 | PsPM-VC7B dataset
==================
Repository Version: 2018.03.23
This dataset includes pupil size response (PSR) and skin conductance response (SCR) measurements. Also included are CS and US information, keypress responses, keypress response times, key correctness and shock ratings for each of 21 healthy unme... |
27a60284307bc864a41895b9f78d507fa05e7a20bfd9e76877cab6408514ad63 | Text | 3,716 | 87 | # Memristor-Model
[](https://doi.org/10.5281/zenodo.20150590)
SPICE models and testbenches for **Diffusive Memristor** and **Drift Memristor**.
## Overview
This repository provides reusable core model netlists and ready-to-run test circuits:
- Diffusive memristor core... |
046515ce596aa6313d8b1656c63cabccd77c66946a214f60f3ed9434e4dddfee | Text | 3,724 | 76 | ## Molecular Contrastive Learning of Representations via Graph Neural Networks ##
#### Nature Machine Intelligence [[Paper]](https://www.nature.com/articles/s42256-022-00447-x) [[arXiv]](https://arxiv.org/abs/2102.10056/) [[PDF]](https://www.nature.com/articles/s42256-022-00447-x.pdf) </br>
[Yuyang Wang](https://yuyan... |
36c173d8f1a95a81fde76b15d11c5661970e4e21bc7d806dd365c0fe4a5d6856 | Text | 3,729 | 84 | [](https://doi.org/10.5281/zenodo.20865767)
# DeorphaNN
DeorphaNN is a graph neural network that prioritizes peptide agonists for G protein-coupled receptors (GPCRs) by integrating active-state GPCR-peptide predicted structures, interatomic interactions, and deep learning ... |
4f4910605e0aac61714695e07ecc7097d58e80b74fcf94d8054d4b05a0ea811d | Text | 3,729 | 104 | # CryptoVision processed lab image dataset
This Figshare package contains the processed model-input dataset used for the
CryptoVision laboratory-image analyses. It is intended to provide the minimal
dataset required to reproduce the reported model training and evaluation
results with the public CryptoVision code.
Thi... |
1973a420b9f906330fdca50b7be838b1e5ed0b12ff748903491b1768a9db9f00 | Text | 3,731 | 125 | # ECG Preprocessing
Scripts for preprocessing the 12-ECGs for deep learning.
This preprocessing is used for generating the data for the models in:
- https://github.com/antonior92/ecg-age-prediction
- https://github.com/antonior92/automatic-ecg-diagnosis
Some of the datasets from our group are made available after th... |
ddeb7b25651cdb61891dcd1b725d113d89ecc968f59135ebce04dadf6c2eb40a | Text | 3,739 | 41 | # Neural stem cell (NSC) aging lipidomics
This is the repository containing code for pre-processing, normalization, quantification and data presentation of lipidomics data included in the following manuscript:
>Reference: <br>**Lipidomic profiling reveals age-dependent changes in plasma membrane lipids that regulate ... |
1cd6594a5ecd9ed8f01f81dc254adcc53a4ac9c780fe6135d9233d4d8864234b | Text | 3,743 | 90 | VOXELIZED VERSION of the MOREL ATLAS of the HUMAN THALAMUS
*************************************************************
is a digital image file that represents the 3D anatomy of the thalamus, transformed to the Montreal Neurological Institute 152 anatomical reference space.
