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189f6192bdaeecb5cc0e276ed9446ea9b9fdef24fd064b293c1e5d1bb80bf4d1 | Text | 473 | 4 | # umcuEpi_ioECoG_SpectralEntropy
This code contains the script to calculate spectral entropy in different frequency bands on 2s-epochs of intraoperative electrocorticography (ioECoG). This code is used by Schaft et al. (2026) - Spectral entropy variability of intra-operative electrocorticography predicts outcome after ... |
0078f19e0af3c6012ce6bbb87d052fe638c7522db392dffaca0d008a916f5d74 | Text | 485 | 22 | # Space Mice Small Non-Coding RNA Analysis - Figures
Reproducible plotting scripts for all figures in the Space Mice SNC RNA manuscript.
## Quick Start
Part 1:
Run snakemake Pipeline:
```bash
# Stage 1: Run Snakemake pipeline
snakemake --snakefile results_generation.snakefile --cores 4
```
Part 2:
Run Rscripts:
... |
78efd40acb6490721f010a96916dcc770a431f374b869272ffb05be6b7a2de22 | Text | 488 | 3 | Code for the CellChat and LIANA signalling analysis of the developing dopaminergic niche accompanying the paper "Midbrain Dopaminergic Neuron Development is Regulated by Two Molecularly Distinct Subtypes of Radial Glia Cells"
Additional data files needed to replicate the analyses in the paper (notebooks in this repo):... |
f5fc4707661ba3f70a7eb7a7296e0d7af39b049d9948974fe702147d569673e9 | Text | 496 | 8 | # GeneTissueSpe
Source code of the shiny application available at : http://nathanprovin.shinyapps.io/GeneTissueSpe/
Implements the SPM/CTM/Ib scores as well as the Tau index to measure the level of tissue-specific expression of a given list of genes.
Results are displayed through histograms to show tissue specificit... |
d539c5de321100c9a04b7c3776e3d9ac20b5adcd1162f8d53586e2ee70417558 | Text | 501 | 5 | This is the analysis code for the paper "An Open fMRI Resource for Studying Human Brain Function and Covert Consciousness Under Anesthesia" by Zirui Huang, Vijay Tarnal, Panagiotis Fotiadis, Phillip E. Vlisides, Ellen L. Janke, Michael Puglia, Amy M. McKinney, Hyunwoo Jang, Rui Dai, Paul Picton, George A. Mashour & Ant... |
0203c3aa84b6566889709cd4a2b5fc99d2380ed17e27ce2e3eda80eef51c9075 | Text | 503 | 4 | # FXS-alpha
Repository for the code used in "A human electrophysiological signature of Fragile X pathophysiology is shared in V1 of Fmr1-/y mice." The code generates an improved 1/f fit of power spectra from human and mouse EEG/LFP data to isolate periodic signals and show conserved disruptions of alpha oscillations (i... |
826c51e6a68a242b3ab3d3d0d7e8ec61243fff8bb3dbdff31ecec7b29a9b9f41 | Text | 504 | 4 | # huah
This repository contains the code used to generate the data presented in Figure 7 of the manuscript of Glovaci, Vervaeke, & Hu, which is currently under consideration for publication in Nature Communications. Simulations were performed using Neuron 8.0–8.2 running on a high-performance computing cluster under a ... |
e0c49555ee81be1ccd49cecbbb525348a59cbe32bf617d8c435ce19ba4126a9a | Text | 540 | 13 | This repository contains the neural/behavioral data for the paper:
"Sharpened visual memory representations are reflected in inferotemporal
cortex" (published in J Neuroscience).
Contains the finalized processed data files as well as all the code
that generates the figures for the paper.
Analyses and plotting funct... |
1ef7d278fdec6cbf847678355c7501bb24f29a3a3e1ea383a7010db0b03fda99 | Text | 541 | 17 | ## Convert t-types to me-types
Download t-types.nrrd (if necessary)
```bash
sh dl_t_type_nrrd.sh
```
Run on BB5
```bash
sbatch process_t_types_job.sh
```
it will call the convert_t_type_nrrds_to_me_type_nrrds.py python script
The development of this software was supported by funding to the Blue Br... |
a95f5999f00a4f3e0d4f5c85a4e0c818830b925f31546a00a959a7ebb0461055 | Text | 555 | 10 | # 🔥 **FIRE**: <ins>F</ins>iber-seq <ins>I</ins>nferred <ins>R</ins>egulatory <ins>E</ins>lements
[](https://zenodo.org/doi/10.5281/zenodo.10023811)
[](https://github.com/mrvollger/FIRE/actions)
A S... |
82120ec3cff7556db88a9825deccd788efabfdaf6516d8729927b1fa1bc35f31 | Text | 557 | 15 | This repository contains all the codes required to reproduce the results of _van den Ende & Ampuero_ for the analysis of the PoroTomo experiment (phase II). Run `prepare_data.ipynb` to download and prepare the data (once). After that, the other notebooks in this repository are used to analyse and visualise the data for... |
2e70e65ededa6cd917e1f8af22e56e754c09132cfd597ec4b3e0211ccc9612e8 | Text | 565 | 24 | # MyelinAge
Model to predict the myelin age in infant MRI images.
This is the code for the paper: https://pubs.rsna.org/doi/10.1148/ryai.220292
The training data can be found here: https://doi.org/10.5281/zenodo.6556134
Install dependencies:
* Docker (needed for brain extraction with `freesurfer/synthstrip:latest`... |
e9f8caf5d4564ef08ca65a45dabd4fda874b7b42344125db35f2faa1b8e78e76 | Text | 572 | 24 |
Hybrid SCNN–OeSNN–ELM MATLAB Implementation
This package provides a modular reference implementation of the proposed framework:
Spiking CNN + OeSNN-UAD + Extreme Learning Machine.
