sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
10d2fb5fa6d18b73f18dfd0d39a514d939f3e6af7107694fd2d948c64c1a9f89 | Text | 1,055 | 28 | This small script is based on a [github repo](https://github.com/lab11/pyVisa_Tek_MSO2000) by Ye-Sheng Kuo. Thanks for giving me the permission to use and share your code!
Currently, this script works for Tektronix TDS2014B, RIGOL DS1000Z and SDS1104X-E scopes
and all scopes that share the same programming interface a... |
b6b8b21ef604ac628653944f932233632458a4f227055036e8a12874a2a843bd | Text | 1,077 | 23 | # Welcome to Muscle X Application Suite!
The Muscle X program suite is a collection of programs intended to assist with analyzing diffraction X-ray images.
# The collection includes:
- X-Ray Viewer (xv)
- Equator (eq)
- Quadrant Folding (qf)
- Projection Traces (pt)
- Scanning Diffraction (di)
- DDF Processor (ddf)... |
19179e273e3b6c4b62817c2f7810a824dc14318db6203cf94db790dad3e9d59a | Text | 1,081 | 45 | ===============================
Dynamont
===============================
.. image:: https://img.shields.io/travis/JannesSP/dynamont.svg
:target: https://travis-ci.org/JannesSP/dynamont
.. image:: https://circleci.com/gh/JannesSP/dynamont.svg?style=svg
:target: https://circleci.com/gh/JannesSP/dynamont
.. i... |
560955c7b59efbdea397e3cff790f417f63f0a072ae3da9925f7b8df36e773e8 | Text | 1,091 | 43 | # Fast and Efficient Zero-Learning Image Fusion
This repository provides an **opencv** and **pytorch** implementation of the paper "[Fast and Efficient Zero-Learning Image Fusion](https://arxiv.org/abs/1905.03590)".
## Usage
```bash
pip install -r requirements.txt
cd code/
# --imageSource specify a sequence of sou... |
7d060e81d43195a44e0c096a6bf6c6a04f228357d1181aa6bcffd2f8d1488e4e | Text | 1,105 | 42 | # 2025_published-code
Repository for codes used in publications from the Muenzberg Lab in 2025
Food Intake Analysis Suite - README
===================================
Author: Laura Kaiser
Overview:
This R script processes feeding event data from Promethion systems. It includes functions to:
- Clean and load data
- G... |
249c4d4a5d4c0c17b3ffe7a76a9105088dafb1f81dda5f72a5c54f3b04828720 | Text | 1,113 | 14 | # The Resting-state Pain susceptibility Network signature.
Please refer to the website: https://spisakt.github.io/RPN-signature
[](https://github.com/spisakt/RPN-signature/blob/master/LICENSE)
[
The outline of the deepJPRESS model architecture. TE-specific representations are generated by a combined use of WaveNet and GRU before being aggregated to create the JPRESS representation. This representation serves as the output of the encoder and maps the input FIDs to metabolite concentrations and T2... |
416d6c0748e3a84e3679341dffd0ecee82272b3ec5f3507abd2b3a6987873e3f | Text | 1,123 | 23 | # Granular Phenotyping of Neuromuscular and Cortical Adaptation in Elite National Judo Athletes
Repozytorium zawiera wszystkie dane, skrypty analityczne oraz ustawienia parametrów wykorzystane w badaniu:
"Granular Phenotyping of Neuromuscular and Cortical Adaptation in Elite National Judo Athletes: A Three-Group Exper... |
c72484520a11e9c964ac2df894abc178c5e94aa4e8c9ab02659eac031225187c | Text | 1,123 | 25 | MS_ABM_Weatherley
This code supports the manuscript “Therapeutic targeting of oligodendrocytes in an agent-based model of multiple sclerosis.” This article is published open access in PLOS Computational Biology, available here: https://doi.org/10.1371/journal.pcbi.1013273. This repository contains MATLAB code of an ag... |
3b79050dadd3af4e87d23eb4daea88e34b27d577ba69b93ebfe67186e1182720 | Text | 1,134 | 25 | # SVDEnsemble
==============
by Shuting Han, Feb. 2018
Overview
--------
This is the code for defining neuronal ensembles using singular value decomposition (SVD). Conceptually, we view neuronal ensembles as representative population vectors in N-dimensional space, where N is the number of neurons. SVD is used to fin... |
bf24fd408f8224f1b93e11f30e416f60994c864f8e4553f289d8893b3a23d4f1 | Text | 1,136 | 42 | # fly spotter
This repository contains code that was used for extraction of fly locations in "MED13 and glycolysis are conserved modifiers of α-synuclein-associated neurodegeneration"
## Installation
Download and add the following to your MATLAB path:
```
https://github.com/sg-s/movie-analyser
https://github.c... |
fcec3a5cf54c0b359ed6eb0bc56b35b4f2924a5f5fb21cf06620cff53d9139c3 | Text | 1,156 | 40 | # Lobster
## Overview
Analysis scripts and schematics for Lobsterbot project
## Publication
This code accompanies the following paper:
**Population analyses reveal heterogeneous encoding in the medial prefrontal cortex during naturalistic foraging**
Ji Hoon Jeong & June-Seek Choi
*eLife*. DOI: https://doi.org/... |
4a907efd4dd1ffa11d06663aec019a2301cd7abf769e2f6acff2eb1b671cff8d | Text | 1,168 | 33 | # networkSpreadFVM
Finite volume simulation of concentration profiles spreading over network structures
Public code is currently under construction and more examples and implementation details will be provided at a future time.
