sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8694774b0b54fe5ef1c5d4f5621f8963c015bca566f29b456772006d0208bdfb | Text | 3,086 | 114 | # Scripts for Co-occurrence analysis in ASD
Analysis Scripts for Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity for ASD
This repository contains analysis scripts for identifying and characterizing co-occurring rare variants in autism spectrum dis... |
b74daeee7a8b1d85579a6a10c5efb8eff6869bf0cc32da59c75172daf4cfa882 | Text | 3,087 | 58 | # HeMoVal aSAH CSF dataset (clinical + spectroscopy)
## Overview
This Zenodo record contains two deidentified datasets from a preregistered multicentre prospective observational cohort study of aneurysmal subarachnoid haemorrhage (aSAH) conducted at eight neurosurgical tertiary centres in Switzerland, Germany, and Aus... |
6940bafa7b71a5d5e6f0f32da54df76160b20ed943ec6408d3d8fdf2bc0dd0e3 | Text | 3,099 | 46 |
This repository contains code utitlised in the analysis of data for the publication BLANK. It was written to transform raw fast5 files produced by Oxford Nanopore Sequencing and produce quantifiable expression matrices.
NanoFlow1.sh and NanoFLow2.sh were ran on linux within conda.
cDNA_DE.yml cotains conda environm... |
e501660e402173d84e732f62c0378b908fc3fb44f0dfc888fe4fa6002663c3dc | Text | 3,103 | 56 | # snRNA-seq analysis pipeline
#This repository contains the scripts used for the snRNA-seq analyses described in this study.
The code can be used to reproduce the results either starting from raw fastq files or from the processed Seurat object (.rds).
#The data generated from this study can be downloaded from:
https:... |
6661c33c9aa668b1298abafc34f19a795a0c5143a0cb58c7fa98715094a79886 | Text | 3,121 | 67 |
# scCustomize <img src="man/figures/scCustomize_Logo.svg" align="right" width="150"/>
[](https://cran.r-project.org/package=scCustomize)
[](https://cran.r-project.org/packag... |
2eb8ec6beb1fdab0f73d64f458485c28e702a35e8e292eef569d431f36280b34 | Text | 3,122 | 80 | # Benchmarking machine learning for bowel sound pattern classification – from tabular features to pretrained models
This is the official code repository associated with the paper:
📄 **Benchmarking machine learning for bowel sound pattern classification – from tabular features to pretrained models**
✍️ *Zahra Mansou... |
a2adb97e65f7078c71e3d6dcd7b9229760dde7c3bb2d0c4a7d9a121d0b8b8776 | Text | 3,124 | 94 | # Temporal Video Tampering Detection in Automotive Dashcam Videos
## Overview
This repository contains the implementation and resources for the paper:
**"Temporal Video Tampering Detection in Automotive Dashcam Videos Using Frame Difference Features and a 1D Convolutional Neural Network"**.
The project introduces a l... |
17cf001102a98cddf0cfa938125774d89a1e1b9b79fcd38a6d478b6cd3da1665 | Text | 3,125 | 98 | Installation
============
% ./configure
% make
# As root:
% make install
To install in a custom directory:
% ./configure --prefix=/my/dir
% make
% make install
Then make sure the following environment variables contain the correct
paths:
PATH -> /my/dir/bin
LD_LIBRARY_PATH -> /my/dir/lib
MANPATH ... |
90f938be8af4926dd02f2101637cdba8504dfbca7df3fdf2e546e0a1f6938720 | Text | 3,131 | 80 | # nsddatapaper
This folder contains an archive of code used in the manuscript "A massive 7T
fMRI dataset to bridge cognitive neuroscience and artificial intelligence",
which is informally known as the Natural Scenes Dataset (NSD) data paper.
================= Part 1 (Author: Kendrick Kay)
"main" - This folder cont... |
1fd708f5703e18a9ca9240e401977c750ea6c280a19ed5abff27ce81ddb8301a | Text | 3,138 | 88 | [](https://zenodo.org/badge/latestdoi/297969672)
ImpedanceFitter
===============
Impedance spectroscopy (IS) is a great tool to analyse the behaviour of an electrical circuit,
to characterise the response of a sample (e.g. biological tissue), to determine the dielectric ... |
ca160033f60223123ee8aaf27c1ba4e63a5f6e4f33053cbed0ff9b6ecea36e6b | Text | 3,152 | 55 | *(See a better-formatted version of this page at https://alleninstitute.github.io/mfishtools/)*
# mfishtools
R functions for gene selection and analysis of mFISH data
mfishtools includes many functions that are used for analysis of data for the CZI SpaceTx project, and mostly relies on correlation-based analysis wit... |
4241c96427f7d5100a5284fbdb5452452cd2f84644023db6bd97c9dc8055c75b | Text | 3,153 | 80 | # NucFreq plots
[](https://zenodo.org/badge/latestdoi/142181949)
Script for making nucleotide frequency plots
# Usage
```
usage: NucPlot.py [-h] [-d] [--legend] [--zerostart] [-a] [-r REPEATMASKER]
[--regions [REGIONS [REGIONS ... |
f4fc19696414a53d3ab5a51d6413b47235e62cf2df5c3d36d604fe8313e1354e | Text | 3,157 | 48 | # Decay_Analysis
A physics-informed framework using metaheuristic optimization, Runge–Kutta simulations, and physics-informed neural networks (PINN) to extract quantitative parameters from luminescence decay dynamics.
