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8311f7f86ad6517ae2b998be354702874cd2afeb3320415eba09cc9a3d92677c | Text | 190 | 2 | # progression_to_MCI
This repository included the scripts and code used in our publication: "Prediction of mild cognitive impairment progression using time-sensitive multimodal biomarkers"
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8faf463478f3fcef6c70502d57bd3545fa0a42b30cca632a821b6b86f902854c | Text | 192 | 2 | # NeuralMarkerPain
The codes used in the paper 'Accurate and Efficient Prediction of Pain: A Comparative Electroencephalography Study of Functional Connectivity and Cross-Frequency Coupling'.
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b943af68c8e6cb80c0f3290a5c1763c3ebb542028f6859ee771d3d0f1eef85b1 | Text | 214 | 1 | This repository includes the code used for the analysis in the publication titled "Notch mediated lateral inhibition is shaped by morphological differences that bias cells toward signal-sending or receiving roles"
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55546685e5aed3a12238d05c14a16367910696f25f4b8d9a5d542d48360c537e | Text | 229 | 8 | # unirna-tools
A universal toolkit for RNA structure and function
## Installation
```bash
cd ./unirna-tools/src/mse && wget http://contra.stanford.edu/contrafold/contrafold_v2_02.tar.gz && tar -zxvf contrafold_v2_02.tar.gz
```
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b55179fb3fa1f352bb9ef40ae2c634b4def5be3bdcefe6ad924568c53cb343f0 | Text | 239 | 2 | This code implements the model of distinct egocentric spatials in retrosplenial cortex and postrhinal cortex.
Datasets used to train the model and Results generated by the model is available at https://doi.org/10.6084/m9.figshare.32446644
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60e98b6da7490bb045569434f7ce047cdad3c9ea83d30504b9006a177f41cc62 | Text | 281 | 13 | # Simulation_SpineAlterationFocalCorticalDysplasia
tested on Ubuntu (in parallels)
need NEURON simulator [this](https://www.neuron.yale.edu/neuron/),
recommend to use Anaconda [this](https://www.anaconda.com)
## about spine modeling
see the [figure](figure_for_spines.png)
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53fd5bd5cae87718d21b394d74b7e300cef2e27c7226c56b2104b87bda6d147a | Text | 283 | 5 | # GD-Ls
Code for GD-Ls analysis of human cortical layer parcellation using Stereo-seq data.
Open the .ipynb notebooks and run the cells in order.
Some notebooks contain R code, others contain Python code.
Required R and Python packages are listed in the comments of each notebook.
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31e742da44c16cd17b20514e01f509f2430d1dff8f21089394d764fe4c100a1a | Text | 289 | 4 | # Anahí Binagui-Casas et al., 2026
Contains source code for data analysis shown in Binagui-Casas-et-al.-2026.
If you want to run the notebook please note it uses Python 3.12.3 and the libraries numpy, scipy, matplotlib, pandas, sklearn, random, seaborn, math, warnings, pylab and copy.
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3c7e9e76a31240bc6e4967f247fee30f614c1e9654876f4b19f76422e6e9ff95 | Text | 297 | 5 | Code base for the manuscript "Synthetic Alzheimer’s disease dataset generation and evaluation with privacy protection".
pyhton code was used for synthetic data generation and utility and privacy evaluation
R code was used for creating the real datasets, and generating the plots of the paper.
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da56b95d8217729fc0e65e14c9d20a113f7020a7fe774d1882c4526c4c50b69d | Text | 303 | 5 | #Spatial-jitter simulations
This GitHub repository contains the scripts and code to reproduce the results of the paper 'Spatial-jitter model for magnetoencephalography sensor arrays' by Iivanainen.
Main script is Bspectrasphere.py which produces most of the simulation results in a spherical conductor |
f58900f23615fb02d1ef7bdeaa21e56a958cd4529923c6eb724b1f56e413fe52 | Text | 317 | 4 | # python_BphP_MSOT_sim
A forward model to produce time-series photoacoustic images of bacterial phytochromes (BphPs) for my PhD :)
This model uses Python over MATLAB as it is easier to run inside docker containers (necessary to use many HPCs), Python is also open source making the project more easily reproducable.
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19d75eb16e857795fd8cb8c98c0a8b8922563f5ca6df0df08b0425cb374b3e27 | Text | 331 | 11 | # alvin-aperiodic-stressinduction-analysis-2026
Code for the paper: "Beyond Neural Oscillations: Stress-Related Aperiodic Activity and Aperiodic-Oscillatory Spectral Covariation".
DOI:
## Usage
Run the scripts in this repository using Matlab, Python, and R to replicate the analysis.
## License
Licensed under the MI... |
46108ff112cf21e23c45b34a84c821fc0a817857413519d59cead63ab631a78f | Text | 348 | 7 | Overview:
ReadMe's are present in each zip file
CURCI-G contains the data and analysis for the primary dataset
CURCI-G procrustes contains data and analysis for procrustes transformed primary dataset
CURCI-NG contains data and analysis for supplementary replication experiment
R figure script contains the script that ... |
298c2ab158ee0da4329b79222498cacaea9ba892e9698ab06eab094ba14e6cb5 | Text | 357 | 17 | This folder contains input data for the analysis.
The Seurat object is not included due to file size.