# Basic starter guide:
1) Acquire the gfortran compiler
2) Go into source/ and time "make... |
81ff3f5463734aaff107d683b11f3dd01cadde35d89cb8b0223a884e1013d01a | Text | 1,172 | 25 | # A Neural Circuit Framework for Economic Choice
This repository contains the code associated with the manuscript:
**A neural circuit framework for economic choice: from building blocks of valuation to compositionality in multitasking**
*Aldo Battista, Camillo Padoa-Schioppa, and Xiao-Jing Wang*
bioRxiv (2025)
#... |
6c13b43c4a31e65e2885693a2eabc11dc1beee5f159d166d8cd7c2cf6250a705 | Text | 1,175 | 24 | Automated Segmentation of Retropharyngeal Edema in Acute Neck Infections
Overview
This repository contains code and resources related to our study on retropharyngeal edema (RPE) quantification in patients with acute neck infections. RPE visible on magnetic resonance imaging (MRI) has been associated with disease sever... |
a8182445efd845ee589e22b993896b808406c39db2420e6be885c355b625b158 | Text | 1,176 | 25 | hole
====
A program to analyze the pore dimensions of ion channels.
Please see the homepage http://www.holeprogram.org/ for further information.
Supported platforms
-------------------
* Linux
* macOS (experimental, Intel chips confirmed to work)
Installation
------------
* **Source code** is available at https:... |
9c08bbb2fe5ec69dd22b50b694751e9105cbc05dc0ab45bda12be1fa9552c0a6 | Text | 1,186 | 29 | # CPDtissuesXray
The code in this repo supports the plots and findings presented in this study:
> **Critical point drying of brain tissues for X-ray phase contrast imaging**
>
> Safe Khan, Jonas Albers, Artem Vorobyev, Yuxin Zhang, Jakob Reichmann, Angelika Svetlove, Fabio de Marco, Ksenia Denisova, Yikai Yang, Flore... |
5c97a1dc3ec42dc29d8a35071b369be90722b08790b290124feed329577d3182 | Text | 1,192 | 29 | # Gonzo: Human brain MRI data of CSF-tracer evolution over 72h for data-integrated simulations
This repository contains the processing pipeline for the Gonzo dataset: dynamic contrast-enhanced MRI images following intrathecal injection of gadobutrol in a healthy human volunteer.
## Resources
- **📚 Documentation**: ... |
522ce5d8551f360b2a91f52ca429ed28c3aee6ca16dcd654b6cafd7f6cab084c | Text | 1,197 | 14 | ### Information about files in this figshare repo ###
# volumes.csv
Spreadsheet containing all structures assocaited MDVC (pc_lod), paternal HF/HSS diet affect as relative change (%, paternal_pc) and absolute volume change (mm3, abs_pat), direction of change (larger 1, or smaller -1, pat_dir)
# absvols.csv
Data file ... |
587007ca61319613e3a1564f7b28cb31067f4dafe06fef2df5823afa39d5a2b5 | Text | 1,197 | 14 | [](https://doi.org/10.5281/zenodo.18672975)
[](https://github.com/PTRRupprecht/Duss-et-al-2026/tree/master/LICENSE)
[![Size](https://img.shields.io/github/repo-size/PTRRupprecht/Duss-et-a... |
d1534637e19d55997c59e8ee4620f479f35cbf331f13495e95d1b2b475b08e29 | Text | 1,197 | 26 | # Alcohol impacts an fMRI marker of neural inhibition in humans and rodents
## About
This is the codes to replicate the analysis in *"Alcohol impacts an fMRI marker of neural inhibition in humans and rodents"*.
