sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
808f50e1fb19c952a11e935dc95eab7ea8973ee623aa804e25b7eb7816095b76 | Text | 1,223 | 52 | # [An R package `PI4AD`](https://github.com/hfang-bristol/PI4AD)
## @ Overview
> The `PI4AD` is an R package enabling genetics-led, systems biology-driven therapeutic discovery centering on Pi.
## @ Installation
### 1. Install R
Please install R (version 4.3.0 or above); see https://cran.r-project.org
If installe... |
7f432daad39c6245f0647412f67f6d535a3c05b28902aa6b393b6aa2365f8864 | Text | 1,231 | 39 | # Tutorial on (s)BLISS Downstream Analysis
Welcome to this tutorial. The aim is to provide a guide to the
preliminary downstream analysis of (s)BLISS data. A [Nature Protocols
article]() provides a summary of the sBLISS technology and a walkthrough
on the analysis of the results.
## Getting Started
### Requirements
... |
9b2e600d7c82308f732f6cdcede759d311a4dbaa78ac9a4426c03c08da34058d | Text | 1,236 | 27 | # l0-sparse-NMF
This package reproduces results from
Robert Peharz and Franz Pernkopf,
"Sparse Nonnegative Matrix Factorization with l0-constraints",
Neurocomputing, vol. 80, pp. 38--46, 2012.
In particular, it provides algorithms for approximate non-negative matrix factorization with l0-sparseness constraints.
P... |
f038c7b14349afa48e5719f948806fd1bc711eaa68580b2893e7d57ad1ecbb42 | Text | 1,267 | 7 | # CanineGutMicrobiomeStudy
Companion scripts for the manuscript [Pellowe, S.D., Zhang, A., Bignell, D.R.D. et al. Gut microbiota composition is related to anxiety and aggression scores in companion dogs. Sci Rep 15, 24336 (2025)](https://doi.org/10.1038/s41598-025-06178-4)
The first step to reproduce our analysis is t... |
929906d206f257feb116247529532e780ce0a1a898485ca4397ff69ddee86d8c | Text | 1,298 | 28 | # AI-ThermPpt
AI-powered prediction of critical properties and boiling points: A hybrid ensemble learning and QSPR approach
## Installation
To install the necessary packages run the following command:
```bash
pip install -r requirements.txt
```
# Example
A complete example file is provided in the "Example" fold... |
1c267e05c8f71774ebf88fce2c999ae529f61bc2ac7e4a4c07fc5ebc32a6c43e | Text | 1,315 | 35 |
# JaxKineticModel
Python package to simulate, build, and train kinetic models.
### Installation
Install the package using
```
pip install jaxkineticmodel
```
Or the latest version using
```
git clone https://github.com/AbeelLab/jaxkineticmodel.git
python -m pip install .
```
### Documentation package
Documentatio... |
39e622d5ff33b55c397768a7a1351b6d7930ca56e62f6955169ad34c0074ac55 | Text | 1,317 | 57 | # Schizophrenia EEG Detection Pipeline
This repository provides a complete pipeline for schizophrenia detection using multichannel EEG, following the methodology described in:
> **"Enhanced Schizophrenia Detection Using Multichannel EEG and CAOA-RST-Based Feature Selection"**
## Features
- EEG feature preprocessing... |
62e9402091051f0f12221d8d1d03d756d218be1a9501b02b759e519369da6a2b | Text | 1,329 | 21 | # ImageJ Macros
A collection of random ImageJ/FIJI macros I use at the lab for analysis of microscopy images.
## How to use
1. Click on the ImageJ/FIJI script (".ijm" file) you want to download.
2. Click on "Raw"
3. Save page as .ijm file
4. Drag and drop the ijm file onto FIJI (or install macro in ImageJ)
## How to ... |
e509684553c4e20dca74d129f0d84dcc314ef69bb1f5abc5953b140cefd97fda | Text | 1,349 | 24 | # Protocol design of PGSE
[](https://doi.org/10.5281/zenodo.15312803)
The code implements protocol design of PGSE developed in [Gabriel Ramos-Llorden, Hong-Hsi Lee, ..., Susie Y Huang, Nature Biomedical Engineering, 2025](https://doi.org/10.1038/s41551-0... |
fb30054be5bc112388901828432770a273daf93c43f3d57ca0be91558020a24a | Text | 1,381 | 35 | # BRWExtract #
BRWExtract is an automated tool for reading multielectrode array data from .brw (BrainWave) files. It parses the raw quantal data into voltages for each channel, reshapes into channels, and writes to an (open-source) .hdf5 file with metadata embedded.
## Prerequisites ##
BRWExtract requires h5py and ... |
ea6270fc3454b627113ff91155681ab1411bf8909e3d3c5564fb8b3874c29719 | Text | 1,384 | 60 | Build Prerequisite
===================
+ Qt 4.8.0 or later
+ SQLite (including Qt plugin)
OpenCL is not required for runtime operation.