Details are found in the following publ... |
80b76783bf2ed7f3ee110899b1ecce27767c33e0a09db26f5360ed53d732e2b2 | Text | 3,744 | 49 | PsPM-RRM1-2 dataset
====================
Repository Version: 2020.11.23
This dataset includes skin conductance response (SCR), electrocardiogram (ECG), respiration and eye tracker (including pupillometry) measurements for each of 29 healthy unmedicated participants (7 males and 22 females aged 23.5 +/- 3.6 years... |
896cb42f4d4c5db8005be6f76d5a8c8a7c9f7bb391e6bf6ea4b662591b24346f | Text | 3,753 | 49 | **Package for MRI. Supports:**
- Reconstruction
- non-Cartesian regridding
- iterative SENSE (Cartesian or non-Cartesian)
- iterative SENSE for higher order models that may include:
- a B0 map
- time varying spherical harmonics of phase accrual
- trajectory design
- spiral
- LOTUS (... |
33d714c2408ba4b1dd2ad0925b20f6c706e3d7b113d701dda49d4e8fe10aa708 | Text | 3,764 | 120 | netneurotools: Tools for network neuroscience
=============================================
|
.. .. image:: https://zenodo.org/badge/375755159.svg
.. :target: https://zenodo.org/badge/latestdoi/375755159
.. :alt: Zenodo record
.. image:: https://img.shields.io/pypi/v/netneurotools
:target: https://pypi.pyth... |
7889e9485f3b4ae8c581f5c1ea482d01e853a9736c3d0b0b5794cdae87dd85e1 | Text | 3,764 | 113 | # Reproducibility Package
This package contains the scripts used to reproduce the paper workflows for:
- AGAR split reconstruction
- curated dataset download
- Detectron2 and YOLO training
- Detectron2 and YOLO evaluation
- inference speed benchmarking
- bootstrap confidence intervals
- ensemble search with Weighted ... |
f5cf84d4be1c445255d43d842acbc3274508c0d95fc86a7855f1bb1aa1ad8bb8 | Text | 3,764 | 86 | # diffBloch
Hybrid Physics–Machine Learning Models for Quantitative Electron Diffraction Refinements. Code accompanying the paper [Hybrid Physics–Machine Learning Models for Quantitative Electron Diffraction Refinements](https://arxiv.org/abs/2508.05908), Shreshth A. Malik, Tiarnan AS Doherty, Benjamin Colmey, Stephen... |
a0618ecb32da2d9790af7c205a8d655cb7ba5275e607328718bd52114fd6ea66 | Text | 3,770 | 35 | # Benchmarking MS/MS spectral featurization methods
## Introduction
This repository serves as companion to the upcoming article to be published in JASMS, which focuses on comparing different strategies for MS/MS featurization to train ML models used in molecular structure annotation tasks.
All results and figu... |
c200d0ed5c171e7b5d558324b0cbc1ac8f155f455e657ea0b3ea5cc66f6aed6d | Text | 3,775 | 36 | # EEG-ImageNet-Dataset
This is the official repository for the paper "**EEG-ImageNet: An Electroencephalogram Dataset and Benchmarks with Image Visual Stimuli of Multi-Granularity Labels**".
<img width="776" alt="image" src="https://github.com/user-attachments/assets/55ac9916-e6ff-4f27-afbe-21a5d8206df2">
**Figure 1... |
cfe0aa495a6c345d30d7bfa7c36aa5d20e806925b53109eab4403861388d5dcc | Text | 3,779 | 141 | # MEGaNorm
[](https://www.python.org/)
[](https://www.python.org/)
[ repository maintained by [dair.ai](https://dair.ai/).
**Deep Learning Visuals** contains **215 unique images** divided in **23 categories** (some images may appe... |
db91281ee7c2b9b955413211c1b96aab016fd41299c2be0447f47700bc69e399 | Text | 3,782 | 30 | # SARS-ALIculture
## A multi-scale multi-cellular model for Air-Liquid Interface cultures
The provided code defines a multi-scale individual cell-based model to simulate and analyze viral infections within the pseudo-stratified epithelium of Air-Liquid-Interface (ALI) cultures of human airway epithelium. It relates t... |
689fcc85ed14b3eca129df1e42feea4986fd1cfe319d8c21a5074c4fecf063a8 | Text | 3,806 | 32 | # ClinicalNetDynamics
Code supporting: Brain network dynamics reflect psychiatric illness status and transdiagnostic symptom profiles across health and disease. Cocuzza C.V.*, Chopra S., Segal, A., Labache, L., Chin, R., Joss, K., and Holmes, A.J. (2025).