Contents:
- Data preprocessing (normalization + GRF)
- Spiking convolutional layers
- OeSNN-UAD reservoir evolution
- Analytical ELM opti... |
f7ef4eb66a5dbc34a30470584f36dfbb54dc3819355b4a61c081915569be63ce | Text | 581 | 29 | # ``BrainTrace`` experiments on spiking neural networks
See [braintrace](https://github.com/chaobrain/braintrace) repository for more details.
## Requirements
```bash
pip install BrainX[cuda12]
pip install BrainX[cuda13]
pip install tonic
pip install h5py matplotlib msgpack prettytable numpy -U
pip install tor... |
38e8e7704f3a7493b6080fd8f26d5b02514fdce4558478982262d4f5bcbb5fe7 | Text | 586 | 14 | # AUD_microstructure
[](https://doi.org/10.5281/zenodo.15438434)
A repository for the creation of figures and plots for an AUD population study.
## Downloading
The code is in P... |
91d93072fd6faa4810a2c12699ff8da1eece5ca8f10972d3c38e8e5b21773ca7 | Text | 587 | 5 | # Predicting cell-type-specific PSI values
This GitHub repository can be used to reproduce the results to predict cell-type-specific PSI values using long-read single-cell sequencing data. Information on how to train linear regression (LR) and deep learning (DL) models can be found in the corresponding folders. How to... |
76e75cc7379391ec13d895507d1b8a5445f54609edb084ee4edb07c9d7c68d3b | Text | 598 | 6 | # Distinct roles of cortical layer 5 subtypes in associative learning
This repository contains the code for the 'Distinct roles of cortical layer 5 subtypes in associative learning' submission.
The `ValueBased_model` directory contains all the files to train the value network on the cue reward association task. This ... |
8c8e269d10c7c9180ca0b278936707bfa7f11389743383aa8f5009495a0ab6c2 | Text | 615 | 8 | # l6cthns
Custom-written analyses for Gutman-Wei et al., 2025
# License
Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 [CC BY-NC-ND 4.0]
# Description
RunTracingAnalysis.m lets the user set the input files and metadata for axon and dendrite tracing in .swc file format, with an additional rightmost... |
691f252906f4a1716c0fa37957b71fc60647d3bfbde8a7a84bb5a2a254258f8e | Text | 621 | 21 | # EulerGPU
Pytorch-based implementation of Euler registration using GPU acceleration.
## Installation
To install, simply clone this package and then install with `pip`:
```
git clone git@github.com:flavell-lab/euler_gpu.git
cd euler_gpu
pip install .
```
## Citation
If you are using this code, please cite this art... |
61894cf17954fcf3f0afba28220ce368b475c4c3233dabc514c34327f0d29ef8 | Text | 641 | 7 | The repository hosts the code and analysis for the paper **"In silico model of basal ganglia Deep Brain Stimulation in Parkinson’s Disease captures range of effective parameters for pathological beta power suppression"**.
The code for simulation of the BG model is written in Python and uses ANNarchy library which is a... |
46d32909b303db852ffc0cd5d550e64455b8324d7d37de435521f73e610ad5c3 | Text | 643 | 8 | # AggregateStats
The Fiji macro SeriesThunderstorm.ijm provides batch processing of (STED) images using the Fiji plugin Thundestorm [1].
The Matlab script AnalyzeThunderstormFiles.m reanalyzes the 2D Gaussian fitting to allow anisotropic tau aggregate shapes. It also performs statistical analysis of location and shap... |
a962398917a3c1b785440e270c402d640e431c8feb047e38ab4d2f2cbf6be68a | Text | 648 | 7 | This is the anonymized data, analysis, and plot scripts used for the study entitled
"Localization of free-field sound sources in the chronic phase of mild ischemic stroke"
by Mathias Dietz, Anna Dietze, Peter Sörös, Karsten Witt, and Henri Pöntynen.
The study is conditionally accepted for publication in Trends in He... |
68955283bb624a907536b2d85784b9677262132c62f207369385e41bdc243526 | Text | 652 | 7 | # R-scripts-for-small-intestinal-enteric-glia-analysis-Muppirala-et-al.-2025
Code generated to analyze bulk sequencing data and single cell sequencing data present in the manuscript "Tachykinin signaling defines distinct populations of glia in the enteric nervous system"
There are three separate sequencing scripts:
1) ... |
2c7d99eb852f3807e75a314daaec71171bd8c315be2c87f032562f4a002ea2af | Text | 657 | 13 | ## stretchable_conductor
Codes for "Machine Intelligence-Accelerated Design of Conductive Interlayers for Ultrastretchable Electrodes with Strain-Insensitive Performance".
### Notebooks:
- ```design_boundary.ipynb```: Feasibility design boundary
- ```data_augmentation.ipynb```: Data augmentation for model training
... |
5400edd9e117bd7750bc5dddf25e58c7f880d1fdb0bbe80675235d73a8cc678a | Text | 665 | 9 | # Code_AD_simulations
In this Repo you can find a code for simulating brain signals from a mean-field model of the cortex.
The model is set to simulate activity in various stages of Alzheimer disease.