Distribution
============
To distribute as a ZIP archive (windows), the following files are
required (specific subdirectories, if specifed),
bshouty_model.exe
vessel_int... |
3db41b53a5efe329a121f4fdc18c7a02b4192dd5d00be6420e24d0710c501800 | Text | 1,424 | 26 | # Generative AI for weakly supervised segmentation and downstream classification of brain tumors on MR images
Code for training and running weakly supervised brain tumor segmentation models and weakly supervised evaluation of segmentations using non-cancerous variants from generative models.
Simpy pathway model for stroke thrombolysis and thrombectomy. This models compares the outcome difference between two models of care:
## Models of care
### Drip and Shaip
```mermaid
flowchart LR
A[Stroke\nonset] --> |Delay| B(Call 999)
B --> |De... |
1a9f62e8ede4f8c7cf01cc785d320290874b61079ce44be9ca09cd9ce2ca0721 | Text | 1,436 | 42 | # MassCube
[](https://github.com/huaxuyu/masscube/)
[](https://pypi.org/project/masscub... |
f7d8721e7727e8c4ff61ddaec4b4bf35ea58efeaad4f171606e592d4536c28da | Text | 1,481 | 27 |
# TockyRandomForest: Machine Learning R Package for Flow Cytometric Fluorescent Timer Analysis (Beta Version)
**Author:** Dr Masahiro Ono
**Date:** 21 January 2025
<img src="vignettes/assets/LogoTockyRandomForest.jpg" align="center" width=25%>
The **TockyRandomForest** R package is part of the **TockyMachineLe... |
ffef6ce2231470ae3ab160b2206f7d7292c918f920ba5f9a845c657e1cd0d125 | Text | 1,484 | 32 | # pji-ml-prediction
Predicting Periprosthetic Joint Infection with Machine Learning
This repository contains the source code and methodology used in the research article:
"Predicting Periprosthetic Joint Infection: Evaluating Supervised Machine Learning Models for Clinical Application"
Manuscript ID: JOTr-D-25-00307
... |
b17d8a821be1a510a0e0a112af08cccbef6c528ae4d00244dfb208eafe9cbe1e | Text | 1,485 | 41 | # RVINN
**RNA Velocity-Informed Neural Networks (RVINN)** is a PINN-based framework for modeling mRNA dynamics and inferring transcriptional and post-transcriptional regulation.
---
<div style="display: flex; justify-content: center; gap: 40px; align-items: flex-start;">
<figure style="text-align: center;">
<i... |
be62195c0a1ce1cd7c0343ed8d9395276e5c1f332f2b3e6794ab72d6fd942c8b | Text | 1,489 | 33 | # Single-Cell and Stereo-seq Spatial Transcriptomics Analysis Workflow
This project includes the complete workflow for single-cell and Stereo-seq spatial transcriptomics analysis, covering data quality control, integration analysis, spatial domain annotation, and main figure generation. The workflow is divided into th... |
8db3af24b105cf3aeb592cdf03941a1465ea9082baebe195296ed9952fbc6a2b | Text | 1,521 | 20 | # Image analysis pipelines for analysis neuronal protein aggregates
These pipelines use a combination of morphological segmentation, pixel classifier, intensity measurments and cross correlation analysis to quantify various spects of intracellular and intranuclear protein aggregates.
[This repository](https://github.... |
b2ef90430bcb851133c75871ab74426bc5a20f0f178b7a068a34115ede423164 | Text | 1,549 | 37 | # Faulkner-et-al-2024
This repository includes code for reproducing main results and figures for the paper "Context flexibly modulates cue representations in visual cortex" submitted to Nature Communications.
## System Requirements
### Hardware requirements
The provided code can be run on any standard computer with... |
71951ce35d110aa231d78b65b85387be3515aedff65a476d20c4ec507ed1cdeb | Text | 1,574 | 39 | # circHomer1-models
Code used in supplementary figure 4 for modeling circHomer1 dynamics.
## Installation instructions
1. These instructions require:
2. a recent Python distribution, preferably anaconda
3. an installation of git.
4. The correct environment yamls.
#### For a windows machine:
1. Open a command promp... |
766d5408e5da51da782c8bde18249c82abb1c43f40cf775d11f532fbd513ae75 | Text | 1,577 | 26 | Partial Least Squares - MATLAB
------------------------------
This repository hosts the MATLAB version of McIntosh Lab's Partial Least Squares implementation.
### Installation
```
git clone https://github.com/McIntosh-Lab/PLS.git
```
### Usage
See the [PLS User Guide](https://github.com/McIntosh-Lab/PLS/wiki/User-G... |
e570fa45c0d4059114263f31c186d5a0519ee7d8f6104794e41cee1e8010d601 | Text | 1,585 | 43 | # InterDependence Scores (IDS)
Code to compute IDS between sets of variables. Supports both numpy only users and PyTorch users.
## Prerequisites
Python version >= 3.7.
## Installation
Clone the repo and run the following command to install ids:
```bash
pip install -e .