In bioRxiv (p. 2025.05.23.655864). https://doi.org/10.1101/202... |
ba08bb568ce85c4fc950ccc3cc06ff67387b62af60f8669809c55a3f82799002 | Text | 3,809 | 102 | # UNet2D for Object Detection
This repository provides a 2D U-Net-based pipeline for segmenting fluorescent microscopy images. It is designed for images where object boundaries are unclear or ill-defined. My specific use case concerns the anterior pharynx of the nematode C. elegans, the outline of which is not labelle... |
c6fb371dd6a557d2d588d87053a0154f7b48d851312f6f7db2d7a4c81ae3427e | Text | 3,810 | 133 | # CAME
[](https://zenodo.org/badge/latestdoi/367772907)
**English** | [简体中文](README_CH.md)
CAME is a tool for **Cell-type Assignment and Module Extraction**, based on a heterogeneous graph neural network.
For detailed usage, please refer to [CAME-Documentation](https://x... |
b879953b3d22ef13360468067c7c678a669de12b6c30c8e9269139249a33ab7f | Text | 3,812 | 72 | - [Version 2](#version-2)
- [Benchmark](#benchmark)
- [Prediction of pCBS binding numbers of mouse C2H2 zinc-finger proteins](#prediction-of-pcbs-binding-numbers-of-mouse-c2h2-zinc-finger-proteins)
- [Install](#install)
- [Usage](#usage)
- [Dataset](#dataset)
- [Weights](#weights)
- [Space](#space)
- [Method](#method)
... |
f7e41d64fe6f3b6d5f6c4e962cf205d3bf8d098ea545c278e157ecbc71e2b232 | Text | 3,822 | 85 | BrainSMASH
==========
BrainSMASH (Brain Surrogate Maps with Autocorrelated Spatial Heterogeneity) is a
Python-based computational platform for statistical testing of spatially
autocorrelated brain maps. At the heart of BrainSMASH is the ability to
simulate surrogate brain maps with spatial autocorrelation that is ma... |
9cd24d22591cffff7ddd211773b190c91a180f56f8001613f235c75388eadbf0 | Text | 3,825 | 58 | # Glycan-Atlassing
**Summary**
This code is intended to cluster the multidimensional super resolution data within a given radius, perform nearest neighbor analysis and GlyCo. Localization data from each cell should be saved in a folder with the filenames starting with the corresponding lectin followed by underscores.... |
12e12c3a1c1f90cd3dca469a46a6e3854815e67dada837e6f164cf2fb1cbd26d | Text | 3,831 | 161 | # TwinRNN
This repository contains code associated with the paper:
**Independence and Coherence in Temporal Sequence Computation across the Fronto-Parietal Network.**
The main entry point is a Jupyter notebook that loads a pretrained Twin RNN model (stored in `RNN_models/`) and reproduces activity under perturbatio... |
26964bbc3da7363693beb835678b485ab04ae78c1b190827e9d2f3352e44bae7 | Text | 3,860 | 94 | # Single-cell Hierarchical Poisson Factorization
## About
scHPF is a tool for _de novo_ discovery of both discrete and continuous expression patterns in single-cell RNA\-sequencing (scRNA-seq). We find that scHPF’s sparse low-dimensional representations, non-negativity, and explicit modeling of variable sparsity acros... |
bd309c4a281ae29caf7f1ba6243a100fae9c6fd34e7f695a431476d317679a02 | Text | 3,871 | 117 | # accs-workflows
### Goal
A series of Prefect workflows for training, tuning, and evaluating machine learning classifiers based on DNA methylation microarray data.