Download it from:
GEO Repository with the accession code:GSE233163
Original file name:
GSE233163_seurat_object.rds
After downloading, rename it to:
ganglia_seurat_object.rds
and place it in:
data/
"Figures will b... |
9de83f1e265b7afaa44aaa77c17e49b35074cd189fb54136b0647412187c7e4f | Text | 369 | 8 | # FRACTAL-MSI
Code and data used to create images in FRACTAL-MSI
Frac_MSI_IF_register.py is the code to register immunofluorescent and LA-ICP-MS images.
frac_image_process.py is the code to do image fusion by the CDFIF and PRIF methods of the registered multimodal images.
Example images used to make figures in the m... |
1609cb3791c25463732d0f4eae1dacac45946be69d9a42ce423120d09b2a3a55 | Text | 371 | 11 | # alvin-aperiodic-stressinduction-analysis-2026
Code for the paper: "Beyond Neural Oscillations: Stress-Related Aperiodic Activity and Aperiodic-Oscillatory Spectral Covariation".
DOI: https://doi.org/10.5281/zenodo.21207822
## Usage
Run the scripts in this repository using Matlab, Python, and R to replicate the ana... |
e8b7b1bde49414b5b3556453a33068debe65c69d0cf61f2093b1236b306dcda7 | Text | 371 | 4 | For processing of in vivo data and wildtype organoids after 2 days of BMP4 treatment, see "GA" code.
For transduction efficiency analysis, see "CA" code.
For dendrogram generation from control and perturbed organoids after 4 days of BMP4 treatment, see "JC" code.
For all other processing of control and perturbed organo... |
ad1a8fe0176a63f6e1af59afb5c928bd7c74289da75e7628a6c5692f1a5b6548 | Text | 401 | 7 | ## Neural activity profiles reveal overlapping, intermingled subpopulations spanning area borders in mouse sensorimotor cortex
This repository contains code to recreate the figures associated with the manuscript by Salimian, Grier and Kaufman published at eLife: https://elifesciences.org/articles/109240.
Data to repr... |
f457bbf8a914787358da67d7bad2afa6f6ac077bfb5453e634ff42ed3395215d | Text | 445 | 19 | # MPVNN
MUTATED PATHWAY VISIBLE NEURAL NETWORK FOR CANCER SPECIFIC SURVIVAL RISK PREDICTION
Author : Gourab Ghosh Roy
Maintainer : Gourab Ghosh Roy <g.ghoshroy@pgr.bham.ac.uk>
The Python code, the input data and the output files are in the respective folders.
We use Python 3.8.6 with TensorFlow 2.4.1 and Keras 2.4... |
0abc94b67b2dbd3acf00dbea96122e1f08e57b07035edb300a84f11402e876e8 | Text | 474 | 9 | # Indoor Air Quality Research
Indoor air quality research and exploration
List of Data Analysis Steps:
1) Environmetrics Analysis (classification of health risk areas)
2) Randomization of the groups as training and testing (including validating)
3) Training stage with the multiple ML Algorithm
4) Selection of high CA ... |
b30fcd6c66f3614c53a3fec3d10080f87dc34a000af621b6a0b5aad2fb213581 | Text | 477 | 4 | # Code repository for Liu et al. (2026) Targeted stool metabolomics suggests exploratory catecholamine- and tryptophan-linked metabolic features in autism spectrum disorder
Citation:
Liu K, Li H, Zhang S, Xi M, Zhu J, Chen J, Xu W, Xie A, Makriyannis A, Guo JJ and Kong X-J (2026) Targeted stool metabolomics suggests e... |
ef3b2bea75531f3e65ba7373fddc4f3e75c59c79268712cf64103b1a2804fed2 | Text | 507 | 7 | # The SubcellularDistribution Pipeline
This pipeline was created by Pearl V. Ryder and Dorothy A. Lerit to investigate the distribution of subcellular structures in fluorescence microscopy data in three dimensions.
The [documentation file](https://github.com/pearlryder/subcellular-distribution-pipeline/blob/master/do... |
8c4f67bc821dbec26e33ed4184693283b92e9285bd6fbb654f7bbb79c8e9b820 | Text | 518 | 11 | # Dipolar order mapping based on spin-lock magnetic resonance imaging
This repository contains MATLAB simulation code for the paper, published in NMR in biomedicine:
"Dipolar order mapping based on spin-lock magnetic resonance imaging"
Authors: Zijian Gao, Qianxue Shan,Ziqin Zhou, Ziqiang Yu,Weitian Chen
https://doi.... |
96993937c08436392c25f95a3f26579632063570a761d0d81e12dd99634e785d | Text | 546 | 8 | # Human Brain-Wide Activation of Sleep Rhythms
Dataset DOI: 10.5061/dryad.2fqz612x0
Article DOI: 10.7554/eLife.103956.3
Description of the data and file structure
Simultaneous 64-channel EEG and whole-brain fMRI were recorded during the first half of the night in 138 healthy young adults (107 retained after quality ... |
4b0a2be8645298c9305aa26517b55b7ac51fe485def88f541dd09ec80cd709c2 | Text | 584 | 11 | # SMI-FSM
Single Molecule Imaging – Fluorescent Speckle Microscopy (SMI-FSM) analysis
SMI-FSM is a software (written in MATLAB) for the analysis of simultaneous two-color imaging data of plasma membrane proteins (via SMI) and cortical actin (via FSM). In brief, it is designed to:
1. Extract dynamic properties of sin... |
f65c080619aca4289ad48a83515b60b7cf33e48a37793532f6bee5c602c8a57d | Text | 589 | 14 | # Goal-Directed Theta Sweeps in Honeycomb Maze
This repo contains the source code used in "Hippocampal theta sweeps indicate goal direction".