```
## Example usage
The following t... |
1de606d71af19142cd3830c480b86ae2a80523a359e75292f95829f0b16809e4 | Text | 1,594 | 13 | # Two pathways to resolve relational inconsistencies
[Arxiv](https://arxiv.org/abs/2411.05809v2)
## Authors
Tomer Barak and Yonatan Loewenstein
## Abstract
When individuals encounter observations that violate their expectations, will they adjust their expectations or maintain them despite the observations? Naively, ... |
11c598704cfa8672cf18679be38b53b7803ff6f9edb8978df144efd5c54f4f9c | Text | 1,640 | 43 | # README #
## Basic usage
### Pre-process and filtering `MATLAB`
- `make_fluo_data.m`: Launches the pre-processing of the fluorescent Calcium data with the parameters
- `preview_image_stack.m`: Crop, rotate, and other basic pre-processing functions.
It requires a basic set of parameters.
... |
c50a884ccf81c0ecaa84256d9e256a9e42e1c544b91b834833f4c42e82d9a2ee | Text | 1,656 | 57 | # MCANet
Paper is available at [Briefing in Bioinformatics](https://doi.org/10.1093/bib/bbad082)
<img src="assets/Model_Overview.jpg" width="800px" height="400px" title="Model Overview" >
## Dependencies
Quick install: `pip install -r requirements.txt`
Dependencies:
- python 3.8+
- pytorch >=1... |
28cd029cf5ccff9a43252ddaf67f4988ff3dc2bb982c134a23a6680cae71e567 | Text | 1,687 | 39 | # cas9-similarity-search
DNA similarity search using Cas9
# Repo overview
The oligos ordered for the database can be found in database_oligs.csv
The alignment data for the baseline database and experimental queried databases can be found in `data/sequencing.`
The feature vectors we start with come from the preceding... |
49c2dae8a1d371953448bbf7102de1263187ef4f1ebfcdea95462e59d08d0578 | Text | 1,690 | 38 | # Glioblastoma TCGA-WSI-Annotations
This repository contains manually curated annotations for over 60 Whole Slide Images (WSIs) from the **TCGA dataset**. The annotations are provided in JSON format and can be matched with the corresponding TCGA images.
## 📂 Dataset Structure
- **annotations/**: Contains JSON f... |
b543cc6bd69b80f3eded0ddb2df548b920548c32d219f94faceba083aa0f25aa | Text | 1,694 | 74 | #Deep Learning based color fundus Imaging for Diabetic Retinopahty
This repository provides a complete pipeline for Deep Learning based color fundus Imaging for Diabetic Retinopahty , following the methodology described in:
> **"Deep Convolutional Neural Networks (DCNN) Model using color fundus Imaging for Diabetic R... |
78ed66bbbe8bc97a1cbafb2c38f3d9f3566bb5a7f5832787a33e52ff57068cad | Text | 1,707 | 33 | <h1 align="center">
Pep-TCRNet
</h1>
**Pep-TCRNet** is a novel approach to constructing a prediction model that can evaluate the probability of recognition between a TCR and a peptide amino acid sequence while combining inputs such as TCR sequences, HLA types, and VJ genes.
## Requirements
To successfully run Pe... |
8d74066213f1c5b741675054b0908ef973ff7cbae5408e9a6ddb2dc8dfdf4d56 | Text | 1,736 | 33 | # Neural Topology Optimization Via Active Learning for Efficient Channel Design in Turbulent Mass Transfer
The data and code for the paper [C. Kou, Y. Yin, M. Zhu, S. Jia, Y. Luo, X. Yuan, L. Lu. Neural Topology Optimization Via Active Learning for Efficient Channel Design in Turbulent Mass Transfer, *Advanced Science... |
35040c2391fa9224d4ad50f1fec7925c3acd1f712f0926441cdd0448d29eae0c | Text | 1,783 | 53 | # ISOSNet
This is the repository for our paper [ISOSNet: a unified framework for cone photoreceptor detection and inner segment and outer segment length measurement from AO-OCT B-scans](https://opg.optica.org/boe/fulltext.cfm?uri=boe-16-8-3237&id=574353).
Please cite the papers listed at the end of this document if y... |
53a065186580f4fcb0b6a47bae8cc4d1d4b1aa90afec7887251d2817a229fec8 | Text | 1,783 | 35 | Code accompanying Leupin and Britz, Pre-stimulus microstates and bodily signals independently influence perceptual awareness at the discrimination threshold.
We here provide the code for preprocessing, epoching, and pre-stimulus analysis of EEG data. EEG data can be made available upon request.
## Code organization
Ea... |
8a7e3f8e4175f9884d2b9f8521287daf7715e25d80a697901793f8b3391f1764 | Text | 1,786 | 42 | .. image:: https://github.com/h5py/h5py/actions/workflows/build_wheels.yml/badge.svg?branch=master
:target: https://github.com/h5py/h5py/actions/workflows/build_wheels.yml
.. image:: https://ci.appveyor.com/api/projects/status/h3iajp4d1myotprc/branch/master?svg=true
:target: https://ci.appveyor.com/project/h5py/h... |
221c72b4efde69d24df2ca0f95f349028df658fc4f1c7f537051536091ef50c8 | Text | 1,795 | 34 | # Homophilic wiring principles underpin neuronal network topology *in vitro*
This repository contains all relevant code to replicate our findings.