There are some rudimentary analytic tools to investigate functional connectivity and power spectra distribution of si... |
fd5ffccbdf8d112fe824c95ad318b78c5d08e6abf38d2b240e398bf7b06048cf | Text | 670 | 11 |
# Decoding intended speech with an intracortical brain-computer interface in a person with longstanding anarthria and locked-in syndrome
Justin J. Jude, Stephanie Haro, Hadar Levi-Aharoni, Hiroaki Hashimoto, Alexander J. Acosta, Nicholas S. Card, Maitreyee Wairagkar, David M. Brandman, Sergey D. Stavisky, Sydney S. Ca... |
96db9c877684997df11a5dc80abb8a3cf707b8adbb713186a5eb4055f64fa041 | Text | 675 | 15 | Integrative analyses of single-cell transcriptome and immune profiling reveal clonal expansion of T cells in the blood and cerebrospinal fluid of Parkinson’s disease.
1. counts.rds
A unique molecular identified (UMI) count matrix.
The values in this matrix represent the number of molecules for each gene (row) tha... |
63e5230ef646571b55047bb1739090afea04fa4aab7accc2d29bde12fc26fcae | Text | 684 | 9 | # Guide for NovaScope Exemplary Downstream Analysis (NEDA)
This is an exemplary downstream analysis for Spatial Transcriptomics data from [NovaScope](https://github.com/seqscope/NovaScope/tree/main).
Please see detailed guidance at https://seqscope.github.io/NovaScope-exemplary-downstream-analysis.
Reference: Kim, ... |
2f65f3e5a2469a2693dfe6de3f6826f7b72e7aee945aa5f5fbe323e4552a79e8 | Text | 685 | 5 | # A novel cis-element enabled bacterial uptake by plant cells
## Publication
<div>Cathebras et al. 2026 Nat Plants https://doi.org/10.1038/s41477-025-02161-z</div><div><br></div><div>Authors: Chloé Cathebras 1, Xiaoyun Gong 1, Rosa E. Andrade 1, Ksenia Vondenhoff 1, Jean Keller 2, Pierre-Marc Delaux 2, Makoto Hayashi... |
239b1bb9396215098ade7581f0e191d731d33e5134c529a209f45cf3700b2ad0 | Text | 688 | 29 | # DVDSA
Python Code for Deep Learning Analysis of Voice Biomarkers for Treatment Response in Adolescent Major Depressive Disorder (Communications Medicine)
## Statistical Analysis
Analyze the acoustic characteristic with:
```
$ python feature_analysis.py
```
## Binary Classification with Machine Learning Models
T... |
94c611a204436e704349961dee46b860842126079e8099e2851f1cccd19e29a1 | Text | 689 | 15 | # monolayers
## Description
Repository for **"Physically-informed machine learning framework enabling accelerated screening of high-refractive index 2D materials"** article.
Here we provide trained models, subsets of data and inference script. Training scripts and full datasets are available upon reasonable request t... |
34d9cc06453fc1b39bbb473e587636f0c7a662ae107d37836885c631ab0ba705 | Text | 692 | 17 | # olfactory-ec
Code for Fernández del Castillo et al., "Convergent motifs of early olfactory processing are recapitulated by layer-wise efficient coding".
For details, please see [our paper](https://www.pnas.org/doi/10.1073/pnas.2524661123), for which the BibTeX is below:
```
@article{fernandezdelcastillo2026converg... |
2706cf8f0d93546ee3bb860a12e2ba2a5e94ceccbd55084d91f98b5d643f0692 | Text | 694 | 16 | # Increased baseline pupil size enhances uncertainty avoidance in decision making.
Behavioural and pupillometry analysis of Kakaei et.al. 2025.
## Citing ##
Kakaei E., Schlecht A., Hauser T.U. (2025) Increased baseline pupil size enhances uncertainty avoidance in decision making.*Under review*
## Requirements ##
- ... |
771c6e23d4beea6e18cf5430740b324d057ae793c58455c849394fceb1cd7b53 | Text | 700 | 13 | # BIDS_spm_preprocessing
Group SPM preprocessing script for longitudinal data in BIDS (Brain Imaging Data Structure)
Script and functions are prepared for preprocessing of fMRI data obtained for my research project:
"Temporal dynamics of functional connectivity changes induced by cognitive training",
in which parti... |
1fdadc732dd052d6de26fe63a562da14bfcbdeb60cf651e87f6ba9f96b31c466 | Text | 707 | 23 | ------------------------------------------------------------------------------------------------------
# SCILD: Advancing spatial cellular communication inference in spatial transcriptomics
## Authors
- yujiating@amss.ac.cn
- lywu@amss.ac.cn
- dcsun@sdu.edu.cn
---
## SCILDdocs
**SCILDdocs** contains the full docum... |
ef2082cf309c25a68b2cb48c68f9b8bd27e5ced95965f4d17d8b0404eb3fd627 | Text | 707 | 13 |
[](https://doi.org/10.5281/zenodo.18021731)
# Identification of Chlamydia pneumoniae and NLRP3 inflammasome activation in Alzheimer’s disease retina
This repository contains the code used for:
1) predicting pathological measures in the brain of subjects with varying lev... |
42224f6b4ab2f0c945c2f169b9a87c9b91cd45d1e91abc50b35887cc3896877b | Text | 716 | 14 | # functional_controllability
This toolkit is for computing the controllability measurements, minimum control energy, and kernel ridge prediction for behavior tasks.
## Test environment
1. Matlab 2018a
2. Python version 3.6.7
3. sklearn version 0.19.1
## minimum control energy
Use Energy Efficiency/pipelineCompareSta... |
ac5281b2f9ef90506f47ffac34ee0d49aa23fc3b837e1991a9e8980536427072 | Text | 719 | 10 | CMRR-MB
=======
Welcome to the support page for CMRR multi-band pulse sequences.