A demo on the continuous attractor network simulation can be found in this [notebook](notebooks/can_simulations.ipynb).
You may need to install necessary python libraries befo... |
4d06d0d3c04358c027b4238572579dd69a3f59e6cab36af8f6df70aaa45f3480 | Text | 615 | 20 | Woodward, D. J., Reay, W. R., Wormington, B., Diaz-Torres, S., Ong, J.S., Gerring, Z. F., Thorp, J. G., & Derks, E. M. (2026).
Dissecting pleiotropy between major depressive disorder and physical disease comorbidities
MDD_Disease_Factor.tsv.gz = Disease-MDD Second-order Factors
MDD_Disease_Factor_withQSNP.tsv.gz = Di... |
c94414c1df2a583901c3c84d959fc9065baf74855ab13373da24312f95d0c906 | Text | 662 | 10 | This repository contains code for a minimal computational study of bilateral sensing and symmetry-breaking processing in directional inference.
Stage 1 evaluates how bilateral sensor geometry shapes Z2-equivariant Fisher-information profiles across auditory, binocular, and tactile models.
Stage 2 evaluates how delay-... |
4af4d5dccbc13f1d81feef03d032ed96d8bac39614ab46ccf3e6060840dd492f | Text | 683 | 14 | Synthetic Multi-eccentric Hartmann–Shack Dataset
This repository contains the synthetic datasets and MATLAB scripts used in the manuscript:
Contents
DataSet_llum_10/: Synthetic Hartmann–Shack images generated with a phase modulation of 1.0 rad.
DataSet_llum_14/: Synthetic Hartmann–Shack images generated with a ... |
d052872528f3672d51dafd5430a057de799a7c5033549e5ed757a2bb60afb44d | Text | 696 | 10 | # 3D Digital-dynamic-histomorphometry
MATLAB script that processes binary masks from registered in vivo microCT scans of mouse long bones to enable 3D rendering and quantification of dynamic histomorphometry-like parameters, including mineralizing and eroding surfaces, bone formation rate (BFR), and bone resorption rat... |
4f4dbb751cc35d2ea92ad1c0b351085a9bd9edc7d8b843bda4384e4f53f4b874 | Text | 724 | 12 | # Test-retest reliability of sensorimotor activity measured with spinal cord fMRI
This repository contains code accompanying publication: [https://doi.org/10.1101/2025.09.07.674708](https://doi.org/10.1101/2025.09.07.674708).
## Contents
Full detail of the pipeline are availble in the above manuscript. Briefly, the ... |
5ca9f6dbf16d817d52a4b9ed43112c6a01794a4b41c9bb98ea1366f56d96e78d | Text | 726 | 21 | # Neurite Kymograph Tools
Scripts to generate multi-channel kymographs from ROI sets and analyze neurite tip position and intensities.
Included scripts:
- `NeuriteKymoGeneration.py`
- `NeuriteKymoAnalyzer.py`
Key features:
- Multi-channel kymograph generation via `KymoResliceWide`.
- Manual threshold dialog with liv... |
fbd759518e79309df73a5be9eb539ffdbb64f38fc85c378cdb5e9e87ed095b73 | Text | 733 | 9 | Table 1 and Table 2 list the insects identified in the bat diet based on 16S and CO1 analyses, respectively, and correspond to Figure S1.
Table 3, Table 4, and Table 5 summarize the behavioral responses of crickets to bat odor, a blank control, and limonene, respectively, and correspond to Figure 1B.
Table 6 pres... |
a817bb5ef2bfe0839433920d95cdb6b3bcb3d08caa423c619f46e10a2811b8c6 | Text | 734 | 9 | **Detection of Early Stage Parkinson’s Disease Using Wearable Sensors at Multiple Body Locations and Convolutional Neural Networks**
This repository contains the analysis code used in the manuscript:
“Detection of Early Stage Parkinson’s Disease Using Wearable Sensors at Multiple Body Locations and Convolutional Neur... |
ba063cd0408b5f6df6348a3eac18c73a15ec7fdc2f711a1dacc9e9268fe5cf3a | Text | 740 | 15 | # Active vertex model with cell-cell viscous adhesion
This repository contains MATLAB code to simulate the shear-driven behavior of epithelial tissues using a Vertex-based model. The code supports research published in:
This model simulates cellular mechanics in the presence of cell-cell adhesion force, capturing the... |
23d53006092c7094cc611a591762419178cc520f72288246753289208c9e090b | Text | 743 | 13 | # 3D Digital-dynamic-histomorphometry
DOI: https://doi.org/10.5281/zenodo.19225261
MATLAB script that processes binary masks from registered in vivo microCT scans of mouse long bones to enable 3D rendering and quantification of dynamic histomorphometry-like parameters, including mineralizing and eroding surfaces, bon... |
5565a4c50ef3bc1ce1e82b14d8e2691b6937f54703d16a3f0241c040bfbd0e37 | Text | 745 | 7 | # Kara-Lab
Studying the Neurobiology of Neurodegenerative Disease
The mission of the lab is to follow a network-based approach to understand the pathogenesis of neurodegenerative diseases, with the ultimate aim being to utilize this strategy to develop combination treatments. This strategy distinguishes our lab from ... |
f98943a8f11b0d014147974b40b98a243efd775a3bb8625311c257bf1aa0d117 | Text | 747 | 21 | # Neurite Kymograph Tools
Scripts to generate multi-channel kymographs from ROI sets and analyze neurite tip position and intensities.