## Overview
Many LED phosphors exhibit multi-peak emissions due to activators at distinct crystallogr... |
f8add5dc8762182d06b523956e280083e86e8786171f1e77d5ad05284a686a00 | Text | 3,164 | 65 | # TRM-of-Wind-Turbine-Blades-with-CNNs
This repository is part of the article "Explainable Machine Learning for Tower-Radar Monitoring of Wind Turbine Blades: Fine-Grained Blade Recognition Under Changing Operational Conditions" submitted to *MDPI Sensors*.
The work investigates convolutional neural network (CNN)–bas... |
520892f26a31b0d2a2041b42dfbaa019235c531896ba34483c60183fbea1c4c4 | Text | 3,173 | 102 | <h1 align="center">
<img src="https://raw.githubusercontent.com/pyapp-kit/magicgui/main/resources/logo_long.png" alt="magicgui" />
</h1>
<p align="center">
<a href="https://github.com/pyapp-kit/magicgui/blob/main/LICENSE">
<img src="https://img.shields.io/github/license/pyapp-kit/magicgui" alt="magicgui is r... |
27cd8db15c5993180bd6c20a32b0b343e1736d16ce96fcc33b16d25691187c88 | Text | 3,177 | 58 | # Cell Communication Energy (celcomen)
[](https://github.com/stathismegas/celcomen/stargazers)
[](https://github.com/stathismegas/celcomen/netwo... |
2f26aa83bccbc6a97a13ea4a3b40b4ca0db86ae3ed22b077809b21c066a2206c | Text | 3,179 | 83 | # PRIQA---Parasite-ResNet-101-Image-Quality-Assessment-Study
Code and resources for PRIQA, an Image Quality Assessment (IQA) framework for Cryptosporidium and Giardia microscopy images.
The framework supports multiple CNN backbones for feature extraction and uses regression models to map features to Mean Opinion Score... |
7a922978ff5dc4b7bdbe0249329e995743022fe6bade0ccfe68bd6a3da96b493 | Text | 3,179 | 113 | # rscvp
[](https://rscvp.readthedocs.io/en/latest/)
- Pipeline for RSC visuo-spatial project (rscvp) analysis
- Data are acquired using internal customized package [Stimpy](https://bitbucket.org/activision/stimpy/src/master)
- Core a... |
1758588617e631b3246ccbd1072fcb7b7b2014ce7c7722cbc31442bce118be8c | Text | 3,184 | 53 | # NextClone for STICR
NextClone is a Nextflow pipeline to facilitate rapid extraction and quantification
of clonal barcodes from both DNA-seq and scRNAseq data.
DNA-seq data refers to dedicated DNA barcoding data which exclusively sequences
the synthetic lineage tracing clone barcode reads using Next Generation Sequ... |
50117de687f1a3b4d95c05be8671b5ac4ab99cee166dc42edc4618453cf6b3d5 | Text | 3,197 | 119 | # Scripts for Co-occurrence analysis in ASD
Analysis Scripts for Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity for ASD
This repository contains analysis scripts for identifying and characterizing co-occurring rare variants in autism spectrum dis... |
87b1eee5539a518451c9b647ff083eb6ad19e1a93057b5a27b58a187a57a06d7 | Text | 3,198 | 65 | This repository contains the data and MATLAB code required to replicate the findings of “Immersive NREM2 dreaming preserves subjective sleep depth against declining sleep pressure” by Michalak, Marzoli, Pietrogiacomi, et al.
If you use this code or data, please cite the associated article and the Zenodo record.
The... |
d05d4bcad809477796d8bdc8dc21374baed2128412fcd13593953838a20335a3 | Text | 3,199 | 95 | # MRAi_P3: Magnetic Resonance processing with Artificial intelligence for Peak Probability Presentarion
## Authors
* [Amir Jahangiri](amir.jahangiri@gu.se)
* [Vladislav Orekhov](vladislav.orekhov@nmr.gu.se)
## License
This package is licensed under the MIT License. See the LICENSE file for details.
## Citation
Pleas... |
bb824eabc3186d91b462031b72307b7e81d79702fe5835b2cda1fb6fcd9e0987 | Text | 3,200 | 93 | [](https://datalad.org)
# Project <insert name>
This repo is made with
[cpp-lln-lab/template_datalad_fMRI](https://github.com/cpp-lln-lab/template_datalad_fMRI).
[⚠️ CHECK THE GUIDE ON HOW TO USE IT ⚠️](./how-to-use-me.md)
## Add below documentation ... |
faccbb95eac0091e03a30317be72d48cbba529934eb3863de1e472e359cc059a | Text | 3,206 | 50 | # gallantlab/motion_energy_matlab
motion_energy_matlab is a software library to calculate motion or static energy features of visual stimuli (movies or images).