For any questions regarding the use of this repository, please get in touch at danyal.akarca@mrc-cbu.cam.ac.uk or da434@cam.ac.uk
If using the code, please consider cit... |
3a1d351b5664dbbb2bd85cca7634f4e0872ca8b20e31e46b6e44121b8505c3b3 | Text | 1,797 | 33 | Directed Rod Simulation for Drosophila Class IV Dendritic Arbor Morphogenesis
This repository contains a C implementation of a simulation model that recapitulates the mean-field picture of Drosophila Class IV dendritic arbor morphogenesis using *directed rod dynamics.
Model Description
The simulation models the stead... |
0853a248aaab62151c567a1a3aad6368bfa56d70516ac54ccb92fb6f63841a17 | Text | 1,803 | 49 | # CACHE
This repo contains our code for paper Counterfactual and Factual Reasoning over Hypergraphs for Interpretable Clinical Predictions on EHR, in Proceedings of 2nd Machine Learning for Health symposium 2022 (ML4H 2022).
## Model Framework
## Data
**[IMPORTANT, PLEASE READ!]**
... |
8138040d5fca3a907b9663ff9fb408f19b877cf519afa9d5206fffcc14c86065 | Text | 1,808 | 21 | # eICU Collaborative Research Database Code Repository [](https://doi.org/10.5281/zenodo.1249016)
This is a repository of code shared by the research community. The repository is intended to be a central hub for sharing, refining, and reusing code used for... |
28690bb4b613dfe0daa1e88d397ccddfb7cdd5814437413d6e91d58ba58cf205 | Text | 1,821 | 39 | # Context flexibly modulates cue representations in visual cortex
This repository includes data and custom code for reproducing the main results and figures from the paper "Context flexibly modulates cue representations in visual cortex" published in Nature Communications.
## System Requirements
### Hardware require... |
1c60b78846a1814a637291b8d421e741dd33a90ae6bbd0ec4475a1ff02721d3d | Text | 1,836 | 20 | # Human short association fibers are thinner and less myelinated than long fibers
[](https://doi.org/10.5281/zenodo.15601201)
This is a collection of all scripts, sample data, an... |
1bdb097ee2ad9d5073a029b34206955825ceeda828d7de3cf6f1a751777c9b2d | Text | 1,846 | 26 | # E-I-SNN
Codebase for the work Biologically-Informed Excitatory and Inhibitory Balance for Robust Spiking Neural Network Training
# Simulation workflow
Due to the massive workload of processing hundreds of training sessions (and then multiple layers of processing) this workflow is designed to enable massive batch com... |
b177c33921edcebb6e24a040b3c42a43d9b3d069079235a1de8b42edacc9c967 | Text | 1,863 | 31 | # The effect of spherical projection on spin tests for brain maps
This repository contains scripts and functions to reproduce the results presented in [The effect of spherical projection on spin tests for brain maps](https://doi.org/10.1162/IMAG.a.118).
## The main script
[main_script.py](main_script.py) contains a ... |
6040a43f46e21060e73ddc1fd70b0a749b0e24e787d6a24237d6f7bb23916a67 | Text | 1,869 | 35 | # Project Description:
Acute Kidney Injury (AKI) can harm multiple organ systems, including the heart, brain, and the immune system. Stage 1 AKI (AKI-1), though mild in presentation, represents a critical subset of AKI patients with distinct outcomes, warranting further investigation into its subphenotypes. In this stu... |
9b611a024cd0fcd7aefeaebfc8ca0354c630bcb92ecb4546fcc28609ff0dc07b | Text | 1,887 | 17 | 
# Benchmarking Peak Calling Methods for CUT&RUN:
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has rapidly gained prominence as an effective approach for mapping protein-DNA interactions, especially histone modifications, offering substantial improvements over conventional chrom... |
c729504af80ab6451028f8b204ed42cca7aba4171672e81d4068bdc69398efbb | Text | 1,889 | 59 | # GASTON-Mix
GASTON-Mix is a spatial mixture-of-experts (MoE) model for learning domain-specific _topographic maps_ of a tissue slice from spatially resolved transcriptomics (SRT) data.