Included scripts:
- `NeuriteKymoGeneration.py`
- `NeuriteKymoAnalyzer.py`
Key features:
- Multi-channel kymograph generation via `KymoResliceWide`.
- Manual threshold dialo... |
45fe958d17d3d2f650a391c70dd3d607e42edfa972408d9227bac99a345cb624 | Text | 749 | 30 | # CaLM
## The Codon adaptation Language Model
This repository encapsulates all code required to reproduce the results of the paper ["Codon language embeddings provide strong signals for use in protein engineering"](https://www.nature.com/articles/s42256-024-00791-0), by Carlos Outeiral and Charlotte M. Deane.
## Cit... |
83d861e0de7e2f19f7e29d7b8a6dc1fae752bfa134b3b4bf7c112f7cd87e6dd5 | Text | 757 | 7 | # Vetere-et-al-2026-Cell-Reports
Original code developed for Vetere et al. (2026), Cell Reports
In this repository you can find all original matlab scripts used to preprocess and analyze the neurophysiology data in Vetere et al., 2026. You can also find all raw data in the manuscript in .xlsx or .mat format, along wit... |
891fa18f7d1bba073c8cbe33c57c14cd79d53f507c544616890c41bc6c72f899 | Text | 789 | 12 | # gNODE
gNODE: gLV model-informed neural ordinary differential equations for modeling microbial community dynamics
## Framework of eNODEconstr
## (A) Training module
Longitudinal microbial abundance data are used to train a NeuralODE whose dynamics ... |
3f6644d1b16ffab806ec9e9c35efa1bf930e4618e02c57db74c8f7f22e7353f6 | Text | 817 | 18 | # Mitochondria Segmentation Project
It provides scripts to segment and analyse mitochondria on Electronic microscopy brain images.
## Overview
The project provides several tools and pipelines for image segmentation and analysis:
- **Cellpose_pipeline**: Includes scripts for training and detection using Cellpose, alo... |
88c92f3569508f65724d4253cbc7dbe5a6ce01f172255124e43df1ae7beea864 | Text | 847 | 17 | # Revised Aurelia Atlas vs3
Revised Scripts necessary to reproduce the analyses in Link et al. BioRxiv [https://doi.org/10.1101/2023.08.24.554571v4]
- published in PLOS Biology (2026)
1) Linketal.Ac.generate.data_REVISED.R : R script for importing mapped count matrices from Cellranger 'out' directory after mapping an... |
2fa3e86c550cb756e538538f4a65389759838a50ec8d0c3b009ace055eb0faec | Text | 861 | 13 | # Data Repository
This repository contains the MATLAB (.mat) files with the experimental and numerical data supporting the figures presented in the article:
Alessandro Petrini, Claudio Conti, and Davide Pierangeli,
"Degree-of-polarization modulation for high-dimensional optical computing",
Nature (2026). https://doi.... |
92aa9be8519f5d99753ad95648a2152c67b088843b072c9ab9f8b5b7084da225 | Text | 863 | 19 | # MiNet
### MiNet is a gene- and pathway-based deep neural netowrk for multi-omics data intergration to predict cancer survival outcomes.
# Get Started
## Example Datasets
To get started, you need to download example datasets from URLs as below:
[Train data](http://dataxlab.org/MiNet/gbm_std_imputed_train_15.csv)
[V... |
d73c3057a0522a2fce2bc5ab5b66cd4f8aed589c5c68288ef49929484b561302 | Text | 867 | 26 | README
This repository contains the source data underlying the figures in Binagui-Casas, Granes et al., 2026.
Each folder corresponds to one or more figure panels, as listed below.
FOLDER-TO-FIGURE MAPPING
fig1F_data - Figure 1, panel F
fig3B-S2A,B_data - Figure 3, panel B; Figure S2, panels A and B
fig... |
d68031039f3abe9736ae316aa3a1f80100638f5e876adb062fc6abbbec5c7e6e | Text | 900 | 11 | # CATractography
Cellular Automata Tractography: Fast Geodesic Diffusion MR Tractography and Connectivity Based Segmentation on the GPU
The method is presented in:
[Hamamci, Andac. "Cellular Automata Tractography: Fast Geodesic Diffusion MR Tractography and Connectivity Based Segmentation on the GPU." Neuroinformatic... |
6fee40e45401c51e4ae4bfe5d58f008f054458551925d3781e40c92fa2650f5a | Text | 904 | 19 | # A Hierarchical Navigation Framework Implementation
## Project Introduction
This project is the open-source implementation of the paper titled "A Hierarchical Navigation Framework for UAVs ..."
## Project Structure
├── video/ # Directory for vedio
├── code/ # Source code
├── environmen... |
5bd24a22b8a50dc7bad1f86b77c25c28a1e750948e24a965770fa89b4c292199 | Text | 949 | 66 | # scKANFormer
## Environment
- python >= 3.8
- PyTorch >= 1.8
- `numpy`
- `pandas`
- `scipy`
- `scikit-learn`
- `scanpy>=1.8.2`
- `anndata>=0.7.2`
- `matplotlib`
- `seaborn`
- `numba`
- `louvain`
- `umap-learn`
- `einops`
- `tqdm>=4.62.1`
## Installation
```
git clone https://github.com/nathanyl/scKANFormer
```
## R... |
488c17bc90e3ee6c9b6636e25efc242f864f7e60326d825075c44a359d4a305f | Text | 999 | 17 | Compiled standalone software and source code: MATLAB, code included in the 'example_code' folder
Dataset: in the Sim3_p0.1_mini.mat in the 'example_code' folder, for large-scale dataset, please refer to https://cloud.tsinghua.edu.cn/f/88a9ede6051544d3aaf8/.