## QUICKSTART/USAGE
The main functions accept movie/image stimulus inputs and return the energy featu... |
8ed82c0e27bbe3a9b28333399069cb8531650ff6a3bceebc862f690aed1123fa | Text | 3,207 | 137 | # ASKIVIT-Project-WoodVIT-V1-training
Training and inference scripts for CNN-based models on the **WoodVIT V1** dataset.
This repository focuses on:
- computing dataset statistics (channel means) for normalization,
- training models (GPU),
- evaluating trained checkpoints,
- running inference on the test split.
---
... |
da4fa763f7787fcae660053421dea62e2d02dc1b73fe10e6a4275e8c34b4f4b2 | Text | 3,212 | 53 | <p align="center">
<img src="https://raw.githubusercontent.com/yetinam/pyocto/main/docs/_static/pyocto_logo_outlined.svg" />
</p>
[](https://github.com/yetinam/pyocto/blob/main/LICENSE)
[ https://rdcu.be/bjxAg
High Dimensional-Differential Evolution (HD-DE) by Michelle Kim and Julie ... |
286f302eff733bed38343784ef84adb67e1880d456a6e5e0b73d3b8d79f66aa1 | Text | 3,224 | 134 | # Multi-omics prediction of pMCI vs sMCI (Reproducibility Repo)
This repository contains code and documentation to reproduce the pipeline described in our paper for predicting progression from MCI to Alzheimer's disease using blood-based multi-omics data.
Because the original ADNI datasets are sensitive and cannot be... |
2bca9ac5fd21b9c6b1951fb3f947363be9cb1c7b7187439d4f43fd9c3c48eda8 | Text | 3,224 | 71 | ______________________________________________________
This page contains public-domain data required to reconstruct simulation results in the manuscript "Predicting dominant terrestrial biomes at a Global Scale: Assessments of machine learning algorithms, climate variables indexing, and extreme climate," submitted by ... |
ea6cb51d419c27b5129a82481568302ba1ac00d0b0cd2838db110241c167e065 | Text | 3,231 | 44 | # MooneyScripts2024
## Download other required data to reproduce our results
To produce results, go our OSF page, download and decompress the `data.zip` file and the model checkpoint `model_checkpoint.tar`. Put the contents of data at the root, and create a folder `results/checkpoints` and put the checkpoints there. Th... |
79b4134061f21aa3baed67fa656f055686db77adb08ac0ebe2dd6c8a5d4fb92b | Text | 3,233 | 108 |
# Genomic Similarity via Normalized Compression Distance (NCD)
This project implements a Python pipeline to compute pairwise distances between genomic sequences using **Normalized Compression Distance (NCD)** — a method rooted in Kolmogorov complexity and approximated via gzip compression. It supports both genome- an... |
6ebba860bdc94aa7f021a2885ea7afdb9f431ad86b959a0b341053a90f5a1f53 | Text | 3,248 | 32 | OVERVIEW
This readme file contains information regarding files uploaded to the Zenodo page for “A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types”.
Uploaded files include:
1) “Auxiliary_functions_script” containing all custom functions utilized by the Main_Script.
2) “M... |
f9e874e79c8bd6956d8dc1b33816b306102e9922390b6a13af844814987383d7 | Text | 3,257 | 115 | # **Defacing Evaluation Pipeline**
---
## **Setup**
### With Pip virtualenv
* Step 0: Set up virtual environment
> pip3 install virtualenv # or sudo apt install python3-virtualenv
> virtualenv .venv
> source .venv/bin/activate
* Install cmake
> sudo apt update
> sudo apt install cm... |
34fb233c92f53e062fadd11119fdf5f29f2ba0cfb54f0c8445e4176fae412df5 | Text | 3,272 | 85 | # hybrid_rnns_reward_learning
This code fits "hybrid RNNs" to behavioral datasets. Behavioral datasets will
usually be bandit tasks performed by humans.
## Interactive Usage
The Colab train_models.ipynb provides a simple example of running this code
interactively.
## Installation
To install the code and requiremen... |
b47c719de459db275b55372cfd5be74a3bb8cd652b18bbe4a3f14c924210e18c | Text | 3,290 | 76 | # Slice Display
## Overview
Slice Display is a MATLAB toolbox for visualizing fMRI data. Besides standard fMRI displays, it can make dual-coded images (simultaneous display of contrast estimate and unthreshold t-statistic maps). Data visualizations can be entirely scripted, so that generating figures is easy and repr... |
1840684e7d653120d84214957e8b97568c2250c9e61abb2489ced47279d67412 | Text | 3,292 | 33 | [](https://www.mathworks.com/matlabcentral/fileexchange/109840-ezcalcium)
# EZcalcium
Calcium imaging analysis made easy. EZcalcium is a flexible, user-friendly toolbox for analysis of calcium imaging data, contr... |
52bba07bef05969ec9b38c3f87615c2fc2018a6c8b10aafa83c24f461444188b | Text | 3,295 | 87 | # NAcInhib
Codebase accompanying the manuscript: "Accumbal calcium-permeable AMPA receptors orchestrate neuronal ensembles underlying social attachment"
# Author(s)
Mostafa M. El-Kalliny, J. Keenan Kushner, William M. Sheeran, Olivia E. Neilly, Kelly E. Winther, Liza E. Brusman, Michael A. Kelberman, Charles A. Hoeffe... |
58ec23c19d29a575157118e7e2c864aa1206aede212553cd7f0b3d2beb1ca297 | Text | 3,360 | 99 | # Emotion-Expression-fMRI
Analysis scripts accompanying:
> Mano, Y., Nakaya, K., Komeda, H., Toyama, A., Fukuda, H., Miyamoto, Y.,
> Kitayama, S., & Suzuki, S. (2026).