If you have noticed a bug or have a request for a new feature in a future release, please [open a new support request](https://github.com/eauerbach/CMRR-MB/issues). Be sure to include the sequence version number (e.g. VB17A R006a), seque... |
60d45d26c1ed7ad79ddc15668e5dc48baa2595e0b90a5541835ef3f3f620cc37 | Text | 728 | 31 | README for lmbench 2alpha8 net release.
To run the benchmark, you should be able to say:
cd src
make results
If you want to see how you did compared to the other system results
included here, say
make see
Be warned that many of these benchmarks are sensitive to other things
being run on the system, mainly from ... |
726a5e99fb80cfbdafa1b1927af871bd57e005fbfe3198e4cf4625572412e939 | Text | 731 | 15 | # ScalingSmoothing
Scripts to scale and smooth repli-seq data. Could probably be used with any chromatin profile data.
# Usage
Run this command for each or your log2 ratio bedGraph file:
`Rscript /path/to/scaling.R /path/to/Input_log2Ratio.bedGraph /path/to/Output_log2Ratio_scaled.bedGraph /path/to/Ouput_log2Ratio_sc... |
0e0c6f4e585ad1ff0e1735aa89cdbbff9152fd345e73c42eedad5bc619b72586 | Text | 735 | 14 | 
# Neural General Circulation Models for Weather and Climate
NeuralGCM is a Python library for building hybrid ML/physics atmospheric models
for weather and climate simulation.
- **[Paper](https://arxiv.org/abs/2311.07222)**
- ... |
bfd75733dc88d0e626358dd45a94806b36c8c473144763431cfc2075cac775f5 | Text | 743 | 25 | # NEOSTI - A Neuromorphic Electronic-Opto Spatial-Temporal Hybrid Image Sensor
This is a sample code for training NEOSTI model on a demo dataset, UnityEyes dataset.
## Requirements
* Python 3.7+
* numpy >= 1.21.0
* torch >= 1.1.0
* torchvision >= 0.3.0
* pillow >= 9.1.0
* scipy >= 1.3.0
## Instructions
1. Enter the ... |
b67251cd80a1cb358602c27fb4d0476802d9e86aea077be99ba1e2ecc490d375 | Text | 744 | 25 | # NEOSTI - A Neuromorphic Electronic-Opto Spatial-Temporal Hybrid Image Sensor
This is a sample code for training NEOSTI model on a demo dataset, UnityEyes dataset.
## Requirements
* Python 3.7+
* numpy >= 1.21.0
* torch >= 1.1.0
* torchvision >= 0.3.0
* pillow >= 9.1.0
* scipy >= 1.3.0
## Instructions
1. Enter the ... |
a7c1966424b2ea2bef8a14797b02ab555122ee1905fd5fd722028fdf98d1d115 | Text | 746 | 25 | # AlzheimerShortTermMemory
This repository contains analysis code for the study:
Li, Chia, Xu et al. Vulnerability of short-term memory in a mouse model of Alzheimer’s disease.
### Supporting code
This repository includes helper functions from https://github.com/joao-semedo/communication-subspace:
Semedo et al. (20... |
d26c7768a4b319065364f8f1d9508e23edd50347188fe6ebde0bd60cb5779fee | Text | 752 | 14 | # 2026_Fisher_et_al
#### Scripts for:<br/>
#### ASCL1 Promotes Nuclear Shrinkage in Transdifferentiation by Suppressing *NUP37*<br/>
DOI: 10.1016/j.stemcr.2026.102823 <br/>
<br/>
Authors:<br/>
Emily Fisher<sup>1,2</sup>, Zhongjiao Jiang<sup>1</sup>, Li Li<sup>1</sup>, Gaurav Chhetri<sup>1</sup>, Komal Saleem<sup>1</sup... |
cb44e3eb95a5cc7bacd7bf5632871d7f698561e6010160b4f3c77e9efd2f5f2d | Text | 753 | 19 | # CEST-fMRI
CEST-fMRI codes
including scripts processing experimental data, generating simulation data and display the cosrresponding results in main text.
gen_figures: including functions required for visualizing partial results.
scripts\processing: including the processing of experimental data and the presentation ... |
afd62d549f4f0936888872d9c7c4fd48efa51e54354ce85a7566beca258b1c4c | Text | 756 | 18 | 
RANGE is a model-agnostic framework that employs an attention-based aggregation-broadcast mechanism to significantly reduce oversquashing effects in message-passing neural networks.
## Prerequisites
It is recommended to install the `mlcg` package (version 0.1.0) in a clean environment by following... |
48f692fcfde47803ebb1f811f02c8cbbb62f47f6e9485539ee84145e38efbaab | Text | 763 | 29 | ### Run code: training, inference and figures
[Colab](https://colab.research.google.com/drive/1Z2KtSNWx9FxDrNDeLqsMihVGNMum059V?usp=sharing) with training example from scratch for Apis cerana.
[Colab](https://colab.research.google.com/drive/1h7yygrz1L0Sd3FlHMJREgv2B8cQIf-Wf?usp=sharing) with model for Homo sapiens - e... |
faf97bb824d8c1d049f975eee61af8514745497557f246dc6179964b1e2ab7b9 | Text | 766 | 20 | # SNARTomo
<img align="right" src="https://user-images.githubusercontent.com/12241752/222498175-f95029e1-5a6e-4a41-99e5-b035c480468b.png" />
SNARTomo is our set of scripts for on-the-fly tomographic reconstruction.
The name is derived from the programs that were originally run by it:
* **S** ee-tee-eff-find-four... |
adef8931c79b279ec773fc0415e9a96119f9656a8a6f5657647baae168b674e4 | Text | 768 | 11 | The enclosed .png files show single-cell isolations as described in the listed manuscript: https://doi.org/10.1101/2025.10.02.680067.