System requirements:
1, Software: MATLAB R2022a
2, ... |
64109ecd671a1969576826bd7a8122e5fe1637f0275c8baab89f159abdcf3e85 | Text | 1,013 | 36 | # Multi-Scale OSH Core
This repository provides a compact reference implementation of the deterministic
multi-scale Optical Scanning Holography (OSH) representation described in:
**Multi-Scale Optical Scanning Holography for Robust Manipulation Detection in Satellite Images**
## Included
- The OSH transformation us... |
3bba13e9da357b263dfe750b59a5a471c9466eebf8dad24b34d56bea26ea2454 | Text | 1,019 | 26 | # FM_V1
Code for macaque visual cortex cell atlas.
Comprehensive whole-cell profiling of primate primary visual cortex unveils new cell types and species differences in gene expression
Jia-Ru Wei1, Zhao-Zhe Hao1, Chuan Xu, Mengyao Huang, Lei Tang, Nana Xu, Ruifeng Liu, Yuhui Shen, Sarah A. Teichmann*, Zhichao Miao*, ... |
4fcc05c9fca4a1d65c6a434c956a9b89cee895d778ebe742eb14249d636e4dfe | Text | 1,052 | 28 | # D3Text
Entity recognition, entity linking and relation extraction over the BRENDA
enzyme literature, with distant supervision from BRENDA's own entity tables.
## Install
Python 3.13 and [pdm](https://pdm-project.org). Pick the lockfile matching
the machine's torch build (`cpu`, `cu126`, `cu128`, `cu130`):
```bash... |
9ba3a02d8c19a2b18f3341d2d9ec66f509121c2ca239fb722dfacdb6fcf95aca | Text | 1,077 | 8 | Title: Metadata files supporting the study "Effects of Gut Microbiota on the Susceptibility of Ischemic Stroke in Mice"
Associated manuscript: Effects of gut microbiota on the susceptibility of ischemic stroke in mice
Author: Guangyan Wu#, Huidi Wang#, Qianyi Zhou, Jingxiang Fu, Feng Zhang, Zhuo Duan, Shuo Wang, ... |
ed36d6784c07afe550399d5249157d069fae80fa3029a111ac1a65899dbac99a | Text | 1,088 | 32 | # gradient\_analysis
[Link](https://nbviewer.jupyter.org/github/NeuroanatomyAndConnectivity/gradient_analysis/tree/master/) to view this repository.
# Requirements:
## Python2.7:
### standard packages
numpy
scipy
pandas
h5py
matplotlib
seaborn
gdist
### Neuroimaging
[nibabel](https://github.com/nipy/ni... |
9d4d2ac0872badaff3104b6db745066dde6c944e1d51f5d7f02e7fa6c9a55141 | Text | 1,101 | 38 | # Luminex-Data-Cleaning
Automated pre-processing of Luminex data to remove outliers and measurements with low bead counts
Please be aware that the current packages in R must be installed prior to using said pipeline. There are specific packages necessary for both R script files, each are lsited below. For a more detai... |
b76b72fdec7fc9a048751d187f9dc4b62ab45bfa527a137d923c39e195c21acb | Text | 1,179 | 35 | # BrainTumorSegmentationEnsemble
Overview
--------
This repository contains a simple script for predicting brain tumor segmentation masks using an ensemble of convolutional models. The steps below explain how to prepare pretrained weights, install dependencies, and run the script to obtain predicted masks in the `out... |
be447789f48299df039dee47c06a114cf4534a7676fa1286c9a76ac8fc884cce | Text | 1,190 | 27 | # brenda_references
The BRENDA reference corpus: the training / validation / test DataFrames and
the relation preprocessing behind them. `d3text` consumes this as a library.
## Running the scripts
`scripts/` holds the ad-hoc data-collection drivers that build and repair the
document database — pulling references out... |
530d4bff631ee61896ee0aedefe2ea31d397551c5a992f2632b1b3155c57f64a | Text | 1,191 | 46 | # ASL-Bigbrain-CCSI
Code for analyzing CBF-CSI similarity index (CCSI) study using 7T MRI and Bigbrain
## Cite this study:
Guo, F., Zhao, C., Bhatt, R.R. et al. Assessing molecular, cellular and transcriptomic bases of laminar perfusion and cytoarchitecture coupling in the human cortex. Nat Commun (2026). https://doi.... |
2218fdd82b20e587a8963a9eba5c77a86d1960d3485279ae59646b2d822ed062 | Text | 1,199 | 28 | A quick and dirty viewer for the ICs generated by FSL Melodic
This program lets you quickly classify 'bad' and 'good' components and saves them in separate files.
These classifications can be further used for denoising using fsl_regfilt or fsl fix.
Written for Python 2.7, using Tkinter and PIL.
Instructions:
Fir... |
8b5a889eb45e171f6e603f974fb9ee642302f41e1a1aa342625fcc48cad15710 | Text | 1,209 | 7 | #### Extended data for Heimburg et al. (2026). Thalamocortical bursts encode reward contingencies and drive associative learning.
**Data**: The dataset is accessible for download in two formats from a Dryad repository (DOI link will be made public upon acceptance): A version with all necessary data for MATLAB scripts ... |
2b9a49dbaed92ca85f19647d9ae785e27506eb8e886298d53743b20337331cbc | Text | 1,218 | 36 | # ClinicalTrialLLM-Extractor
A tool for extracting and analyzing clinical trial data using Large Language Models.