> **Neural mechanisms underlying decisions to express or suppress emotions.**
> *Social Cognitive and Affective Neuroscience.*
> https://doi.org... |
d9e06aafa8f4cb3d75e63157db3ceaa72dd247644d6647b800dd5a6df5acfa13 | Text | 3,363 | 171 | # Language Assisted Learnable Hyperdimensional Computing Framework for Retinal Disease Classification
## Introduction
This repository contains the implementation of the language assisted learnable hyperdimensional computing framework for retinal disease classification.
The pipeline consists of thr... |
f380fed3bf7967209e3e6bf3f7acc10c9f4ef286ffcb306c4462a17ee4689121 | Text | 3,364 | 56 | # Blackmer-Raynolds et al., 2026 Code Repository
This GitHub repository contains the code for the paper titled: "Indigenous gut microbes modulate neural cell state and neurodegenerative disease
susceptibility." For a detailed description of the methods and results, please refer to the [paper](https://www.cell.com/cell... |
0d22f8f3510e4bc39da2ab11f409a69c7383880ca8dc6e3d042f631cbd893d60 | Text | 3,367 | 61 | # cancer-nac-ensemble
Ensemble machine learning pipeline for predicting neoadjuvant chemotherapy response in breast cancer using bulk RNA-seq. Features a validated 17-gene signature with external validation (AUC 0.78).
# Ensemble Machine Learning for Neoadjuvant Chemotherapy Response Prediction in Breast Cancer
[](https://doi.org/10.5281/zenodo.13379191)
This pipeline is now to ready to run from a dependency complete docker image hosted here:
https://hub.docker.com/repository/docker/jbrenton191/rnaseq_splicing_pipeline/general
## 0. Pull the docker image
... |
9213917417efd8dfb4ea0ba2271a74f473981bb6ca4f8d45564dd32dc2e9c7cf | Text | 3,396 | 119 | # A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity
## 🚀 Introduction
The approach achieved over a 10-fold increase in DNA cleavage activity in two complex multi-domain functional proteins (Kurthia massiliensis Ago and Pyrococcus furiosus Ago, refer... |
6a3703ca43ea27b6048ef7ca127a0b13952850f6dbdaf4f74816e1092ca55b8e | Text | 3,402 | 69 | # CEC 2017 Python
Python 3 module containing a native implementation of the CEC 2017 benchmark functions (single objective optimization). The implementation is adapted from Awad's original C implementation, available on [Suganthan's GitHub repo](https://github.com/P-N-Suganthan/CEC2017-BoundContrained), along with the... |
74a970db041a2b6bf4bf3735253877607d881ae6027eeab33008a9da7a802c08 | Text | 3,404 | 104 |
Cell Type Estimate For Seurat Object (CTE4SO)
=======================
```
Cell type annotation tool for single cell data
Author and Maintainer: Hua Sun
Version: v0.3.1
```
Description
----------------------
CTE4SO is a cell type annotation tool adapted from ScType (Ianevski et al., Nat Commun 2022). It was develo... |
67a013f5eaf008f6025a95ec601d183aa201b09b5e8c4f7252df762a8c372702 | Text | 3,406 | 90 | [](https://zenodo.org/badge/latestdoi/297969672)
[](https://results.pre-commit.ci/latest/github/j-zimmermann/ImpedanceFitter/master)
<p align="center">
<img src="log... |
2a6684aeaa5bb64fb2c3d8f01a45e1815ca575d9af13d4890f75b77c9f9fd73b | Text | 3,459 | 110 | # Mc_GNN_analysis
This repository contains the codebase and experimental pipeline for morphology-guided Graph Neural Network (Mc-GNN) analysis on SARS-CoV-2 nanoparticle imaging data. It includes preprocessing scripts, baseline comparisons, and ablation studies for both the TargetDNA and ViralRNA datasets.
---
## Da... |
27e5e91d49d2d1747bf27dae7a132f7e411df28701111cc89fe15baf4442e98b | Text | 3,469 | 137 | # Macular
## For Users
### Linux.
The user can download an installation script by running the shell command:
``` bash
wget http://repo-sam.inria.fr/sedsam/macular/macular-latest-Linux-x86_64.sh
```
Then, type:
``` bash
bash macular-latest-Linux-x86_64.sh -b
```
The command creates a directory ~/macular where Mac... |
7dc6ec5d457bab8ff381723b6fd4f3f4bbc6f9057357020fa641ec0ce150844f | Text | 3,483 | 47 | # Analysis of clinical, dosimetric and radiomic features for predicting local failure after stereotactic radiotherapy of brain metastases in malignant melanoma
This repository contains code, models and radiomic features used for the paper "Analysis of clinical, dosimetric and radiomic features for predicting local fai... |
202438fdebabe443395620e506d4ca5b563b17ed1e98d27954440d86e8f70cb0 | Text | 3,484 | 86 | # Reproducible Package — PCA–ANN Surrogate + Multi-objective Window Optimization (Tehran, Hot-Dry Climate)
This repository contains the cleaned dataset, reproducible scripts, and documentation required to reproduce the main analyses reported in the manuscript:
**“An AI-driven multi-objective framework for optimiz... |
af24c59ce789478c1de66c71004f10226d6865f74f27010ea2fa26a318d40e4a | Text | 3,486 | 133 | # sharp
A single-cell demultiplexing pipeline.
the sharp (♯) from musical notation similar to the hash (#) in hashtag.