Background images are provided for HMC3 and microglia isolation experiments (Background_hmc3.png and Background_microglia.png). Please review these backgrounds to differentiate cells ... |
276832af44d7f6365596598ab84dd9950aad41956639c85689ae11347416860b | Text | 780 | 6 | ## Installation
This project uses the [uv](https://docs.astral.sh/uv/getting-started/installation/) python environment manager. The virtual environment will be created the first time you run `uv run script.py`.
## Mechanics-Based Model
The mechanics based model is contained in model_v7.py. This script is set up to run ... |
bd6abd773676462a13c308c9d9ebcaecfa7b40f4c436265541bf15b23993b62e | Text | 783 | 25 | # MoAGNN: Hierarchical Multi‑omics Graph Neural Network with SAGPooling
## 📦 Project Structure
```
save_graphs.py # Convert CSVs → PyG graphs (.pt)
data_load.py # 5-fold stratified split loader
networks.py # MoAGNN (GCN + SAGPool + MLP)
layers.py # SAGPool layer
main.py # Training & evalu... |
7c7c7cbd27556f82002a88f6f1b818332dd11507f54bf6ec84ba1b8c0d898c8a | Text | 784 | 10 | PGC3-BIP GWAS Summary Statistics - Oct 2019 Freeze
Filename: daner_bip_pgc3_nm.gz
Created by: Niamh Mullins niamh.mullins@mssm.edu
Description:
Meta-analysis of 41917 BIP cases, 371549 controls from 57 datasets.
Results in Ricopili daner format (for column description see: https://docs.google.com/document/d/1TWIhr8-q... |
96cafe7c069a8ce83b0123229dd8fee7af43e9aeb1d48de7a22eb8996b48f0e0 | Text | 787 | 11 | # Code and Data for "Autogenic spinal excitatory circuit ensures skilled hand movements in primates"
This repository contains the data and code associated with the manuscript by **Kim et al**., titled **“Autogenic spinal excitatory circuit ensures skilled hand movements in primates.”** (Manuscript currently under revie... |
67575c2731099bf9cdd029a62911501cbb5f08c2854dd7a520b51d9406eaf3c2 | Text | 796 | 13 | # Data-driven denoising in spinal cord fMRI with principal component analysis
[](https://github.com/BrightLab-ANVIL/spinalcompcor/blob/main/LICENSE)
<br>
----
### Guide to this repository:
There is one script, `SpinalCompCor.m`, that is used to perform PCA... |
46f316320b05998c0e551f9b5f7bb2cc9a123be0058e1522afe06e2d54bbe7bc | Text | 804 | 9 | [](https://pysinglecellnet.readthedocs.io/en/latest/?badge=latest)
# PySingleCellNet: a computational toolkit for the single cell analysis and comparison of embryos and embryo models
PySingleCellNet (PySCN) predicts the 'cel... |
ea981b8b304cfd31469d6c5ea6adbabed25c9c71dafc7c9fa625f3032aa8c4b3 | Text | 805 | 16 | Tractography issue demonstration
================================
This repository contains a series of Jupyter notebooks that demonstrate
multiple issues that can arise when dealing with tractography data.
- ``tracking_spatial_mismatch.ipynb``: Issues that arise when the wrong spatial
information is used when track... |
5e4d8d0089c7b77cfdeaaf5d6f83ce99543c461f31a1aff5f016ded2374d6b2a | Text | 810 | 16 | # Sleep-Alters-Neurovascular-and-Hydrodynamic-Coupling-in-the-Human-Brain
This repository contains script used in research article "Sleep Alters Neurovascular and Hydrodynamic Coupling in the Human Brain"
Currently available at Biorxiv: doi: https://doi.org/10.1101/2024.10.16.618430
The analysis requires following e... |
0848b40e3d1a6586ef947227f5c28b2786e61e8e03c1b35f73871d96ab5b4921 | Text | 812 | 33 | # Voxface
Fast voxelation of the face in 3D structural MRI data combining spline downsampling with nearest-neighbor upsampling to
deidentify the face while retaining some signal intensity to guide whole-head registration.
### Latest Version
2025.5.19
## Installation
### GitHub Installation
1. Clone this branch to y... |
28d9d877ff4c5772c49c2d698648fe59f5868c93951e6eb646287e1e6c7efa24 | Text | 826 | 17 | # Predicting scores from video
Pose estimation code adapted from: [Open MMLab: MMPose](https://github.com/open-mmlab/mmpose)
Feature computation code adapted from: [Chambers et al 2020](https://github.com/cchamber/Infant_movement_assessment)
Score prediction code adapted from: [auto-sklearn](https://github.com/aut... |
8b549eeb7102d9aa564226079daba2fea705de21a1e52469735c5d054f7eb819 | Text | 828 | 15 | # ReAlnet - Human EEG/fMRI-aligned Artifical Neural Network
Achieving more human brain-like vision via human EEG representational alignment
ReAl = Representational Alignment
Train the models - "Train_ReAlnet.ipynb"
Load the models - "Load_ReAlnet.ipynb"
Conduct RSA - "RSA.ipynb"
Download our model weights f... |
c158526371a55fb483d3a3b87a0114512fe92198a59f0d2d074f0c44433968d9 | Text | 829 | 18 | ## Repository Structure
**Data and analysis code for the study:**
*Rubber Voice Illusion exposed neural correlates of voice perception and vocal adaptation across the Continuum of Psychosis.*
### Folders and Contents
- `data/`
- `Dat0_Demo_SPQ_PDI.csv`: Demographic information, SPQ and PDI ratings
- `Dat1_il... |
7234892f15b9626e6a8ae3e972b771b88420f3bb53af8e8d6fa6f1ca0c5a0e44 | Text | 840 | 22 | # cerebellar-cortex
Specialized pipelines for the segmentation of cerebellar
surfaces at ultra-high resolution in-vivo and post-mortem
used in the article:
"Mesoscale imaging of the human cerebellum reveals
converging regional specialization of the morphology,
vascualture and cytoarchitecture.", N Priovoulos et al.,... |
7d46017a587d72cac6d8c51ce5952a75e8f867786d2f7ea595325b813eeaf007 | Text | 844 | 11 | # Energy Landscape Analysis Toolbox (ELAT) for MATLAB