## Overview
This project extracts structured information from clinical trials using LLMs, focusing on key parameters and outcomes. The pipeline includes data acquisition, filtering, LLM-based information... |
2ada4151c8a854b1a9a80647f6aa1faa70c9d23340d5e7482d760eeeda935fe9 | Text | 1,240 | 29 | # OIA-DDR
A General-purpose High-quality Dataset for Diabetic Retinopathy Classification, Lesion Segmentation and Lesion Detection
You can download OIA-DDR from either Baidu Drive or Google Drive.
- OIA-DDR on Baidu Drive: [DDR dataset](https://pan.baidu.com/s/1560JK2pzxTN9Ny1TcmNasQ "悬停显示") PWD:ue0t
- OIA-DDR on Go... |
63e2bc9361f758819ffa0707013e2902c3a093c808f21c8d52ae014f785680df | Text | 1,276 | 20 | # beats_sides_olfactory_circuit_Drosophila_Duan_PlosBio2026
R scripts for the analyses presented in Duan et al. (2026) Deciphering the Combinatorial Expression and Genetic Regulatory Mechanisms of Beats and Sides in the Olfactory Circuits of Drosophila.
This work is soon to be published in PLOS Biology. The BioRxiv ... |
1b28ccc7d3e9bd40e86ada3e9e12c7227458c5fafdeaa8ff531ff66f9915466a | Text | 1,294 | 48 | # TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments
This repository contains the source code ,the data and trained models.
## TransformerCPI
## Setup and dependencies
Dependencies:
- pytho... |
c02fd3db11f1f9e484ea20fdd46f98fa73393c0d33f01c9b361f125ae5a9a6f5 | Text | 1,314 | 20 | # Long-term Reliability of Aperiodic and Periodic EEG Features
Reanalysis of the [Dortmund Vital Study](https://doi.org/10.18112/openneuro.ds005385.v1.0.2) resting-state EEG dataset examining the five-year test-retest reliability of aperiodic and periodic EEG measures across the adult lifespan.
## Overview
Raw... |
0379f8c10918f51da75ef46d234368a93222c8d04fb4eeba56d182bb2ec16ee7 | Text | 1,316 | 31 | ## Brain image registration with implicit neural networks
This repository includes several code examples presenting how implicit neural representations (INRs) can be used for brain image registration.
INRs serve as a continuous, coordinate-based approximation of the deformatio... |
64d93cdeb28b130f3a75cfb85782b7163b304480e78160bf054c732243e4395b | Text | 1,335 | 18 | # Introduction
[](https://www.mathworks.com/matlabcentral/fileexchange/97142-probability-density-functions-distance-and-similarity) [![Open in MATLAB Online](https://www... |
dd04df94fba6905c78f9aaa1ba709a42adb53b6217e79e31133227de4b66f286 | Text | 1,348 | 40 | # Additional Python Files for the Kvasir Hybrid Transformer Repository
This package contains:
1. `xai_analysis_full.py`
- Full XAI implementation for:
- SmoothGrad
- Integrated Gradients
- Occlusion Sensitivity
- LIME
- Grad-CAM
- Grad-CAM++
- Score-CAM
- Generates a paper-sty... |
cefe705cf6b407f732ee46b91b2eccf4eb5ae7b71b913a8bb55980a2fea314db | Text | 1,357 | 22 | # BELT
This is the repository for the "Bayesian Edge Cloud Architecture" BELT. The repository is structured as follows:
1. If you want to run the codes that support the paper, start from the following section.
# Dataset
The dataset is available in GDF [Click here to open the link to the dataset](https://drive.google.... |
d9bfbe4598f135b58f5cff193e79eed10995ca85365bca451312b11e04d0cea6 | Text | 1,367 | 71 |
# 🧠 PANDA: Patch-based Unsupervised Deep Learning for Brain Anomaly Detection via Age Prediction in Fetal MRI
Under Revision at *Imaging Neuroscience*
---
### 🎯 **Multi-Disease Fetal Brain Anomaly Detection Using Brain Age Prediction: A Patch-based Deep Learning Framework**
<p align="center">
<img src="Figure ... |
a82df1596adb6c02d0d0f089f6d7e1a8a4131f0f094e443f544b76e44696d27a | Text | 1,393 | 47 | # A python code of CoNNECT: Convolutional Neural Network for Estimating synaptic Connectivity from spike Trains.
## Preparation
Install cython and tensorflow at your PC if you have not done before.
***cython***
```
$ pip install cython
```
We have confirmed that our algorithm runs with the cython version 0.29.6.
*... |
b8e18bc55769072caea09bd93b4f757e7fd7422c8598472d86a2d98792f4a906 | Text | 1,399 | 39 | # Individualized Atrophy and Network GOF Analysis
This repository contains Python scripts for individualized gray-matter atrophy mapping, network goodness-of-fit analysis, ROI-level result aggregation, and group-level statistical testing.
## Requirements
- Python 3.10+
- NumPy
- pandas
- SciPy
- NiBabel
```bash
pip... |
5aa7cff2747ffff96d4a689304b9d9a6dc21b31174f5bbdbc9b14172c1c05113 | Text | 1,405 | 5 | # SeismicGNN
Most seismological analysis methods require knowledge of the geographic location of the stations comprising a seismic network. However, common machine learning tools used in seismology do not account for this spatial information, and so there is an underutilised potential for improving the performance of ... |
902466e7ef2fd191ee04c4d6d483a3eee672cfaf804547f124ddc392cfd147d5 | Text | 1,407 | 35 | Dataset title:
Source data and analysis code for “A Nose-to-Brain Circuit Underlies Anxiety Regulation by Nasal Afferent Frequency in Mice”
Overview:
This repository contains the source data supporting the main and supplementary figures of the associated PNAS article.