## Installation
We will make GASTON-Mix `pip`-installable soon. In the meanwhile, you can directly install the conda environment fro... |
32a47491b9b6d0653dd7decf8b1792f267775b56191688bbfbcc58e0e4a81d4c | Text | 1,897 | 46 | =============
**HeuDiConv**
=============
`a heuristic-centric DICOM converter`
.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:latest-brightgreen.svg?logo=docker&style=flat
:target: https://hub.docker.com/r/nipy/heudiconv/tags/
:alt: Our Docker image
.. image:: https://travis-ci.org/nipy/heudiconv... |
4a88a3064d7e6876e83b328f1bd2531ca9c2567d122241e9728588acc098f3a3 | Text | 1,915 | 51 | # fvcore
fvcore is a light-weight core library that provides the most common and essential
functionality shared in various computer vision frameworks developed in FAIR,
such as [Detectron2](https://github.com/facebookresearch/detectron2/),
[PySlowFast](https://github.com/facebookresearch/SlowFast), and
[ClassyVision](... |
1f2f5870082b00b47aab0fd8ae3a5e139a82cbe87a5f7fb9ebb19d594aa60854 | Text | 1,922 | 45 | # sbcdata
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[, Hessian analysis, and Variational Bayesian Gaussian Mixture Model (VBGMM). T... |
31cb2975d696018a465725cd2ed0434623f0555d700585e75b892ae6dd7b1e7d | Text | 1,941 | 36 | # Organoid-Robot-Control
*This is code accompanying the publication*
Molokanova E. _et al._ **Graphene Optoelectronics for Non-Genetic Neuromodulation in Disease Modeling, Stem Cell Maturation, and Biohybrid Robotics** (2025)
## Installation
* Download and install [Anaconda](https://anaconda.com/download)
* For ... |
255a2c7ce7905ac9592bc9cb0dc35d74e35f5436baf795d4cc69ea304491cd58 | Text | 1,942 | 31 | # Madden et al. 2025
This is the code repository associated with the publication titled: Serotonin and Psilocybin Activate 5-HT1B Receptors to Suppress Cortical Signaling through the Claustrum
## Whole-Cell Patch-Clamp Data Analysis
This code is a simple application of the pyABF library created by SW Harden https://... |
38a4e2c0b04c0954b448364b72e6f8b74c4256d5a72ddb4f0713d509e3f749c7 | Text | 1,945 | 51 | # shortvideos
### Purpose
The goal of the short videos task is to produce data capable of training a sensitive and specific neural signature of self-reference.
### Paradigm
In this task, participants complete 21 blocks of 3 trials.
In each block, they are asked to make one type of j... |
8b6f594799f54f1d477caf74e2816fea70183f5255b39e5f0897f575553c4402 | Text | 1,947 | 23 | # ICA-AROMA
ICA-AROMA (i.e. ‘ICA-based Automatic Removal Of Motion Artifacts’) concerns a data-driven method to identify and remove motion-related independent components from fMRI data. To that end it exploits a small, but robust set of theoretically motivated features, preventing the need for classifier re-training an... |
9e0fab9c8dcadf988866e0e2cdd9409e94dbec559d5d96a60ac72b0f64766ed1 | Text | 1,948 | 47 | # 2025_epe_eeg
Behavioral data and analysis script for "Separable neural signals for reward and emotion prediction errors"
The manuscript is published in Nature Communications at the following [doi to add]().
# Setup
Clone repository or simply download in a zip file.
The R Markdown file in the Analysis folder conta... |
509264a56461518401a1626140aec4a7046f0d8f3315756c006169205e750a24 | Text | 1,960 | 56 | # eNOS Signal Intensity Measurement
## Overview
This repository contains a MATLAB-based pipeline for analyzing **eNOS (endothelial nitric oxide synthase) signal intensity** in fluorescence microscopy images. The script processes `.tif` images, identifies the largest segmented area in each image, and extracts its mean ... |
a5399d7ec6ee943d915239d6f8b5943239155d978433cc0147b897719af5e796 | Text | 1,985 | 20 | # sptmsfmri
## Referenced Work
This repository holds the preprocessing and QC code for the publication **Concurrent single-pulse (sp) TMS/fMRI to reveal the causal connectome in healthy and patient populations** Find the preprint here: [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.09.25.614833v1)
## Contribu... |
2df5bf3ba6fdae8c87186216fa5acede216c0244d79d9074bd7eb84cf0b7f217 | Text | 2,004 | 34 | ### better algorithm/implementation for fast-oopsi now available
- the standard toolbox for calcium imaging and analysis is [CaImAn](https://github.com/flatironinstitute/CaImAn), which extends our work in several nice ways (they have Python and MATLAB)
- a very nice R package: https://cran.r-project.org/web/packages/L... |
1ead0dbf1ec53e71b79b21491dc667adf97708e17062e5d212ddc422f68e6176 | Text | 2,021 | 48 | # ggvenn
An [R](https://www.r-project.org) package that draws modifiable venn diagrams in [ggplot2](https://ggplot2.tidyverse.org/). The venn diagrams can easily be modified and added to an existing ggplot object. ggvenn uses base R functions to convert the data into a format that is than vizualized using ggplot2's ge... |
93bb9bb7372c899aef3ccd3507a647ea97e35eb57d0291c1f6b47fb2cefd87ad | Text | 2,025 | 59 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
[](https://cran.r-project.org/package=Rtsne/)
[](https://github.com/jkrijthe/Rtsne/actions/work... |
a47aad01104e5f1ecdbd86a77d6a5954bf82f535f2e485ec3c0d4a2a74373270 | Text | 2,049 | 24 | # Neuromorphic Model of Active Vision
This repository contains the code and resources for implementing a neuromorphic, insect-inspired model of active vision, described in the elife paper “A neuromorphic model of active vision shows how spatiotemporal encoding in lobula neurons can aid pattern recognition in bees”. The... |
94d198d9e848c6fe11ac8ea6e52cdd0461cd60c02ff36373a4514efbe93b13b2 | Text | 2,067 | 31 | 'Read Me' file to the 'Fiber_photom.m' code file.