The workflows primarily use data gathered from GDC (Genomic Data Commons), but can be extended with additional external data (e.g., in-house generated) b... |
1816c60833e4f921271c664b883c650138455c27813e2b7ad3e2420b44ebd3ba | Text | 3,875 | 106 | # fep-benchmark
Benchmark set for relative free energy calculations.
Created by Christina Schindler and Daniel Kuhn, Merck KGaA, Darmstadt, Germany.
December 2018
DOI: [10.5281/zenodo.3360435](https://doi.org/10.5281/zenodo.3360435)
### Manuscript
Schindler et al. "Large-Scale Assessment of Binding Free Energy Cal... |
6cb685cbbbec6a13a5c9d263543b6be2705eb20aba4e27670b83ea870296876b | Text | 3,875 | 101 | # InterFusion
**KDD 2021: Multivariate Time Series Anomaly Detection and Interpretation using Hierarchical Inter-Metric and Temporal Embedding**
InterFusion is an unsupervised MTS anomaly detection and interpretation method. It's core idea is to model the normal patterns of MTS using HVAE with jointly trained hierarc... |
180ec5603cfc591b2a24ca5e278599b3b7f23234de90c0bc3d561e9aaa02486a | Text | 3,881 | 91 | # UMINT
Maitra, C., Seal, D.B., Das, V. and De, R.K., 2022. UMINT: unsupervised neural network for single cell multi-omics integration. BioRxiv, pp.2022-04.
https://www.biorxiv.org/content/10.1101/2022.04.21.489041v1
Now published at Frontiers in Molecular Biosciences
Maitra, C., Seal, D.B., Das, V. and De, R.K., Uns... |
61d66c5783d32ceef3db5b016656360da39f03f941a362135295d4e3b092da67 | Text | 3,898 | 121 | # Human Gloss Perception and Tiny Neural Networks: Figure Generation and Data Processing
This repository contains the source code, example data, and scripts required to process behavioural and computational model data, and to generate all main and supplementary figures for the m... |
e8229f3d91dc2f842fa5f865606aaab42c19ed512e5061e0e81b6b75dd0f5a27 | Text | 3,898 | 110 | # CmeCUT&Tag
This repository contains the analysis scripts used in the **CmeCUT&Tag** paper.
It includes Snakemake workflows, R/Python scripts, and utility tools for processing, analyzing, and visualizing CmeCUT&Tag, CUT&Tag, and WGBS data.
Primary read mapping (BAM and BigWig generation) is performed using the **[... |
eb9a4b11e7deb2bc81a6e39ddb2451b152ae6204adaa33b95f6a8b717e1653a6 | Text | 3,906 | 57 | PsPM-FSS6B dataset
===================
Repository Version: 2022.11.18
This dataset includes skin conductance and eye tracking (including pupillometry) measurements. Also included are CS and US information, keypress responses, keypress response times and key correctness for each of 18 healthy unmedicated particip... |
76306229f7f750ecc062880c3f948f70c2dfa94ba6d5a8d7c2cc9e5f4399ae51 | Text | 3,916 | 49 | PsPM-SC4B dataset
==================
Repository Version: 2018.06.29
This dataset includes pupil size response (PSR), skin conductance response (SCR), electrocardiogram (ECG), electromyogram (EMG) and respiration measurements. Also included are CS and US information, keypress responses, keypress response times, k... |
17357a38774aaa56051fbcc4e853011fbe79e427b60a2102dddfaa7f40386817 | Text | 3,929 | 91 | Overview
pyFLANK is an open-source and automated Python implementation which detects FST outliers using a null distribution inferred from quasi-independent loci inspired by the R package OutFLANK(https://doi.org/10.1086/682949). Our tool integrates three approaches to identify loci obeying a null distribution: graph n... |