Sharp supports the following:
- Hashtag
- CITE-seq
- ASAP-seq
- CellPlex
## Outputs
In addition to cell barcode/UMI correction and quantification, cells are demultiplexed to their sample-of-origi... |
617299b292bd907730affdd0cefda0b579cdf1aede659da672e0bdfd45858198 | Text | 3,490 | 69 | # Kvistiani-lab_Dsort
Dsort spike sorter
Installation
Dsort requires CUDA in order to run. This is because the normalized cross correlation routine is coded in CUDA (no cpu version is provided with Dsort).
What to do to run Dsort?
1. Install matlab R2018a
2. Install cuda 9.0 https://developer.nvidia.com/cuda-90-d... |
4799a9e2b31823d7380e6fde4ead11453c9fbbdbbacd2e733673dc387d66a6a2 | Text | 3,491 | 49 | # HRCHY-CytoCommunity
## Overview
<div align=center><img src="https://github.com/xieBioinfo/HRCHY-CytoCommunity/blob/main/Figures/Schematic.jpg" width="650" height="900" alt="pipline"/></div>
Diverse cell types within a tissue assemble into multicellular structures to shape the functions of the tissue. These stru... |
ea270aec31eb815701f46e1339d64bcb3a13e8cedc3ad905605a5e96a26ed800 | Text | 3,516 | 56 | # Large Deformation Diffeomorphic Image Registration with Laplacian Pyramid Networks
This is the official Pytorch implementation of "Large Deformation Diffeomorphic Image Registration with Laplacian Pyramid Networks" (MICCAI 2020), written by Tony C. W. Mok and Albert C. S. Chung.
\*\* Please also check out our new c... |
b6cfb317287305df767bd21ec3747fd96d1221f67999088560473fb318f460d4 | Text | 3,518 | 71 | # A geometric shape regularity effect in the human brain
This is the code repository for the article "Two brain systems for the
perception of geometric shapes". The repository contains the scripts and
functions needed to reproduce all of the analyses and figures presented in the
article.
If you have any question, ple... |
e72c232d0c51d1a7a5837861a8159849229ea2f15e3cc471f59c811473a79e2b | Text | 3,521 | 42 | ## Improving Micromorphological Analysis with CNN-Based Segmentation of Flint/Obsidian, Bone, and Charcoal
Presented at *Computers & Geosciences*
- Version: 1.0
- License: MIT
## Authors
- Rafael Arnay-del Arco
- Pedro García-Villa
- Javier Hernández-Aceituno
- Sara Rueda-Saiz
- Carolina Mallol
##... |
03c62b5989a3e01fcc3ddb6daf991e1ddccb1e8bfb3946e61c0d6fc648c587d1 | Text | 3,533 | 102 | ![Maturity level-0] (https://img.shields.io/badge/Maturity%20Level-ML--0-red)
# Feature Selection with Stochastic Gates (STG) for PopPK Covariate Search
This is a supporting code for "Stochastic Gates for Covariate Selection in Population Pharmacokinetics Modelling" publication.
**This project is a modified version ... |
6d815bb4f093596a0202884860c56407103d38cf37eca142e426ad96168119cb | Text | 3,533 | 89 |
<!-- badges: start -->
[](https://gitlab.com/lukas.novak/psychtoolbox/-/commits/master)
[](https://gitlab.com/lukas.novak/ps... |
097bb9e72a9f27d284d7a2760f2a2f4bebafe489a120be37c252dd7214aa7bff | Text | 3,542 | 61 | # PSMD (Peak width of Skeletonized Mean Diffusivity)
> [!IMPORTANT]
> **PSMD has a successor: [DELTA-SVD](https://delta-svd.com).** DELTA-SVD is optimised for longitudinal processing and reports PSMD alongside MSMD and the free-water metric MSFW. This repository is archived and no longer maintained. The PSMD tool, its... |
97429c56294296437a067b852777cb90dfe3341e002b01043080d3d024c38b5c | Text | 3,566 | 61 | # Highly Efficient Imaging Genetics (HEIG)
HEIG is a comprehensive toolbox for efficiently conducting joint analysis for large-scale imaging and genetic data, which includes Representation learning-based Voxel-level Genetic Analysis (RVGA) and Representation learning-based Voxel-level Rare Variant Analysis (RVRVA). Com... |
c89a7095e2166897b362702acee0a6919b4ed5625a16a0f4a9e95e93088f9669 | Text | 3,569 | 79 | # TMS Explorer
TMS Explorer was developed to assist with the preprocessing of transcranial magnetic stimulation (TMS) data as part of the study "Transcranial direct current stimulation (tDCS) and mindfulness meditation in fibromyalgia" in the "Non-invasive brain stimulation lab" (NBS) at the University Medicine Göttin... |
660b8ed68a4f9b8da9bdea27c96569f5f740b6a1d0d7c15ecf52b4d3b7d05e3b | Text | 3,585 | 114 | # ATT-CNN Neural Network
This repository contains the implementation of a deep learning model as described in our research article titled **Unlocking azobenzene isomerization mechanisms via an LLM agent-driven workflow integrating simulation, experiment, and machine learning**. The model uses a convolutional neural ne... |
1664906cfd52e44a9d19ef5153500ffac612634eb8275a3af35dc7d8128419b6 | Text | 3,608 | 52 | # SPIDER-seq
Single-cell Projectome-transcriptome In situ Deciphering Sequencing
<img src="https://github.com/ZhengTiger/SPIDER-Seq/blob/main/images/movie.gif" width="100%" />
## Abstract
Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organ... |
df61577dc171fb3b9c083974100b07f3204cbd2cd1b7d21bbc76569cc3aa65f9 | Text | 3,609 | 52 | # Sharpness-Aware-Training
The open source code for our proposed Physical Neural Network (PNN) training method, Sharpness-Aware Training (SAT).