**To reproduce Figure 1**
- `rat/Fig1.ipynb` — Calculates and plots the region-wise T1w/T2w distributio... |
4ed7740c774be471631949100adc4f7678245f4e47034834fa9ac072d2e8c823 | Text | 1,206 | 33 | # bism - Biomedical Image Segmentation Models
This is a collection of generic PyTorch model constructors usefull for biomedical segmentation tasks.
Something akin to the `timm` package for 2D image tasks.
When at all possible, each model will offer a 2D or 3D implementation, however we will not provide pre-trained m... |
ae8e59edb950b571574c5fabbaccf7d7eaba2be58f6af7e460a4bc85c0d48b27 | Text | 1,219 | 38 | # Co-simulation of Arbor and TVB
## Setup
First, you'll need a working C++ compiler (GCC), CMake, and an installation of
MPI (OpenMPI). Your OS likely provides packages for these.
Fetch this repository and install dependencies, as follows
``` bash
python3 -mvenv env
source env/bin/activate
pip install -r requirement... |
a281086f12e3f914222c80dedaac03e91cdbdea81da1e86e275a7b8f2be09806 | Text | 1,221 | 26 | # INFORM_DSP_MultiOmics_Manuscripts
This repository contains code used in the analysis for the manuscript:
**“Integrative Multi-Omics and Drug Sensitivity Profiling Reveals Potential Biomarkers and Therapeutic Strategies in Pediatric Solid Tumors”**
## Overview
This project integrates ex vivo drug screening with ... |
5b693a4f8dcce8ce12dc54bf1d9aa2b31592161f11c182481d74f26dad9d26dc | Text | 1,227 | 14 | ## Beyond single variants: A pathway-based approach to explore the genetic basis of memory
This repository contains all the code used to analyze the GWAS data of the human connectome project to study genetic variants related to memory performance.
The publication is currently under review.
Content:
* ```1_remove_dup... |
42af1d160697b81548256c7d8b37bbdd3a3c1869591ab19db7f660b03479e54e | Text | 1,230 | 26 | # MEG-Harmonize
Code from the paper "Multi-site Harmonization for Magnetoenceophalography Spectral Power Data"
The script is meant for the comparison of multiple harmonization methods. If your interest is solely in
harmonizing MEG data created using the ENIGMA pipeline (or similarly formatted MEG data), we reccommend... |
2ed26cf9bd6f4e724f0fb6618c3c2410dfc98dd5f54be7657ee9978dbf673c37 | Text | 1,242 | 30 | # Enhanced Scanning Pattern-based Imaging Neural Network: ESPINNet
This repository contains an Enhanced Scanning Pattern-based Imaging Neural Network (ESPINNet) for grating interferometry and speckle tracking methods, which is based on a multi-resolution analysis of convolutional neural networks and can extract multi-... |
c9e362aa4d524f166c326322813fa1bb6868ca062f4d803bac80983becceefbe | Text | 1,245 | 26 | # EnContact
EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model
# Model training
We collected chromatin contact matrix of seven cell lines (i.e. GM, K562, HCASMC, MyLa, Naïve, Th17, and Treg) from HiChIP data of Mumbach et al, 2017. We implemented the EnContact model using Keras 1... |
f9f42c6f6207c33a74817819482cbbe5f69ec37eb7f7669ad2fb0c39c170615a | Text | 1,245 | 33 | # CLGNN
## 1. Overview
The code for paper xx". The repository is organized as follows:
+ `data/` contains the dataset in the paper;
* `CTD_chemicals_diseases.xlsx` contain known chemical-disease associations collected and processed from the CTD database;
* `RDA.edgelist` contain known chemical-disease associations... |
0405a95134731a2166c9fc02e79b78590901f61035d7764df41965d2ca50f46f | Text | 1,249 | 34 | # Oyster Hatchery Yield
Code and compiled data for a study on forecasting oyster hatchery larval yield and identifying conditions associated with high and low yields at the Horn Point Laboratory Oyster Hatchery (Cambridge, Maryland, USA).
## Repository contents
- **code**: scripts/notebooks implementing model traini... |
8e97583fee2fdcc6c616f46bda9f8ff8644bf0d07a2555f88927e3375cb177b8 | Text | 1,256 | 39 | # ECG Re-Ablation Risk Predictor
This repository contains a trained deep residual neural network model to predict the risk of re-ablation within 572 days based on 8-lead median ECGs.