e5a2bb3c6e59aa55a8e828780a99c3ec3d5cb638f72de34035de0b5f734e98ad | Text | 3,937 | 102 | # pyDANT: A Python toolbox for Density-based Across-day Neuron Tracking
[](https://github.com/jiumao2/pyDANT)
[](https://dant.readthedocs.io/en/latest/)
[![Open In Colab... |
dc5dbc77e071008a5492e4d1041b40a008a44fa18bad10b89e782761c91e45c4 | Text | 3,948 | 37 | ### *Analysis code accompanying the manuscript entitled*
# Meta-analytic evidence for distinct neural correlates of conditioned vs. verbally induced placebo analgesia
### *by Tamas Spisak, Helena Hartmann, Matthias Zunhammer, Balint Kincses, Katja Wiech, Tor Wager, & Ulrike Bingel, for the [Placebo Imaging Consortium]... |
c70eb09ac9501c78fde2947a60a830281b387bd4d316698cd65a1faf29d425f1 | Text | 3,956 | 57 | # ADHP-maintains-pyloricness
Organized code to accompany the paper: When can local activity-dependent homeostatic plasticity maintain circuit-level dynamic properties? ([Stolting & Beer, 2026](https://doi.org/10.1007/s10827-026-00936-7))
Stable link to this code base:[https://doi.org/10.5281/zenodo.18509900](https://d... |
7eed336c35fa321030b21f863e58e3e2211ad513897ced0a1e051527e78af4b7 | Text | 3,957 | 109 | =========
Tensorpac
=========
.. image:: https://github.com/EtienneCmb/tensorpac/workflows/Tensorpac/badge.svg
:target: https://github.com/EtienneCmb/tensorpac/workflows/Tensorpac
.. image:: https://travis-ci.org/EtienneCmb/tensorpac.svg?branch=master
:target: https://travis-ci.org/EtienneCmb/tensorpac
.. im... |
87ddfc939ee1f297146ba8f490b5e5120356d9e55d3a0f37ef515ab01d86b3ee | Text | 3,957 | 46 | # HyperStackReg ImageJ plugin
<img src="https://github.com/ved-sharma/HyperStackReg/blob/master/Data/Example_hyperstack-before_and_after.gif" alt="Example movie">
**Movie:** A 16-bit multi-channel (blue, green and red) hyperstack movie before and after HyperStackReg registration. The intravital multiphoton movie show... |
980160028a8682863ced884b162ca486a1a6e3702c7bf04135729e41a35cda0c | Text | 3,963 | 74 | # htSMLM
## A user interface for localization microscopes
htSMLM (high-throughput single-molecule localization microscopy) is an [EMU]( https://github.com/jdeschamps/EMU ) user interface for [Micro-Manager](https://micro-manager.org/wiki/Micro-Manager). EMU allows loading easily reconfigurable user interfaces in Micr... |
c2e43615c534c67fa6d1a8dbe2ef0b86a8ceb3fd5f0d94b5a1d826b35ce3e171 | Text | 4,005 | 100 | # GlowTracker
<div style="display: flex; justify-content: center; align-items: center;">
<table style="width: 80%; border: none;">
<colgroup>
<col style="width: 30%;">
</colgroup>
<tr>
<td>
<img src="glowtracker/images/glowtracker_logo.png" alt="GlowT... |
6b11bcf961785772301020b85dcb9fb7aba31b44f2f736a924d9fea9dbf5a9d3 | Text | 4,011 | 112 | # 1. Introduction
COSMOS is a computational tool crafted to overcome the challenges associated
with integrating spatially resolved multi-omics data. This software harnesses a
graph neural network algorithm to deliver cutting-edge solutions for analyzing
biological data that encompasses various omics types within a ... |
9a6a2f7829569f8a7711ad526739a12a58b7cbdcae5976f17ffb2b669f0f1e0b | Text | 4,013 | 81 | # High Gamma Dataset
This is the documentation for the High Gamma Dataset used in "Deep learning with convolutional neural networks for EEG decoding and visualization"
(https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.23730).
See the paper and supporting information for a general description.