Inspired by Sharpness-Aware Minimization (SAM) [Paper](https://openreview.net/forum?id=6Tm1mposlrM) and [Code](https://github.com/google-research/sam), which ... |
0654ac53f9af85000b50f6a5d2297aade8602c507a44e811f8aff602629c2625 | Text | 3,617 | 62 | [](https://colab.research.google.com/github/philshiu/Drosophila_brain_model/blob/main/example.ipynb)
# Model for the _Drosophila_ brain
Activate and silence neurons in a computational model based on the
fruit fly connectome
# Paper
This reposit... |
0e9814a786d2f15b7e8badf49c23467ab5ccd9c5d2b331e475b2e597a9ca7d80 | Text | 3,622 | 51 | # Sharpness-Aware-Training
The open source code for our proposed Physical Neural Network (PNN) training method, Sharpness-Aware Training (SAT).
Inspired by Sharpness-Aware Minimization (SAM) [Paper](https://openreview.net/forum?id=6Tm1mposlrM) and [Code](https://github.com/google-research/sam), which ... |
998ca26f4ebe033d3fef6f08c180cfba1e888f1b243feaae2de9362412b1def5 | Text | 3,624 | 49 | ## miFC-dFC-PET-4-OUD ##
# Multimodal differences in brain function between controls and people with Opiate Use Disorder. #
This study investigates whether there are generalisable differences in connectivity among reward, attention, and cognitive networks in methadone-dependent (MD) people with Opioid Use Disorder (OUD... |
76acce34025dfac5cda8a0a119144b42ae1687a9aeda140f032c8a0b5d18ed58 | Text | 3,630 | 135 | # 3D ViT-UNet for Brain Tumor Segmentation (BraTS 2020)
This repository contains a 3D Vision Transformer UNet pipeline for brain tumor segmentation on the BraTS 2020 dataset.
The project includes:
- dataset preprocessing for volumetric MRI data,
- model architecture script,
- training/validation scripts (with and wi... |
2bbd3c6f052fe4aad2ec5808f771f6a04350519cc242fd503b5bf097c0c198e5 | Text | 3,640 | 46 | # The Lossless EEG Pipeline
**This Project is no longer supported in MATLAB**: Instead, please use the [Python version of this pipeline](https://github.com/lina-usc/pylossless)
## Documentation
A reference manual for the pipeline can be found on the [Wiki](https://github.com/BUCANL/EEG-IP-L/wiki)
A tutorial for usin... |
59a9482f7d885029fbc1fa18019374476a1233fe872186b00a5bb10330a9394e | Text | 3,652 | 57 | 
3' sequencing RNA profiling (3'SRP) analysis :snake:
==============================================
This project is an analysis pipeline using **Snakemake** for 3'SRP.
The pipeline takes as input a **samplesheet** describing your samples, one or multipl... |
639a75a94ea161bf1288f24b8bf4efcd2eedd913ddb3255af74bbd60de0d17ef | Text | 3,653 | 29 | Automatic Behavior Recognition System (ABRS)
Copyright (c) 2019 Primoz Ravbar UCSB
Licensed under BSD 2-Clause [see LICENSE for details]
Written by Primoz Ravbar
Automatic Behavior Recognition System can annotate behaviors of freely moving flies, and possibly other animals, from video. It does NOT require alignment o... |
a3e0f48aeee393b3c5cb7caf041fdba8bb1f13d6ae84e615bf5ae007cda36311 | Text | 3,662 | 65 | # LFP_Analysis
All code can be run from the Start_LFP_Analysis.m file.
All the parameters which need to be set for subsequent analysis are contained in this file.
The code is based upon spike and local field potential data exported from recordings made in Neuroexplorer.