## Overview:
Fiber_photom.m is a simple custom-written MATLAB code to detect peaks in photometry traces recorded by in vivo calcium imgaing fiber photometry (peaks represent activation of a detected neuronal population). The code was originally created by Jae-Chang K... |
758a0c97821130200133697b6428bb1cf2e82d25f8bcb80c4f7216049b6abb22 | Text | 2,078 | 47 | # 2025_epe_eeg
Behavioral data and analysis script for "Separable neural signals for reward and emotion prediction errors".
The manuscript is published in Nature Communications at the following [doi to add]() and references an associated Zenodo [](https://doi.org/10.5281... |
283d27fd4c17b20543f33dc630ec90b36f0a7c3064070bef4d19b3c825c8213d | Text | 2,114 | 45 | # diagnosing-tongue-disease
This repository contains the code for the paper "--" by Yeon-Hee Lee, Seonggwang Jeon. The code includes data preprocessing, model training and testing, Grad-CAM heatmap generation, and activation visualization for the detection of Tongue disease using deep learning techniques.
## Reposito... |
4b3cbe7e902ca43c33ffef9549947b2be5cb0dc6517bfd72d01cae08a16a8c69 | Text | 2,115 | 82 | # Multisyn: Accurate prediction of synergistic drug combination using a multi-source information fusion framework
This repository contains the official implementation of our paper:
**Multisyn** integrates pharmacophore structure, protein-protein interaction (PPI) networks, and cell line omics to predict synergistic ... |
8cee5227b1bd0004fdf8a40d08ddd465355070f181a7ae8a156618689b414a7f | Text | 2,129 | 16 | # Sardine - A method for detecting anomalous regions in spatial transcriptomics data
Sardine is a method that quantifies how anomalous a particular region is given spatial transcriptomics (ST) data between two or more different conditions.
The input to Sardine are the expression matrices and the spatial coordinates... |
e7589c63b22d3abaa4a7824644e6b17929ef3cd5eb11f3f9d1cb727f0e758c60 | Text | 2,134 | 72 | # StrokeGene
## Research Background
With the in-depth research on stroke, a vast amount of academic literature has emerged, posing significant challenges for researchers in literature retrieval, information filtering, and academic organization. To help researchers more efficiently access and understand the latest res... |
aeefb2db0ff548859fda12bad354af3b45c35470769ae326ce9a988f480c7c5f | Text | 2,163 | 46 | # sbcdata
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[ is a deep learning framework designed for accurate prediction of RNA–protein binding sites. It integrates multi-scale sequence features from CNN, CNN-Transformer, and ResNet branches, and incorporates RNA secondary structure information using gra... |
12d160bdadbffbd7345a4e383f3cc00ada04887cef70f56daeee9619a1fc95f4 | Text | 2,167 | 63 | # Paper
See https://academic.oup.com/bioinformatics/article/41/Supplement_1/i449/8199346
Instructions and scripts needed to train NEAR and recreate the results from the NEAR paper can be found at https://github.com/TravisWheelerLab/NEAR/blob/2025_paper_evaluation
# Prefilter
[
* Python 3.9
### Datasets
* Spine Generic Multi-subject dataset version [r20250310]... |
df732baa03f6a99ebc9a6a135381ffa465f992b5530489b8750df705833786e4 | Text | 2,226 | 43 | # emodel-generalisation
Generalisation of neuronal electrical models on a morphological population with Markov Chain Monte-Carlo.
This code accompanies the pre-print:
[Arnaudon, A., Reva, M., Zbili, M., Markram, H., Van Geit, W., & Kanari, L. (2023). Controlling morpho-electrophysiological variability of neurons wit... |
c4e11b1778ed388e31367d153a56581f8eb9f653e191815b203fa09c11098578 | Text | 2,244 | 68 | # RB-SynSubDB - Rat Brain Subregional Proteomics Database
## Introduction
RB-SynSubDB is a specialized database focusing on the proteomics of synaptosomes in rat brain subregions. This database provides protein expression data for six major brain regions (prefrontal cortex, posterior cortex, hippocampus, striatum, ... |
abdb4cfd950ceeae3325e6f80616b92b9be752356ec05b4f10423682cc9e3fe2 | Text | 2,280 | 38 | # GNODEVAE: A Graph-Based ODE-VAE Enhances Clustering of Single-Cell Data
## Graphical Abstract
## Introduction
GNODEVAE is an innovative computational framework that integrates Graph Attention Networks (GAT), Neural Ordinary Differential Equations (NODE), and Varia... |
b989b41ba68553ec9e609d00eb400851fc108b6c2a388c83264f18deb0722632 | Text | 2,286 | 101 | # Cloth Psiturk
This is the psiturk component of the "Computational models reveal that intuitive physics underlies visual processing of soft objects".
## Overview
Following the current `psiturk` api, the folder located at `/psiturk` contains
all the necessary bits to host a psiturk experiment
The main components ar... |
0da138c30ded132c5d07c12e7ab47bc4d663b8a98862a0affc1bb566824ff579 | Text | 2,287 | 62 | # Variability in reported midpoints of (in)activation for cardiac INa
This repository contains the data and code accompanying the paper
> Variability in reported midpoints of (in)activation of cardiac INa.
> Michael Clerx, Paul G. A. Volders, Gary R. Mirams.