Files:
1. Source_Data/PNAS_Source_Data.x... |
a97849b26473fddc451c15ff302a4f2626d7afd6eface9d01cf8d5479a75676a | Text | 1,442 | 20 | [](https://github.com/UU-cellbiology/ComDet/actions/workflows/build.yml)
ComDet
===
[](https://doi.org/10.5281/zenodo.4281064)
<br />
<img src="http://katpyxa.i... |
571c935291cfd1c465e87cf756ebbb7aafb001844aec2585fc38b23a7a2bddf6 | Text | 1,454 | 42 | # Semi-supervised Omics Factor Analysis (SOFA)
[](https://badge.fury.io/py/biosofa)
# Introduction
Here we present Semi-supervised Omics Factor Analysis (SOFA), a multi-omics integration method, that incorporates known sources of variation into the model and focu... |
f54542bb3b4711dd3c1b84521ce1d1462322418edd318bb7565fe90ec20ae859 | Text | 1,491 | 53 | PEER package source distribution.
A complete documentation can be found her
https://github.com/PMBio/peer/wiki/
##Package content##
Source distribution of the PEER library with bindings to python,R,standalone
######## Installation instructions ##########
##Dependencies##
cmake (http://www.cmake.org/)
optional (R/py... |
350b80826131a0e97da2951c24cdda7ab80fc05843084cde9bfc9bd1d3260cac | Text | 1,493 | 27 | # Welcome to the Computational Brain Imaging Group (CBIG) repository!
We are from [Thomas Yeo's Computational Brain Imaging Group (CBIG)](https://sites.google.com/view/yeolab).
CBIG repository is a package that provides the following useful tools:
1. fMRI preprocessing pipeline
2. Brain parcellations and algorithms... |
154a05a343c5f508dd5063e980f6d3cdba3b7eff3847e5b131fdc8e44d6a18a0 | Text | 1,553 | 32 | # Elite athlete structural brain-profile analysis
This is the minimal post-segmentation analysis package for Frontiers manuscript 1904810. It contains only the deidentified analysis dataset, the complete R analysis script, and the package-version lock file.
## Files
- `data/Athlete_Analysis_deidentified.csv` — deide... |
265250a4304446268e2e654989b0b0b8fc26ba4f88c5434f3019bd090cbb4e78 | Text | 1,579 | 41 | MATLAB codes and data for the paper:
"Awake Cortex Stabilizes Traveling Waves for Global and Reliable Information Routing"
Kaio Misawa, Koji Chinen, Akira Kawabata, Taro Kaiju, Takafumi Suzuki & Yutaka Komura
File list:
Main figures:
figure2.m / (data generated by simulation) - Figure 2: Simulatio... |
5b178e60cab5259401ce54a865b17fc16373ef3e53c5f0c003b4453ac213f2c2 | Text | 1,595 | 44 | # locomotion-modulation
Code for the paper "Locomotion optimizes sensory representations through a computational principle shared by rodents and primates" by Jonathan Gant and Wiktor Mlynarski at the LMU Munich.
# Install instructions
In order to run the code, please ensure Python 3 is installed and install the requir... |
455d3cd8ce2952e05ef34638788dc82315c5554d3d2990d8f8b947cb4d09d391 | Text | 1,600 | 21 | # MATI (Microstructural Analysis of Tissues by Imaging)
---------------------------------------------------------------------------------------------------------------
MATI (Microstructural Analysis of Tissues by Imaging) v1.0 is a GPU-accelerated toolbox for microstructural diffusion MRI simulation and data fitting wi... |
9e1f8f8ec316ec7ab06445a3991d1eeb7f5d8abb7996303a69590ddddfdc8cb3 | Text | 1,611 | 22 | Welcome to the Buzsaki lab repository! The goal is to have this repo as your one-stop-shop for code you may need as a Buzsaki Lab member. This will include preprocessing pipelines as well as analysis functions.
IMPORTANT: everything is under collective development by the lab. If you find something that needs changing/... |
622f51026d1f9cf37a3c96283718bb97f9e69fe3be53df83eca8493ae7cccfd7 | Text | 1,616 | 39 | # scMulan
Welcome to the repository for scMulan_v1, featuring our upcoming work: "scMulan: A Multitask Generative Pre-trained Language Model for Single-Cell Analysis."
## Introducing scMulan
scMulan is a groundbreaking foundation model for the analysis of single-cell transcriptomics.
Features:
- **Zero-shot Cel... |
e0dbe99d22fe43f9bbef71c8f7fa3ddf71773a2ceab92aefecc9f502170e4422 | Text | 1,627 | 27 | [](https://doi.org/10.5281/zenodo.15635269)
# Boeken_Tauopathies
This repository contains the analysis code associated with the Tauopathies single-molecule characterisation project, led by Dorothea Böken.