## 🔧 How It Works
The model uses 72 saved TensorFlow/Keras models from a nested cross-validation setup. It averages their predictions... |
7976842072be3d8235f99808c91a25226fd612f82dca8f64157573787f4ece49 | Text | 1,258 | 18 | ## storm-control ##
This is a repository of code developed in the [Zhuang lab](http://zhuang.harvard.edu) for the acquisition of STORM movies.
[](https://zenodo.org/badge/latestdoi/15257214)
[Discussion Group](https://groups.google.com/d/forum/storm-analysis)
Warning! The... |
5a1b4627c844f61e03b142903f60211339ce76fb5b853aa20dfdf52d0aac2dc9 | Text | 1,260 | 21 | # Upf2_migration_2026
This repository contains the data analysis code used in the manuscript:
Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating reelin and ciliary gene regulatory networks<br>
Lin Lin<sup>#</sup>, Naoto Kubota<sup>#</sup>, Yi-Li Lam, Michelle Mingxue... |
6575aabec559c524e62b97e140492608d096a7061659a8167ed981de4a455bda | Text | 1,286 | 25 | WARNING: This repo is unmaintained. If you are interested in pure-python differential expression analysis, please look at PyDESeq2_ .
|PyPI| |Docs|
.. |PyPI| image:: https://img.shields.io/pypi/v/diffxpy.svg
:target: https://pypi.org/project/diffxpy
.. |Docs| image:: https://readthedocs.com/projects/diffxpy/badge... |
9378ab9a92ceaee0fa3c8e3b92e8ab64bb92782a642996cf2a867ba903e44136 | Text | 1,287 | 17 | Comparing five different pipelines post ICA decomposition to find the otimal one for this dataset.
preparation
data
copy ICA decomposed data into yourfolder/derivates/ICA_decomp
Here the data were processed by naj_neurCorGait_master up to and including task_ICA_decomp
(scrips available at https://github.com/Nad... |
a4c39344e5c580dac968c53464ec21c9e250b91a391b3d3c84b0947b8b68a033 | Text | 1,287 | 40 | # Myelin–FC Coupling (MATLAB + Python)
Pipeline to assess how white-matter **myelin** relates to **structural–functional coupling**.
[Nelson M.C., et al. (2026) Communications Biology](https://doi.org/10.1038/s42003-026-09813-6)
## What’s here
- **DATA** derivative connectivity data in 200 & 400 node parcellation — ... |
1bceece05fbb6abbbdc6a5819c2425174aac5ef767731778204785e1a36a26ed | Text | 1,288 | 36 | # Robust Neuroanatomical Normative Models
This repository contains the code used for the analyses presented in:
**Toward Robust Neuroanatomical Normative Models: Influence of Sample Size and Covariate Distributions**
doi : https://doi.org/10.1101/2025.08.26.672402
The project investigates how sample size and covaria... |
563a0732881b52027136334acbdd407680ff45b32e9d6d1aa0e1a2a33fa53f45 | Text | 1,290 | 19 | # furniture_sim
MuJoCo simulation for common furnitures
ventionTable.xml | simpleTable.xml | studyTable.xml |
:-------------------------:|:-------------------------:|:-------------------------:
 | ![Alt text](simpleTable/simpleTable.png?raw=false "simple tabl... |
3cf2d58797933cd03c6d8c8f1f8ce1452f3f07cc560d38237c5942314d262551 | Text | 1,303 | 18 | ## storm-control ##
This is a repository of code developed in the [Zhuang lab](http://zhuang.harvard.edu) and the [Babcock lab](https://hazenbabcock.github.io/) for the acquisition of STORM movies.
[Discussion Group](https://groups.google.com/d/forum/storm-analysis)
Warning! There have been many changes and this soft... |
d636e8a914e4226fd97c5bb925df3e806d5d5e6445c52ca77173111792f1614d | Text | 1,303 | 40 | # Diffusion Flux Model by Paula Giménez Mínguez
This app allows the user to model diffusion of particles in a field of view provided as a tiff image.
Diffusion depends on the pixel intensity so that pixels with high intensity will allow particles to
diffuse freely and pixels with low intensity representy structures ... |
72a144099eb20d4e3011b67125afdc581f72cb5fc14fad57107bcec6c71fc2d0 | Text | 1,304 | 30 | # Neutrosophic-XAI-for-Stereotactic-Neurosurgical-Simulation
Reproducible Python code for the Frontiers manuscript.
This repository contains the full simulation pipeline used to generate the synthetic dataset, all statistical analyses, and all figures and tables reported in the article.