> 2025
The data is all derived from an sqlite dat... |
07b1d86c6a7518c0885378ed401574d1ed9bf661f0a3aa74787cd007fd774654 | Text | 2,299 | 61 | 
ARCADE
======
*ARCADE* is a modular suite of Applications for Real-time Control of subject
Actions and stimulus Diplay for behavioral Experiments. It consists of several
interacting modules that are running in parallel and take advantage of modern
multi-core CPU/GPU archi... |
af992d446e4b86d8e51f1e83380080285da8fa15d7b0a01ce0f9a0347402ea95 | Text | 2,315 | 37 | # seqNMF
Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience
Emily Mackevicius and Andrew Bahle - FeeLab :notes: :bird: 2018
### Description
SeqNMF is an algorithm which uses regularized convolutional non-negative matrix factorization to extract repeated sequ... |
08319a1e960c827e29750a3034909c872c38bbf7155294f5210c44c759bcf75b | Text | 2,316 | 36 | # Kids First Data Resource Center DNA Short Reads Alignment and Haplotype Calling Workflows
This repository contains the Common Workflow Language (CWL) pipelines for the
Kids First Data Resource Center's (KFDRC) Alignment and Haplotype Calling Workflows.
<p align="center">
<img src="docs/kids_first_logo.svg" alt="K... |
6f59895ecbefbc821694e051dd4d73d8b6d26084f03394ecb62ee12ce5e6ce95 | Text | 2,319 | 43 | # NOSA
Neuro-Optical Signal Analysis
NOSA is an analytical toolbox designed specifically for the analysis and interpretation of voltage imaging data. NOSA features baseline fitting and filtering algorithms to extract electrical patterns from high speed recordings with low signal-to-noise ratios. NOSA also includes fe... |
39d158a56f839572af27d9f491d4ba3edba559aea3382c6caddae86c94b78085 | Text | 2,321 | 73 | # 3BTRON: A Blood-Brain Barrier Recognition Network
[](https://doi.org/10.5281/zenodo.15682541)
This is the repository associated with the paper "3BTRON: A Blood-Brain Barrier Recognition Network".
## Files
Here, we provide a description of the files made available in ... |
47593c3ae3e3129cf9f539e047478fffb345121184b9767a9b850483f96232c3 | Text | 2,332 | 72 | # Selection Vector Modulation Low-Rank RNN
This repository contains the official implementation of the paper "Elucidating the Selection Mechanisms in Context-Dependent Computation through Low-Rank Neural Network Modeling" (eLife, 2024). The project implements a low-rank Recurrent Neural Network (RNN) model with select... |
16105a847cca765885586e8d19527e725c2d000d7878aed0d5f3715fb335edf9 | Text | 2,342 | 63 | Nearl
=====
|pythonver| |license| |rtdlink|
`Nearl <https://github.com/miemiemmmm/Nearl>`_ is an open-source machine learning framework designed to mine protein dynamics information from molecular dynamics (MD) trajectories.
The current release focuses on a 3D voxel-based representation for use in 3D convolutional ... |
2a1b346fb799e70838810250889aadaf9ad535887c9f26c2af12e28f2c5914de | Text | 2,345 | 59 | # 🧠 ArEEG: An Open-Access Arabic Inner Speech EEG Dataset
Welcome to the official repository for **ArEEG**, the **first open-access EEG dataset** capturing **inner speech in Arabic**.
This dataset enables research in **brain-computer interfaces (BCI)**, **Arabic language processing**, and **neuro-linguistics**.
... |
160445caffaeec0a9f98eda4ed4cbb952727216ed62ff9ad8f58d5865cf169ca | Text | 2,353 | 38 | Longitudinal changes in brain asymmetry track lifestyle and disease
==============================
This repository contains the code associated with the manuscript entitled 'Longitudinal changes in brain asymmetry track lifestyle and disease'. It builds upon asymmetry patterns described in ["Dissociable brain structu... |
49130f9d8ea821be4b7ca3cc2de792f414031d0c5c8f4e7ae5ec2f9521cbbb82 | Text | 2,353 | 94 | # R5-Helicon Neural Simulation
This repository contains code for simulating and analyzing the interaction between R5 and Helicon neuron populations under different time-of-day conditions. The simulation is based on the Brian2 neural simulator framework.
## System Requirements
### Software Dependencies
- Python 3.8 o... |
4444cf5c7daa99e45e167605ebd814779441e4d73b5ac5d89ebdd1fe0329580a | Text | 2,369 | 29 | # OikonomouCalvaryNerurkar2024
Update - accepted in Development!
Code notebooks and supplemental material accompanying the manuscript doi: https://doi.org/10.1242/dev.204561
### Application of tissue-scale tension to epithelia _in vivo_
[
This code provides an implementation of the Multivariate Variational Mode Decomposition (MVMD) algorithm (1). MVMD is used to decompose multivariate or multichannel data sets, enabling the analysis of complex signals by separating them into modes.
## Features
- De... |
9b07186315fed8ea548558ba3da7f86eda45f15e6079153853f1cedc7c3f963d | Text | 2,382 | 51 | # Overview
## A PC interface for small and simple async and neuromorphic IC test chips
This firmware project is built to have a reusable interface for testing async/neuromorphic chips, also known as Device under Test (DuT).