1. First choose which analysis to perform – for... |
3c83a8c4d974813e7706f015a489d175e2415cca3511d83d4f4e4269ae3c8cf4 | Text | 3,671 | 83 | # 3d-OT
[](https://www.nature.com/articles/s41592-026-03034-9)
[](https://github.com/dbjzs/3d-OT/stargazers)
![Python 3.10.13](ht... |
a6b397eb84c81aaa36a95b54b30dcdaca695ffd0eb65522a914c3317b3f135f8 | Text | 3,686 | 35 | # akinesia_fingerprint_article
Contains code used for the analysis and figure creation of the article "Deep neurobehavioral phenotyping uncovers neural fingerprints of locomotor deficits in Parkinson’s disease". Full article available [here.](https://www.nature.com/articles/s41531-026-01280-4)
The code uses the toolbo... |
8043e0704d0b4253d87f31e05e5f2891fae6e21aeb6b305b449498514b5727c1 | Text | 3,690 | 81 | # Variant effect predictor (VEP)
This project integrates biophysics-based features from Rosetta into existing variant effect prediction models to address data scarcity and improve the robustness of mutational impact predictions for mutational and positional extrapolation.
## Rosetta data preparation
There are two pro... |
71056b12d24ec88dd3df1aab66153f33f75a4cdde520150b45e5c3bf25ada17e | Text | 3,700 | 106 |
# iceDP project description
The iceDP package processes genome interaction data using a density peaks algorithm to identify inter-chromatin interactions. Below is the procedure for using iceDP effectively.
<br>
## Installation
Use pip to install:
```shell
pip install iceDP
```
Or directly copy source code:
```shell... |
4443d16cf84e82c5f349411655f906e83e75e2fa90b0d51c253371c86123883f | Text | 3,721 | 76 | # CVDProc: CerebroVascular Disease imaging Processing
> **⚠️ Important Notice**
>
> This package is intended for research purposes only, to facilitate reproducibility of neuroimaging analyses in our center.
> The authors do **NOT** guarantee the correctness or clinical valid... |
e4bdfb65a16eb97709ad38224f392b8afe5bb740ffaa76136ec0d48eff386a4f | Text | 3,728 | 98 | # Variable Rate Neural Compression for Sparse Detector Data
In this repository, we explain how to train a Bicephalous Convolutional
AutoEncoder model enabling variable compression ratio for Sparse data
(`BCAE-VS`). The motivation for designing the model is to compress highly
sparse data collected from the time proje... |
85c008eea70e282e4580e89021cb8c1ce18262f2af431b38f62961e723cb58f5 | Text | 3,730 | 41 | *This project is in active development and does not have any regulatory approval*
# SlicerNetstim
This repository contains a collection of modules for 3D Slicer on the topic of deep brain stimulation and other applications—see the modules section below for a general overview.
## Modules provided in this extens... |
5d9bc8a4b0db644793022863b7fc6ee94b0df0d52c3679162f8e53a6da08d5d7 | Text | 3,752 | 102 | # Cytosim
Cytosim is a cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It is a versatile base that has been used to study actin and microtubule systems in 1D, 2D and 3D. It is built around a cross-platform C++ core engine running o... |
7575803c62ee6d477db056882177400f8566909a2bc6b55121f121ab6d993d80 | Text | 3,770 | 128 | # HYBRID GRAPH–MACHINE LEARNING FRAMEWORK
## FOR ACCURATE AND INTERPRETABLE BAND GAP PREDICTION
This repository contains the official source code and computational framework for predicting the **electronic band gap of crystalline materials** using a hybrid approach that combines **graph-based structural embeddings**... |
5e1b50ba6f0d06a1e4cddfe84fe06432f06a9316fcd24e2a1a607edf96e4b8f2 | Text | 3,781 | 102 | # dSprites - Disentanglement testing Sprites dataset
This repository contains the dSprites dataset, used to assess the
disentanglement properties of unsupervised learning methods.
If you use this dataset in your work, please cite it as follows:
## Bibtex
```
@misc{dsprites17,
author = {Loic Matthey and Irina Higgin... |
c74403776fd636b37a1da056fa7d530cde6346edd4919acb72f957ca31c2814d | Text | 3,793 | 59 | Jellyfish
=========
Overview
--------
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory... |
5ecd0193d4bf12f0c0488ce86e15fd68481094797bf1865a4e73e1ee69f707f7 | Text | 3,803 | 130 | # rscvp
**Anterior and posterior retrosplenial cortex form distinct visuospatial circuits in the mouse**
Yu-Ting Wei et al., 2026. *Nature Communications*
[](https://doi.org/10.5281/zenodo.18234117)
## Overview
This repository contains the complete analysis pipeline fo... |
020717014e862eeb164aa39f6b3522f54d0ac3c4436e647f0a8dff1e1f5ace04 | Text | 3,826 | 29 | # Human electromagnetic and haemodynamic networks systematically converge in unimodal cortex and diverge in transmodal cortex
This repository contains processing scripts and data in support of the paper:
Shafiei, G., Baillet, S., & Misic, B. (2022). Human electromagnetic and haemodynamic networks systematically conver... |
e6a3cd48d5f81daa1e17f2c2c6a8f40ef4c6c7f186f38e3e47ad3061c12cde64 | Text | 3,837 | 87 | # CHyMErA-seq Analysis
This repository provides comprehensive code and resources for the analysis of CHyMErA-seq data, including data processing pipelines and Jupyter notebooks that reproduce the analyses presented in the CHyMErA-seq manuscript (Dupas et al., 2025).