## Contents
- `neutrosophic_... |
5b91ada66bc6382f1f2abeff6946667e47931c33aa167ec5da4b2624e92ee489 | Text | 1,308 | 24 | # Linear RNN for FMRI
This repository contains the Julia code to reproduce the results presented in the paper:
Di Antonio, G., Gili, T., Gabrielli, A., & Mattia, M. (2026). Linearizing and forecasting: a reservoir computing route to digital twins of the brain. Advanced Science.
The project shows how linear recurren... |
bc59df42fe81d51a07aa38edeb1ec253d218ee28cd561de9802e119d7527e4fb | Text | 1,315 | 28 | # HCP Pipelines
The HCP Pipelines product is a set of tools (primarily, but not exclusively,
shell scripts) for processing MRI images for the [Human Connectome Project][HCP].
Among other things, these tools implement the Minimal Preprocessing Pipeline
(MPP) described in [Glasser et al. 2013][GlasserEtAl]
For furth... |
80fc39adaf165b552bbad22e7b4b1242cf293064bb81c0f3494f7fafba48caa8 | Text | 1,317 | 21 | # europe_tree_competition_publi
This repository contains code for the publication "Loss of competitive strength in European conifer species under climate change"
Data that goes along with the code can be downloaded here: 10.5281/zenodo.19161115
There are several folders:
1. preprocessing:
This folder contains sc... |
e8381d724c0bded9e255faa45c9699f8a71c8e04b7f7b79fc076eca4b8561ad7 | Text | 1,319 | 18 |
# Repository for Identification of suicide brain transcriptomic signatures using meta-analysis of multiple cohorts
This repository contains source code (without source data) for the analyses. Source datasets could be obtained from GEO.
Code was written on a Linux machine and is not tested to work on Windows.
Conte... |
dd999b3094728466964f1c8e3d1df8797cd9be752f5de48a13977d719e80c413 | Text | 1,343 | 27 | # DFT IW Stimulation – Masticatory Function (Data & Code)
This repository contains **de-identified** data and code for the randomized crossover study:
*Interferential current stimulation during dental facial treatment improves masticatory function*.
## Contents
- `data/processed/DFT_glucose.csv` — glucose elution da... |
a12851e46d4743f88b45c9db1f445bf29a42b68bbce4c7e737fbbcd19f6bea20 | Text | 1,347 | 21 | # Hair_Plate_Paper
Code repository for Pratt et al., 2025
This repository contains code to analyze walking kinematics of CxHP8 silenced flies on a treadmill, joint angle encoding properties of CxHP8 neurons, optogenetic silencing and activation kinematic effects of CxHP8 neurons, and hair plate connectivity in motor c... |
825567eef5f8bb47eb411ef6676f6e4a7c62a9e1fcb3a3a79afdcb70e19bdfad | Text | 1,363 | 32 | DTI Playground
==============
DTI Playground is python based NIRAL pipeline software for diffusion MRI: preprocessing and quality
control of diffusion weighted images, fiber profile extraction and analysis, and atlas building. It
ships a web UI (DTIPlaygroundLab) and these command line tools:
DMRIPrep (``dmriprep``)
... |
4bda4089ecdf3292b128b251c2c62152bc7b6d127b1fa19bc7f1eb10ced074bf | Text | 1,366 | 21 | # iAMP-SeE: An Antimicrobial Peptide Recognition Model Based on ESM2 Feature Extraction and Hybrid Attention Mechanisms
## Dataset
<img width="2000" height="1530" alt="Figure2" src="https://github.com/user-attachments/assets/96b3fda9-61fd-4d9e-a47b-11132eb3bacc" />
In dataset 1, the positive samples were collected fro... |
923c02f248088ac958461b6adc0efd2d4e73f4029aec04d7da20a959f6fa6189 | Text | 1,374 | 32 | # CPDtissuesXray
The code in this repo supports the plots and findings presented in this study:
> **Critical point drying of brain tissues for X-ray phase contrast imaging**
>
> Safe Khan, Jonas Albers, Artem Vorobyev, Yuxin Zhang, Jakob Reichmann, Angelika Svetlove, Fabio de Marco, Ksenia Denisova, Yikai Yang, Flore... |
37abd8991bf3353ef324f369ec8c49b7adbc67e7a5a0b2f9a206ad4f316b06a9 | Text | 1,382 | 36 | # NOVAS3D
## What NOVAS3D does
*NOVAS3D* (Network of Vessel Analysis in 3D) is a CNN-based pipeline to extract vascular networks from 3D fluorescent microscopy images and track their morphological changes across time.