## What is this repository?
Energy Landscape Analysis Toolbox (ELAT) provides functions necessary for the energy landscape analysis (Ezaki *et al.* *Phil. Trans. R. Soc. A* **375**: 20160287 (2017)). This software can be run on MATLAB2016 or later versions + MATLAB ... |
93922fb9c97752fefd6d34bde882f06c3ea7f1b3583dff14872df701eb7e1d39 | Text | 849 | 18 | [](https://doi.org/10.5281/zenodo.18459441)
RANGE is a model-agnostic framework that employs an attention-based aggregation-broadcast mechanism to significantly reduce oversquashing effects in message-passing neural networks.
## Prerequisites
It is re... |
77ce7f738128f2dfd30b7093538215fe643b4e46168424e3fa1db532011dd7a9 | Text | 853 | 11 | Code for generating the figures in the article **Auditory-motor surprisal reveals learning across multiple timescales during exploration and production.**
[Preprint link](https://www.biorxiv.org/content/10.64898/2026.03.23.712909v2)
The scripts used to produce the figures are located in ARTICLE_FIGS. Each script lists... |
4e7678d0719380c5b81d3e615c49834c7a35aabba5fce2aca58af0cf2668e67f | Text | 855 | 18 | # Longitudinal 7T MRS of Glutamate and GABA in Alzheimer’s Disease
This repository contains the analysis code supporting the manuscript:
Göschel et al., 2026, "Longitudinal 7T MRS Study of Glutamate and GABA Dynamics in Alzheimer's Disease Progression: From hyper- to hypoexcitation".
## Overview
We analyzed longitud... |
8a0922b62d64c945951686168b1de63e83d81c969dec23049854ec7822449fb9 | Text | 860 | 35 | # Annotation-Free Prediction of Immunotherapy Response in Melanoma Using Single-Cell Transcriptomic Data
This repository contains the code accompanying the article:
**Annotation-free prediction of immunotherapy response in melanoma using single-cell transcriptomic data**
Da Eun Oh, Gaeun Kee, Ji-Hye Oh, Wonkyung Ki... |
84bd519daddd7aa8d988bd332f5ce5bdfae8aa49e81e5a0e884c78f4deb8db7b | Text | 863 | 18 | # headstage_cap
The cap was designed with a smooth surface to avoid any accidental opening in the cage, and to maximise comfort.
3D printable files of the three component cap to protect the neural headstage.
<table>
<tr>
<td valign="top">
<img src="https://github.com/user-attachments/assets/b20b78c1-6d0f-4a... |
87a72bd2fa7270c133c734cb3d4c2401176c33a9ff880dacefd67e679ad8a50b | Text | 867 | 13 | # article-private-public
This repository contains anonymised data and code supporting:
<a href="https://elifesciences.org/articles/56477">Bang, Ershadmanesh, Nili & Fleming (2020) “Private-public mappings in human prefrontal cortex” eLife</a>
FigureX.m files will generate the requested plots and associated statisti... |
55ae3b67720be771760ffc5e822793bc1e08bdac89318177d1a2eb96fceea7a1 | Text | 871 | 7 | # Code for the 2025/2026 Protocol Update
This repository contains code examples corresponding from the paper [Protocol Update: The Normative Modelling Paradigm for Computational Psychiatry](https://www.biorxiv.org/content/10.64898/2026.02.17.706268.full).
The notebooks include the main normative modelling workflow, l... |
43308b1171f6cf45e344246aae98f897b62c39291ed0f5ab4f60013d9fdc0a90 | Text | 872 | 7 | # Kawanolab_CGMD_AMP
The MDP_files folder contains the mdp files used for energy minimization, equilibration, and production simulations.
The Martinize folder contains the ions.mdp file used for the genion step during initial structure preparation, the dat file used to specify peptide coordinates, and template topolo... |
e58fdd484d04524a53e801a666b94798de1b1923552a1cab3b2d9b24cc1fedbc | Text | 909 | 10 | # Zhu_V1_interlaminar-signal-flow
This repository contains the custom analysis functions supporting Zhu, Oh, Trepka, Chen & Moore, 2024 https://doi.org/10.7554/eLife.103255.
./Figure 2/bo_modulation_index.m plot boder ownership modulation index, for each recording session, the histogram and scatter plot of individual ... |
353db17510a9237b3c4cce8cb325cb6385fddbf1d1b52acb42abb534d7460988 | Text | 912 | 33 | # Greeble_PyGame_fMRI_task & customized analysis codes
Related to paper entitled "Spatially Periodic Computation in the Entorhinal-Hippocampal Circuit During Navigation"
## Paper Link: <br />
https://elifesciences.org/reviewed-preprints/107517
## Python environment: <br />
Python `3.9` <br />
PyGame `2.6.1` <br />
P... |
39f9e87d677eda6f2836e08fcc3f8a1931ef7b4f3b091587ec7ccfa1ad8de66c | Text | 914 | 24 | All datasets used in IGPose
https://academic.oup.com/bioinformatics/article/42/3/btag076/8487143
Please check detailed statistics information in the paper.