The associated manuscript is now published [he... |
3778873db9b520f9a3a5636f7613bb51e5800fca502fffcbb944143dc565379a | Text | 1,650 | 33 | # Modeling the influences of non-local connectomic projections on geometrically constrained cortical dynamics
This repository contains the MATLAB code required to replicate the numerical experiments and figures presented in the paper: **"Modeling the influences of non-local connectomic projections on geometrically con... |
02534a59c993bf4d745e0be1ab4d43ff38d554601fc283e42237e95248d6b548 | Text | 1,669 | 36 | # Data Access
## Primary Data (downloaded automatically by scripts)
### GTEx v8 RNA-seq TPM
- **Source:** GTEx Portal / Google Cloud Storage
- **URL:** `https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz`
- **dbGaP:** phs000424.v8.p2
- **Size:** ~1.... |
8da38fe58476342b84912d5eb4407fd49664f7cb7d292e3ba3996c071d1b0896 | Text | 1,681 | 25 | # Code associated with Binagui-Casas and Granés et al. 2026 Figure 4, Figure 6, Supp Fig 5-6
## Figure 4
This repository contains code and data associated with the analysis from confocal images of gastruloids with Tbxt-GFP and Sox2-mCHERRY live reporters in Notch, Wnt, or DMSO control conditions.
Image analysis scrip... |
200db93218bafd6ac182fb98382f71198dd2998ebf1b0e725e13168d0d57c440 | Text | 1,687 | 46 | <div align="center">
<h1><code>PowerLawNoise</code></h1>
<h4><i>Generate power law noise, in Julia.</i></h4>
<br/>
![License][license]
![GitHub Stars][stars]
[![Gitmoji Badge][gitmoji_badge]][gitmoji]
<br/>
</div>
<div align="justify">
This package implements a novel algorithm, following the work in [**"*On
generat... |
f11434b853c986ccbe5b33a549227dc36a7e99c2be958713a45099baf3084be0 | Text | 1,687 | 28 | # Pyap-wing-singlecell-2026
This repository contains the R scripts used for the analysis of insect wing development in *Pyrrhocoris apterus* (SHC) and *Nilaparvata lugens* (HFS).
## 1. System Requirements
- **R Version:** >= 4.2.0
- **Operating System:** Windows, macOS, or Linux.
- **Key R Packages:** `Seurat`, `harm... |
51eab49a78cb09438597242c81c4048d5e85970135899fa5a9b5dfa6b2c134da | Text | 1,688 | 20 | # 💻 Code for DecideNet neuroimaging project
This repository contains code required to reproduce results from my Doctoral project "DecideNet." This project is dedicated to examining and describing functional network reconfiguration during prediction error processing. The analysis is focused on three perspectives: (1) ... |
ae3b6cf6142ba0ecebe30ed587fcf911e4cec30a51b4f170c4a992d55fb8327a | Text | 1,706 | 18 | # niceTFRplot
An alternative visualization for the results of FieldTrip cluster-based permutation analysis on time-frequency data. The code avoids opacity alpha masking by using custom color scales, smoothed by a gaussian filter. Information about the cluster contribution of each individual sensor is outsourced to a 2D... |
6c2734192124339c512c7d753d6a676c4399225be99e4b9dff85aa161f2d9fe4 | Text | 1,719 | 20 | [](https://www.travis-ci.com/mychan24/system_matrix_tools) [](https://doi.org/10.1073/pnas.1415122111)
# System Segregation (graph measure) scripts in R and ... |
92dd6ca316788f5a7a05914e7eea7f663054217d31b303bd2911d70887915aaf | Text | 1,725 | 34 | # Fetpype [](https://fetpype.github.io/fetpype/)
Fetpype is a pipeline for processing *in vivo* human fetal brain MRI
This pipeline is the fruit of a collaborative effort shared across teams involved in the ERANET MultiFact proj... |
6ede884131bbbb6977edaf36dab0705e6cbe7d716a6f74fb9991719215bc5b53 | Text | 1,732 | 40 | # FFAformer: Frequency-Filtered Attention Transformer for fMRI Time Series Prediction
## 📌 Overview
This repository provides the official implementation of **FFAformer**, a Transformer-based framework for fMRI time series prediction.
Functional magnetic resonance imaging (fMRI) signals exhibit long-range temporal de... |
9c56154231793ca1f8085a006439011098446fa1f72c52bd58c1cd275ec9ce1b | Text | 1,746 | 13 | # conditionalColoc
conditionalColoc is a software, written in Matlab, for analyzing the colocalization relationships between objects in three-channel microscopy images.
Conceptually, it divides the channels into target, reference and condition, and addresses the question whether the extent of target colocalization w... |
929718fd8741096858e73723a2eb4dad42c69e9462788e16338ff8bd3a619299 | Text | 1,787 | 37 | # =================================================================
# Laconic Fluorescence Analysis Script
# =================================================================
# This script analyzes fluorescence microscopy data from dual-channel imaging
# It processes both Laconic sensor and pHrodo measurements
# Perfor... |
37b56439cfc4b425308aff8863ee129b6e25240e2f68f8885cf2f33f4be2681c | Text | 1,802 | 51 | # Deconvoluting Spatial Transcriptomics data through Graph-based convolutional networks (DSTG)
This is a TensorFlow implementation of DSTG for decomposing spatial transcriptomics data, which is described in our paper:
## Installation
```bash
python setup.py install
```
## Requirements
* tensorflow (>0.12)
* networ... |
3bea0f7bd78cfdfce9c5a2046573b7d5453bb1562dfa68a8b16998767c6d47bd | Text | 1,807 | 62 | ## Signal probability along line
This program aims to summarize the probability of finding a signal along a line from multiple samples.
To use it, run __main__.py.
You will need @pandas, @numpy and @PyQt5 to run this program.
In essence, given multiple tables, where column X represents a point within a line and colu... |
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