The goal is that the firmware is free of any application-specific integrated circuit (ASIC) o... |
6d93929741e53b4ea5c1f458955d28b38affbe8d9e1d354afdaaa26067e27e67 | Text | 2,416 | 19 | # AI_guided_GDL_PEMFC
# Artificial-intelligence-guided Design of Ordered Gas Diffusion Layers for High-performing Fuel Cells via Bayesian Machine Learning
**Jing Sun**<sup>a,1</sup>, **Pengzhu Lin**<sup>a,1</sup>, **Lin Zeng**<sup>b</sup>, **Zixiao Guo**<sup>a</sup>, **Yuting Jiang**<sup>a,b</sup>, **Cailin Xiao**<sup... |
fcbd139a72197ef6c499f6f17b710609469095d34492f97fb92419dac0ea3485 | Text | 2,417 | 31 | The data archived here correspond to the following manuscript:
Title: The human medial temporal lobe represents memory items in their ordinal position in both declarative and motor memory domains
Authors: A. Temudo, N. Dolfen, B. R. King, G. Albouy
The file "figure_source" reports the individual-subject data u... |
d34263891b8b58f7f8479c9cec487068aa28a670eb86b0f50b7a525678cfa537 | Text | 2,469 | 45 | # Caffe
[](https://travis-ci.org/BVLC/caffe)
[](LICENSE)
Caffe is a deep learning framework made with expression, speed, and modularity in mind.
It is developed by Berkeley AI Research ([BAI... |
efe75b8fc3fa4fa311cf17147b4654e5f626ad5eb2a7bf4c5490e69549f8b871 | Text | 2,474 | 34 | # 2025_moser_et_al
R script and processed proteomics data for:<br/>
**Human iPSC-Derived Mononuclear Phagocytes Improve Cognition and Neural Health across Multiple Mouse Models of Aging and Alzheimer's Disease**<br/>
<br/>
Authors:<br/>
  V. Alexandra Moser<sup>1</sup>, Luz Jovita Dimas-Harms<sup>1</sup>, Ra... |
86afea754511872ea4c1b6fff10630e470d1ccca1ac8d2379fe4066794559536 | Text | 2,476 | 64 | # SMAdd-seq: Small Molecule Adduct Sequencing
## Probing Chromatin Accessibility with Small Molecule DNA Intercalation and Nanopore Sequencing
## Installation
To install dependencies, use the following command:
```{bash}
conda install -f addseq.yml
```
## Repository Contents
This repository contains scripts and data... |
7a38c29339fb7bbf92c1bf12c67ceecd235c115d889b9b77a0c8beaf45e734d7 | Text | 2,544 | 48 | # SWD_AUTOSCORE REPOSITORY FOR SPIKE AND WAWE DISCHARGES (SWD) AUTODETECTION IN SYNGAP1 RATS BY CEPSTRUM ANALYSIS OF EEG SIGNAL
Contact for code: Dr. Alfredo Gonzalez-Sulser: agonzal2@ed.ac.uk
@Gonzalez-Sulser-Team
CDBS - SIDB - University of Edinburgh
CODE WRITERN ON MATLAB R2018b
1. Create folder on C://SCRIPT... |
7acdc125ef5c038c39ca93aa89f9ea2cfb4c6eb6dadf3cba635729285878d6df | Text | 2,546 | 54 | # Rethinking-Methods-Inner-Speech
This repository contains codes for paper titled as 'Rethinking the Methods and Algorithms for Inner Speech
Decoding - and Making them Reproducible'.
The code is divided into following chunks: Preprocessing, training, and testing. The folder details are as follows:
## Preprocessing
... |
83ea0bfb7103533133562cade154e171cb77b7b52e21ffd7d0a9d6b9c3de2b0a | Text | 2,568 | 23 | # An Efficient Implementation of Kolmogorov-Arnold Network
This repository contains an efficient implementation of Kolmogorov-Arnold Network (KAN).
The original implementation of KAN is available [here](https://github.com/KindXiaoming/pykan).
The performance issue of the original implementation is mostly because it n... |
d64129298ccddfe0fb6876875def34286fdb1737fc343cf872f6b427cfc64c01 | Text | 2,588 | 45 | # Yano
- [Yano's user guide](https://shiquan.github.io/Yano.html)
- [Report issues](https://github.com/shiquan/Yano/issues)
- [Discussions](https://github.com/shiquan/Yano/discussions)
## Overview
**Yano** is an R package for spatial dissimilarity analysis（空间不相似算法）in single-cell transcriptomics. It detects features ... |
7ba48063aa0ea47ea03e39f5ba0e517f1d725c87492cdfcc24f05519305b00ad | Text | 2,610 | 66 | # Variability in reported midpoints of (in)activation for cardiac INa
This repository contains the data and code accompanying the paper
> Variability in reported midpoints of (in)activation of cardiac INa.
> Michael Clerx, Paul G. A. Volders, Gary R. Mirams.
> Journal of General Physiology, 2025.
> https://do... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.