In csv files, you will find folders corresponding to specific subsets by removing "_fullgraph" from the folder names.
For more information, please contact the au... |
31b2b7150e39a916d89c906a69e97deda1e2a32b2503d07a55da10055b4c7ecc | Text | 919 | 22 | Individality transfer across tasks
# MDP task
- show_res_mdp.py: reproduce figures in our manuscript
- n_choice_markov: functions for the task
- load_bhv.py: organize recorded data
- bhv_mdp/: recorded data
- train_it_mdp.py: train an encoder-decoder model
- show_it_mdp.py: evaluate a trained encoder-decoder model
- e... |
ff502a5d22ccf0d314d6323e143a1a9bc642cc286f9d5e50df977d27331aac6d | Text | 923 | 12 | # ZebrafishHMM2023
Julia source code accopmanying the paper:
*Mattéo Dommanget-Kott, Jorge Fernandez-De-Cossio-Diaz, Monica Coraggioso, Volker Bormuth, Rémi Monasson, Georges Debrégeas, and Simona Cocco*. ‘**Linking brain and behavior states in zebrafish larvae locomotion using Hidden1 Markov Model**’, Octobre 2024. ... |
b414e599739e235e66a39b050e546fcc0da1e8119330ca40bac2c9965ca288a1 | Text | 926 | 11 | # eveGNN
eveGNN contains all the functions and scripts used throughout the formation of the paper "Parameter Estimation from Phylogenetic Trees Using Neural Networks and Ensemble Learning", Systematic Biology (2025), DOI: 10.1093/sysbio/syaf060
It serves as an archive of our entire exploratory codebase during the past... |
52f2b5f0da0e3f97f38a4049ca1edaf97938dd015eafb38ebd78752aee6cd708 | Text | 927 | 20 | Title: Example scripts used for figure generation
Authors: Matmat and al, 2025
Corresponding author: Karim Matmat matmat@unistra.fr
Description:
This repository contains example R scripts illustrating the types of
analyses and visualisations used in the study. These scripts use fully
simulated datasets and do n... |
55139dfe5b49f56f3605c14255a42f47367c47d7752f7a3149ebd0f1ae8a595e | Text | 927 | 39 | # organelle_transport_analysis
Package for running organelle transport analysis
Requires Python >=3.8
## Installation
Either use `.py` files from `/src/organelle_transport_analysis` directly or install as a local package.
To install as a package, run the following in this directory:
`python -m pip install -e .`
o... |
4302fd82d8a7a911765de682ab50af51eb73b8f1102de7096dc1a32013ed82de | Text | 929 | 12 | # Analysis pipelines for the [GTEx Consortium](https://www.gtexportal.org) and [TOPMed](https://www.nhlbi.nih.gov/science/trans-omics-precision-medicine-topmed-program)
This repository contains analysis pipelines for:
* RNA-seq alignment, quantification, and quality control
* eQTL mapping and annotation
* Allele-spec... |
ab105dbc74393838e108ef76a669e3f365dfc6f67a1bc8025046781bd60ab313 | Text | 931 | 20 |
# Multi-Omics Factor Analysis
<!-- badges: start -->
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/MOFA2)
[](https://bioconductor.org/packages/rele... |
47fd0c0095332be2b538cabf99a61bdcec6b1aaf5cad5fe0c3d66ad0979e161d | Text | 934 | 60 | # MSAT
AClinically Aligned Heterogeneous Graph Learning Framework for Predicting
Adverse Drug Reactions Induced by Chinese Materia Medica
---
## Requirements
```bash
pip install -r requirements.txt
```
Required packages:
- PyTorch >= 1.10
- PyTorch Geometric >= 2.0
- NumPy
- Scikit-learn
- SciPy
---
## File Str... |
cf68e65aebed329a68bde2a97d195434298a637c7bc44fd9c00058cd5f40cd4c | Text | 947 | 8 | # PermCCA
This repository contains a reference implementation for statistically valid permutation tests with canonical correlation analysis.
The paper reference is:
* Winkler AM, Renaud O, Smith SM, Nichols TE. [**Permutation Inference for Canonical Correlation Analysis**](https://doi.org/10.1016/j.neuroimage.2020.11... |
14873c88b6b839b0efd3b0f2bc2147e18d8779687e5bd2d12b3e9b589cca8138 | Text | 952 | 22 | # 2P-FENDO_Toolbox
## Project:
2P-FENDO-II is a fiber bundle based 2 photon miscroscope for all-optical investigation of neuronal functions in the brain of freely-moving mice.
The provided material, although conceived and applicable under a specific hardware configuration, could be easily adapted onto a regular 2 p... |
c7ad30277e10c6de1776c104109bf4588267b4b163a9292307a8182719b3878d | Text | 964 | 33 | # This Repository contains the code to locally run **AxoMetric**
# Order of events needed to run application
## UI.R
This file will create the user interface of the shiny application.
## server.R
This file will create the server of the shiny application.
## main.R
This file will source the user interface and ser... |
772b9b4dad8caf8c105cdcbff13a53714e557ef8af04b67dbd7e9960c6dbe4fd | Text | 968 | 12 | # ChannelDensIGE
Code in support of the work by Stier, C., Loose, M., Loew, C., Segovia-Oropeza, M., Baek, S., Lerche, H., & Focke, N. K. (2026). Comprehensive evaluation of EEG spatial sampling, head modeling, and parcellation effects on network alterations in idiopathic generalized epilepsy. Brain Communications, fc... |
2453ca42071b2b9411c1dad4a60a1203a8257eb8ad90369d5e4283b3008fa734 | Text | 977 | 27 | Matlab code was written and tested on version 2024a
running on Microsoft Windows 11 Pro.