## How to install NOVAS3D
To install the current release run:
```bash
pip install novas3d
pip ins... |
e97e56fe3caf7f21d9788c60764c4b35f4d5b30e3f1398ef304141ebe8ea5fcf | Text | 1,383 | 43 | ## This site
Go here to view this site:
https://biomedia.github.io/dHCP-release-notes/
## Welcome to GitHub Pages
You can use the [editor on GitHub](https://github.com/BioMedIA/dHCP-release-notes/edit/master/README.md) to maintain and preview the content for your website in Markdown files.
Whenever you commit to... |
1ca2070f1d9414855388f077ba6d35821ee1afeabc7a2542744177db2f681482 | Text | 1,387 | 19 | BCI_RW_FBCSP
- This project involves developing a MI-EEG signal processing chain for a Brain-Computer Interface (BCI) application.
- It includes pre-processing, feature extraction and classification stages.
- The main contribution is the development of an innovative feature extraction technique to improve classificatio... |
8aac423b2cfe306f8cfa306740fe3a4bb7734185607510b4c875ba260c6b241d | Text | 1,391 | 40 |
# scPCA - A probabilistic factor model for single-cell data
scPCA is a versatile m... |
598d7af93958369a848b86d17f09107f41aedafa63710ce612e21e23332de2da | Text | 1,403 | 39 | There are 6 zipped files in this dataset.
Normal GWAS for 76 phenotypes in KoGES (See Nam et al. Table S1 for details)
- SAIGE_summaries.zip: summary statistics for 43 phenotypes in KoGES (using SAIGE)
- SAIGE_dietary_summaries.zip: summary statistics for 23 dietary phenotypes in KoGES (using SAIGE)
- POLMM_summari... |
3f95a55e80352acbd8454f58a807396b3189675a6af8a81ca3f98cc05a3ce622 | Text | 1,405 | 38 | # SCALE: Unsupervised Multi-Scale Domain Identification in Spatial Omics Data
SCALE is a Python package for identifying multi-scale spatial domains in spatial omics data. It leverages graph neural representation learning and an entropy-based search algorithm to detect stable spatial domains at different scales, enabli... |
3f3035514fd0de07e57869171c570abcf262c1ef4271d5f085c071f8f95296c7 | Text | 1,413 | 26 | # <img src="https://cs.wellesley.edu/~btjaden/TermNet/img/Hairpin_A.png" width=100> [TerminatorNet](https://cs.wellesley.edu/~btjaden/TermNet) <img src="https://cs.wellesley.edu/~btjaden/TermNet/img/Hairpin_B.png" width=100>
==========
### [TerminatorNet](https://cs.wellesley.edu/~btjaden/TermNet) is a tool for identi... |
9543edfe63e34dfd6dd869f5aa0768df601f3885b41091544944145bb1eab21f | Text | 1,415 | 32 | proteomaps
==========
Scripts and data for generating proteome treemaps (AKA proteomaps)
------------------------------------------
File descriptions
------------------------------------------
- ./data/KO_gene_hierarchy/KO_gene_hierarchy_changes.csv : Table with our own gene reannotations
- ./data/KO_gene_hiera... |
0019bc250e345a31a6924063e4ae0d37c66e5a0f3870ef5210aefd25e89e3cae | Text | 1,424 | 35 | # ElikoPy
[](https://elikopy.readthedocs.io/en/latest/?badge=latest) [](https://pypi.org/project/elikopy//)  from expression studies, or
from curated gene lists mined from t... |
e7891246e9ea5db1e893c17489a4fc84148ea00e8d839c490c8b163f3bfc74c8 | Text | 1,433 | 19 | **********
QDM data
**********
There are three sets of QDM data in this repository, one for each set of samples: human brain samples, rat brain samples, and magnetotactic bacteria sample.
Each set contains folders for each sample and field of view (FOV). Rat brain data is further subdivided into polishes (see p... |
bed3da4b82e6fd481333578f6a99882c7e5b7212d6b8f89f4686586d45705e48 | Text | 1,436 | 70 | # Requirements and Installation
* [PyTorch](http://pytorch.org/) version >= 1.10.0
* Python version >= 3.8
# Getting Started
* Download and preprocess the minimum dataset
``` bash
cd DASA_NMT
bash ./examples/translation/prepare-iwslt14.sh
```
``` bash
python scripts/build_dep_bias.py \
--bpe-src train.en.bpe \... |
e24eea23f93846c6431f20f1d4cb12089191db936de429df3c353a069fe2b6fb | Text | 1,436 | 22 | # Predicting scores from video
🚧 Currently undergoing revisions 🚧
| | Run |
| - | --- |
| Pose Estimation | [](https://colab.research.google.com/github/quietscientist/gma_score_prediction_from_video/blob/main/0_PoseEstimation.ipynb) |
| Fe... |
c3c0e41a7bc092e866bfccbc55961ad93259db647b3ad7a1b6c80be7a85c1d66 | Text | 1,437 | 33 | Code (c) by Paula T. Kuokkanen, Mehnoush Faghani 2025
Code is licensed under a
Creative Commons Attribution 4.0 International License.