## Download
In gene... |
ae9ae5467d32a20527ab1a69a70da75a32742381d0fd956371ccea006db15b3a | Text | 4,019 | 94 | Dimensionality estimation
===========================================
This repository contains code to apply different crtieria to choose the optimal number of Principal Components (PCs) for estimating the dimensionality of a data matrix. It also allow to generate a data matrix as random linear combination of a subset... |
0974a8b88fade85ca0fc85182fc13c738e3849f6c73e2b4634dbc2109d2cb650 | Text | 4,023 | 52 | # EOAD SuStaIn Subtypes Project Repository
This repository contains codes and file specification for the project <i>SuStaIn-based subtyping of early-onset Alzheimer’s disease (EOAD) using baseline Flortaucipir-PET data from the Longitudinal Early-Onset Alzheimer's Disease Study (LEADS)</i>. All components are cataloge... |
da60ca2c7e5367096396aaead36524b07fd580da66f88ebbbe239a721a5bdfbf | Text | 4,034 | 57 | ========================================================================================================================
README: DATA AND CODE ORGANIZATION
Mapping the neuronal building blocks of human language production with language models
Jing Cai, Massachusetts General Hospital, March 2026
========================... |
3ddffd0270fb3a16441bbe34d50946527d9583a020bf81a1c17640757c9c60ad | Text | 4,050 | 77 | # estim_populations
### Neural population dynamics of direct electrical stimulation of neocortex
*(Hickman et al., 2025 — submitted to Neuron on 10/29/2025)*
**Preprint:** [https://www.biorxiv.org/content/10.1101/2025.10.28.685195v1](https://www.biorxiv.org/content/10.1101/2025.10.28.685195v1)
This repository con... |
f277c320c47f30856a7437786c5b21389d8c02a6296ca2721626f134a310f2c4 | Text | 4,050 | 72 | # OpenEQA: Embodied Question Answering in the Era of Foundation Models
[[paper](https://open-eqa.github.io/assets/pdfs/paper.pdf)]
[[project](https://open-eqa.github.io)]
[[dataset](data)]
[[bibtex](#citing-openeqa)]
<https://github.com/facebookresearch/open-eqa/assets/10211521/1de3ded4-ff51-4ffe-801d-4abf269e4320>
... |
42de20b019fa0373d1d8aac747c20e2068dcb203a84ce33db7616ee404ec6e83 | Text | 4,051 | 114 | # SimPlaceCells
is a simulation and analysis framework for studying hippocampal place cells and evaluating the performance of spatial tuning metrics under controlled conditions. It allows researchers to generate synthetic neural data with customizable tuning properties, apply standard place cell detection methods, and... |
65beeadd55325f9b4562813b37a16770ebaf13986efeb88d48cb1ecceb3e3fd0 | Text | 4,065 | 164 | # LUMEN Representative PSD Samples
Representative Power Spectral Density (PSD) samples related to the paper:
> **LUMEN: A Lightweight UAV Multi-Enhanced Network for PSD-Based RF Fingerprinting on Edge Devices**
This repository provides representative PSD examples and preprocessing references for UAV RF fingerprintin... |
d772088c0a937b003e418ac32bbb397c6088e3cd998ce1d99de9c9413eefb722 | Text | 4,065 | 78 | # longitudinal_EEG_timescales
This repository contains the data and code used to produce the results published in XXX
## 📂 Repository structure
| Folder / File | Purpose |
|---|---|
| `Data/` | Contains processed datasets and intermediate files used by the analysis scripts |
| `1_data_matlab_to_python.py` | Converts... |
9517c09fa9ff055be47c8e7f19ae3529bc369e71059a7773cc08ad44b27ca736 | Text | 4,066 | 50 | # Diffusion MRI data analysis assisted by deep learning synthesized anatomical images (DeepAnat)
Keras implementation for DeepAnat
## 1. Pipeline
**Figure 1. DeepAnat pipeline.** DeepAnat utilizes convolutional neural networks (CNNs) to transfer diffusion data to anatomical data,... |
befc27699d7ac966dcd3a044f9eda4c25087e1f082cb211b7abf3cfe8e7da660 | Text | 4,069 | 123 | # ColorMyCells
## A Biological Approach to Cell Type Visualization
`colormycells` is a specialized Python package that solves a common problem in single-cell analysis: **creating colormaps where the perceptual distance between colors meaningfully represents the biological similarity between cell types**.