## Overview
CHyMErA-seq is a pooled CRISPR screeni... |
034140679d68f51623470bf0bd128197ea7084dc31f5f0fd4d59d1ab432515d7 | Text | 3,849 | 34 | # TIMBRE
### ***T***racking ***I***nformative ***M***ultivariate ***B***rain ***R***hythms ***E***fficiently
<img src="Block%20Diagram.svg" width="500" alt="TIMBRE Block Diagram">
TIMBRE is a complex-valued neural network that can recover patterns from multi-channel oscillations carrying information about a variable o... |
ae5f31e259e2fdd98f20ea7533419edf1a3610c777e15c4a3e5f3dc577ce10ba | Text | 3,853 | 119 | <img src="assets/logo.png" width="320" alt="NTAC logo" />
<br>
This is a Python implementation of the Neuronal typing algorithm described in
[Gregory Schwartzman, Ben Jourdan, David García-Soriano, Arie Matsliah. NTAC: Neuronal Type Assignment from Connectivity. Nature Communications 17, 1284 (2026)](https://doi.org... |
76df1722c7fc7496f4100b6e96b9a1d94e5971d3d4b35488c786d9c218e44ed2 | Text | 3,858 | 99 | # UNRAVEL - UtiliziNg tRActography to uncoVEr muLti-fixel microstructure
<p align="center">
<img src="https://github.com/DelinteNicolas/UNRAVEL/assets/70629561/636f7cfa-8718-496c-ab61-7a86b37d774e" width="600" />
</p>
Welcome to the UNRAVEL's Github repository!
[ combined with cognitive training** on cognitive... |
e0b2ae6cd4d5b3d9665b7c2bdbfc10ae3fc611ce37be08a47533bd9705b6474a | Text | 3,871 | 40 | # EFMT_Review
This repository accompanies the manuscript 'Do you match what I match? A systematic review of over 20 years of the emotional face matching task reveals vast inconsistencies in design and implementation.', by Savage and Schlüter
Code to run the analysis and generate the plots in the manuscript are includ... |
9dd8ff39dd43144fa36e626eaf51222854e8e6c5dd597e80ca40cd90c5835db9 | Text | 3,881 | 39 | # DeepISO
<p align="center">
<img src="https://github.com/user-attachments/assets/c8ebddb7-429a-4a55-9d83-76a65b56e8b7" alt="模型架构图3个" width="60%" />
</p>
DeepISO utilizes both sequence and structural information to predict interactions between protein isoforms. To capture the structural information of interacting i... |
6103c6285b8af6b3273a559d4928ce0b9419f783d3174289902311c9468c9e85 | Text | 3,890 | 83 | # BioPathNet: Link Prediction for Biomedical Knowledge Graphs #
This is the official codebase of the paper [Enhancing link prediction in biomedical knowledge graphs with BioPathNet](https://doi.org/10.1038/s41551-025-01598-z) published in Nature Biomedical Engineering.
[]... |
e76396a4e30ac5065f365b66734ac041809b8cb093a093272b3f5f367982b4d8 | Text | 3,890 | 94 | # OptimalBattery
The OptimalBattery project implements the analyses underlying the paper **"Multi-Task Batteries for Precision Functional Mapping"** by Arafat, Nettekoven, Xiang & Diedrichsen (2026).
## Dependencies
**Diedrichsen Lab packages:**
- [Diedrichsenlab/Functional_Fusion](https://github.com/DiedrichsenLab/... |
ca443071a3140ed553a3717add915d570570eee3836eacd578bae2593e1e3940 | Text | 3,897 | 77 | FOCUS (DEPRECATED)
==================
!!! This repository contains the original code and instructions for FOCUS. Please find the updated and maintained repository
[HERE](http://www.github.com/mancusolab/ma-focus) !!!
------------------
FOCUS (Fine-mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wid... |
2741c254353938e9e817800cefa5dbf8fc5b5dafb19cbf34a29c8fe3cc8b781b | Text | 3,912 | 106 |
# speckle
<!-- badges: start -->
<!-- badges: end -->
## Citation
The propeller method has now been accepted for publicaton in *Bioinformatics*.
Please use the following citation when using propeller: \
Belinda Phipson, Choon Boon Sim, Enzo R Porrello, Alex W Hewitt, Joseph Powell, Alicia Oshlack, propeller: testin... |
5a8c1213d6c15767bc16aaabbcd69f9531717fdec689d29a1023885bf0eb3c24 | Text | 3,913 | 70 | # Convolutional neural network models describe the encoding subspace of local circuits in auditory cortex
This repository contains data and example scripts for analysis from Wingert, JC, Parida, S, Norman-Haignere, SV, David, SV. (2026)
Convolutional neural network models describe the encoding subspace of local circu... |
a265bf51c4ac85357997db52ff06ea49aba09cb5bfc9b2548e688bc9b80ea014 | Text | 3,915 | 55 | FmriTools
===
[](https://github.com/haenelt/FmriTools)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://zenodo.org/doi/10.5281/zenodo.10573041)
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.