You should have received a copy of the license along with this
work. If not, see <https://creativecommons.org/licenses/by/4.0/>.
The above copyright notice and this permission noti... |
9fe9f15413eea2bab8a4249d13eec94990515600f933e0dc289394caf8745ee6 | Text | 1,438 | 46 | ### General information
The code provided here serves to systematically benchmark the performance of (Core)NEURON using the busyring test. It has been used to compare the performance of CoreNEURON with Arbor. The Arbor implementation can be found [here](https://github.com/jlubo/arbor_busyring.git). Please see [this](h... |
cce528552bc88a21517b713bb0b09ebd9b67dd158e173088f64696246cfa0d2b | Text | 1,450 | 19 | # dHCP_template_alignment
This repository provides all scripts required for aligning surfaces (derived from the dHCP structural pipeline) to the dHCP surface template space
This needs to be done in three steps:
1) Estimation and application of a rotational transform between MNI space and HCP FS_LR space
2) Estimatio... |
cc99c82335656d331d2e2d60f06f083ea7324b5b6b71ac238b0975f536b6e9f5 | Text | 1,461 | 21 | # A common framework for semantic memory and semantic composition
This is a repository for the publication:
Law, R. M., Lambon Ralph, M. A., & Hauk, O. (2026). A common framework for semantic memory and semantic composition. Imaging Neuroscience. https://doi.org/10.1162/IMAG.a.1131
OSF: https://osf.io/m82nb/
... |
2505c0723d1d620a690b7dfc3313df7971986646f39b6f5695d8b5eeb8710a18 | Text | 1,466 | 16 | # Plastic Arbor
This repository contains a list of example implementations of synaptic plasticity models, from single-synapse to network models. The implementations use the [Arbor](https://arbor-sim.org/) simulator library with recent extensions for synaptic plasticity mechanisms (see [here](https://doi.org/10.48550/a... |
284ba52a40ff4d7e5da881d7aef852522a1d561a065418abca2843d98c93a316 | Text | 1,472 | 26 | # DeepSqueak v3: Using Machine Vision to Accelerate Bioacoustics Research
[](https://www.nature.com/articles/s41386-018-0303-6)
[](https://github.com/DrCoffey/DeepSqueak/wiki)
[-derived pseudo-diffusion volume fraction (f) caused by the differences in relaxation times between the tissue and fluid compartments, and to develop a two-dimensional (b-value-TE) fitting approach for simultaneous T2 and IVIM param... |
76e22e0030b0fa79fe8937f9f5f9f943c6aeb4517b9acc0179f2056e57901fec | Text | 1,486 | 17 | # Tierpsy Tracker
<img src="https://user-images.githubusercontent.com/8364368/41229372-a9e8fcfa-6d73-11e8-877c-de306be55526.gif" width="800">
Tierpsy Tracker is a multi-animal tracker developed in the [MRC-LMS](http://lms.mrc.ac.uk/) [Behavioural Phenomics Lab](https://tierpsy.com) at Imperial College London. The proj... |
490d47b537138758ed5bb34e00f7e97c05804c2e073d7bc62ecea206e07ef68f | Text | 1,495 | 40 | ### Regional and global brain age prediction model
---
- The code in this repository pertains to brain age models that are based on the cortical surface.
- The model was constructed and trained by Gilsoon Park.
- Convolutional graphical neural networks were used (https://github.com/mdeff/cnn_graph).