## The Prob... |
0ffb94b4d6e2b8e6cc2a7c3972fae7c35f27ecd7fa2a1c86109e71b7044187ec | Text | 4,080 | 29 | # Static Optimization in Matlab
This code solves the muscle redundancy problem using static optimization in Matlab. Cost and constraint functions can be defined in Matlab using the OpenSim API. For example, you can track muscle activations from electromyography. Details about the implementation can be found in Uhlrich ... |
2c0800025497f806b3e600336adb272c675b74d634b03494dd32e973e0740929 | Text | 4,100 | 82 | # Deep learning-based prediction of acute pancreatitis based on abdominal CT
This repository contains scripts for predicting acute pancreatitis based on CT scans.
**Note:** Execution of the script requires the trained model. Due to legal constraints, this c... |
94c60e1054cf77dc47eca0d7303565a99239e6aae5e7068976e5f88822be0e77 | Text | 4,112 | 105 | # open-source-rat-behavior
Open source software for controlling operant conditioning chambers, running behavioral experiments, and collecting data.
## Prerequisites
For specific version see `docs\Software Versions.xlsx`
- `Python` If using standalone [Python version](https://www.python.org/downloads/release/python-38... |
94ff2922c24d3add609d6c79bb02a6d92cc791d578f740d04458549ab6fb7cc7 | Text | 4,114 | 80 | # NucFuseRank: Dataset Fusion and Performance Ranking for Nuclei Instance Segmentation
This repository contains the implementation details of the NuFuseRank paper.
Two state-of-the-art models ([HoVerNeXt [0]](https://github.com/DIAGNijmegen/hovernext) and [CellViT [1]](https://github.com/TIO-IKIM/CellViT)) were used i... |
1adc62a49446882c4ce072233760d0271950dbb604e009f60506af74c1a97821 | Text | 4,117 | 53 | # GRU-D
This is a re-implementation of the `GRU-D` model with `Python3 + Keras2 + Tensorflow`.
## Reference
Zhengping Che, Sanjay Purushotham, Kyunghyun Cho, David Sontag, and Yan Liu. ["Recurrent Neural Networks for Multivariate Time Series with Missing Values"](https://www.nature.com/articles/s41598-018-24271-9), S... |
eeacc14b38ad62b23d793140ef6693f396c7974645d45c9c2bac510641ef2643 | Text | 4,129 | 97 | # LargePNet-for-fluorescence-image-restoration
This is the supplementary code repository of the article "Pushing the limits of fluorescence imaging with a restoration neural network aggregating large-view statistics"
It contains a general fluorescence image restoration model LargePNet, and its extended versions.
Its... |
c68b2b5af0fb322356302f05fa26d055d5a092769d32fa2f9aec52cee90e9ee4 | Text | 4,131 | 93 | 
**If you encounter problems running the code, please [open an issue](https://github.com/Dingyun-Huang/tadf-photoluminescence-prediction/issues).**
## TADF photoluminescence prediction
Code repository for curating a dataset of experimental PL wavelengths and predicting them for thermally acti... |
25070ca4e918c2d61e1d7613e99084ad300ab1f4172587f9f329d217128b508a | Text | 4,178 | 88 | # LESYMAP
Lesion to Symptom Mapping (R toolbox)
*****
#### Package details
[](https://github.com/dorianps/LESYMAP)
Version: 0.0.0.9221
Systems: Linux, Mac or [Windows Linux Subsystem](https://github.com/stnava/ANTsR/wiki/Installing... |
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