Python code was written and tested on Conda version 25.11.1 running Python version 3.13.11
Files should be added to a single folder.
No install time is required.
Simple examples of networks include:
Model Manuscrip... |
de245fbf59513f694df2ad8413fe890ec5dc4f9d51db2684b091baf98b35ea2e | Text | 977 | 23 | # Lasso-ML: Machine Learning Code for Stroke Study
## Overview
This repository contains machine learning code focused on a stroke study using Lasso regression techniques. It includes data preprocessing, model training, cross-validation, and statistical analysis.
## Contents
- `externalTest.ipynb`: Code for exte... |
e380c826527b3b514ef29e677a11aaa856c3621821c118586e98ace147aa8abb | Text | 982 | 41 | # spatula : A C++ toolkit for spatial transcriptomics
## Overview
`spatula` is a collection of C++ tools that are designed to help analyze
sub-micron resolution
spatial transcriptomics data such as Seq-Scope.
These tools are under active development, so they may change frequently.
## Documentation
A detailed d... |
1d390049334bfdf0e507fa7fd81fc8f9279b6a64f1fc77c4b1f8d381313acba2 | Text | 994 | 17 | # Joystick
<p align="center">
<img src = "https://github.com/YttriLab/Joystick/blob/master/Demo/JSGithubDemo.gif">
</p>
<p style="text-align:center;">
The above mouse is performing a self-paced center out joystick task for a fluid reward. Following a successful reach, there is a delay to reward followed by fluid de... |
8ad77d04c6bc33da43afb5e021d091db89ae4d99388e2382b000cb46a18cc0ff | Text | 995 | 18 | # Mouse SC orientation selectivity model simulations
Code associated with the study: Shared computational principles for mouse superior colliculus and primate population orientation selectivity
### Usage:
Run each of the functions in the directory "figsNoGUI" to generate the population plots in the desired figure. \... |
745abcd44481a0e81561b7970fdf542afe6a53fce6e2820bde461d559e98badd | Text | 998 | 12 | This small folder contains three pretrained model weights as pth files.
They represent the models used in the research article "Explainable Machine Learning for Tower-Radar Monitoring of Wind Turbine Blades: Fine-Grained Blade Recognition Under Changing Operational Conditions" published in MDPI Sensors.
All three mod... |
546491d81e89f3040a242665433da549dc8114e9fc6915ee44be71934e00356e | Text | 999 | 21 | # SpikeImagingAnalysis
Software to analyze single color, dual-color and dual-polarity in vivo spike imaging.
Run `installSIA.m` to install all relevant folders for a functionnal package.
All functions exist independently and have clear input - output definitions.
# Branches
- master - currently working versi... |
528f7c23f282cd05bd930cc7d5a8944395399e2f2a7084267bf074635972f8f0 | Text | 1,006 | 16 | # Rule_based_xDFAI
## Important note:
Set the required initial values based on your model.
For example: the number of classes, class names, paths, number of layers, and layer names.
## To run the framework on your model, follow the steps:
1- Important features are extracted by Imf_Extraction.py.<br />
2- Traces and t... |
0522dc0efbd7dc19a00adcf673535438efd98122bf9bb13f1bb23d429b5a6cbe | Text | 1,015 | 47 | # Project README
## Environment Setup
Please follow these steps to set up the required environment:
1. **Install according to the Nerfstudio installation guide.**
- Refer to the [Nerfstudio Installation Documentation] for detailed installation steps.
## Data Preparation
Our dataset is located at:
```
sparse_ri... |
69e5fc47744041b7f5921dfccadd328f4cab0aed88e356d95f92154fc2c0a723 | Text | 1,026 | 26 | Post-Processing and Analysis Pipeline for VTK Simulation Results
This repository contains a collection of Python scripts for post-processing, statistical analysis, and visualization of 3D finite-element simulation results stored in VTK formats (.vtk, .vtu, .pvd).
The workflow is primarily designed for brain deformatio... |
4202e81e3398f30662c013aabb42ffb573d37155abdfa25b19ae925c029d850c | Text | 1,036 | 19 | # PROJ-Multiome-EPN-ZR
This repository contains analysis scripts for the integrated snMultiome analyses used in “Dominant clones leverage developmental epigenomic states to drive ependymoma”, [_Nature_ (2026)](https://www.nature.com/articles/s41586-026-10270-8).
<br/>
## Data availability
Raw and processed snMultiome... |
4f742d7f99c08e60bbebcce31aac2285dbc09a05b318254c08c47c94cdd9837f | Text | 1,036 | 39 | # High-throughput-Birds-Vocal-Analysis
<p align="center"><img src="https://github.com/MizukiFujibayashi/High-throughput-Birds-Vocal-Analysis/blob/main/SAIBS_SAT_PCA_v2.png" alt="Figure" width="700"></p>
Now published in : (BioRxiv) https://doi.org/10.1101/2025.05.02.651591
## About
High-throughput software for an... |
b4ab5e1a449a015b707dd9e85390c36f2a08d5455dd9d400d47fe916257bfb4e | Text | 1,039 | 37 |
This repository contains the code and analysis for our study on:
📄 **Pluripotent Stem Cell Plasticity is Fine-Tuned by a Slit-Independent Robo Pathway in a Regenerative Animal**
🧬 Kuang-Tse Wang, Yu-Chia Chen, Fu-Yu Tsai, Catherine P Judy, Carolyn E Adler
---
## 📁 Repository Structure
| Folder ... |
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