### Dependencies
... |
09f8af6bfdf6f7c5791f359694850cf2e191b2b66ce63007941a1af16d954c4b | Text | 1,498 | 11 | # NeuronAging
NeuronAge – Analysis Code for Neuron-Type–Specific Aging
This repository contains the analysis code and selected input tables used in the accompanying scientific publication investigating neuron-type–specific aging trajectories and neurodegeneration in Caenorhabditis elegans and their conservation in the... |
03c3e0aa290e700caa9917015f19aebfffc60f533c3857bf1d01e34444e6d7fd | Text | 1,499 | 41 | # SCALE: Unsupervised Multi-Scale Domain Identification in Spatial Omics Data
[](https://doi.org/10.5281/zenodo.17803418)
SCALE is a Python package for identifying multi-scale spatial domains in spatial omics data. It leverages graph neural representation learning and a... |
a141508cea3720cb948da5dca01fbfb062bf0630e31c668c5d10cc8dbccfc03e | Text | 1,503 | 42 | # Llano-Lab-Analysis-Program
Test
## Installation
### Required Packages
* CaImAn
* Read-ROI
* Shapely
## To-do list
### In progress
* Rewrite the program with class
* Improve comments
* Make sure lines do not go over the 80 char limit
### Future plans
* Change flag for noise response from "Yes" to "Responsive"
* Ch... |
81daf17176066ca425dc833ddfcdc906439076f7b13f3247bb230b51ab22747d | Text | 1,515 | 38 | # CCF streamlines
This package supports projection of Allen Common Coordinate Framework (CCF)
mouse brain volumetric data and coordinate data on to 2D representations. It
also enables other operations that make use of the "streamlines" between
the top and bottom of the isocortex in the CCF.
## Running the tests
The... |
bbd46574c01ccf642d5b4b6fdd5535d962fe66dc97d3494ca1bc2f87a3a2204b | Text | 1,529 | 26 | # Generic Object Decoding
This repository contains the data and demo codes for replicating results in our paper: [Horikawa and Kamitani (2017) Generic decoding of seen and imagined objects using hierarchical visual features. Nature Communications 8:15037](https://www.nature.com/articles/ncomms15037).
The generic objec... |
8cee047033865c8a7517d6cd3d984c522ffce02315c8b1759309c335bbe9f6ed | Text | 1,532 | 28 | # featurevis
Visualize features that activate neurons via gradient ascent.
## Installation
After [installing PyTorch](https://pytorch.org/get-started/locally/), run:
```
pip3 install git+https://github.com/cajal/featurevis.git
```
## Usage
`feature_vis.gradient_ascent` receives a function $f(x)$ to optimize, an initi... |
1278a4b6a9d89aecefa7335ee8c278f6b05e387b000187703c86bd48b3e47500 | Text | 1,534 | 28 | # Matlab code for *"Anatomically aware simulation of patient-specific glioblastoma xenografts"*
## Description
This repository contains MATLAB code and data used in the publication:
*"Anatomically aware simulation of patient-specific glioblastoma xenografts"*
The project implements an agent-based stochastic model ... |
ebf30fa8bad0cf0b2914b3f6c2d845565195eb4607e17048e45f917cc6251664 | Text | 1,548 | 55 | This is the software/code for the letm1 knockout model.
The mitochondrial model is based on Nazareth model, with some
modifications to include the effects of a spike. This part of the code
is nazaret_mito.py, translated to python my Chaitanya.
-----------------------------------
The code is a standalone software and ... |
3f0b76b9bba66baaed4a752b78fb80b6d0c9ea9ed9026ef3662cc5f424a5cd41 | Text | 1,557 | 33 | An archive containing configurations and machine learning potentials of antimony in various formats.
## Folder content
- Training database and the obtained MACE machine learning potential.
- Raw trajectories and snapshots, generated in various ensembles either with Behler-Parrinello or MACE machine-learning potential;... |
867e3ad6a32dbf891aa981bb63384021074a1e1c3752cf0e3524198ec2b3f77e | Text | 1,569 | 46 | This repository contains the finalized Jupyter notebook used for imputation and correlation analysis of trauma patient proteomics data. The analysis was developed to support a manuscript focused on identifying biomarker patterns and subgroup-specific protein correlations in trauma populations.
FILE ----------------
P... |
2ec87b505a6ad5e0e54ad6dc904328194cdeffa8f0f704be15b273cabe630e14 | Text | 1,583 | 27 | # Forouzandehmehr2026-hiPSC-CMs-Model-hiMCES
A computational model of human iPSC cardiomyocytes electro-mechano-energetics with a new oxygen consumption component
This repository contains code associated with:
Li W, Forouzandehmehr MA, McLeod D, Pozo MR, Heinson YW, Kay MW, Li Z, Morotti S, Entcheva E.
Response of hu... |
370073feb07f45fd9b6203d78a98e0754cb1c5737eb7adac0f1ca249c7ea95f9 | Text | 1,587 | 28 | # Meso-MRI with 3DEPI
This repository contains the data processing scripts for **Whole-brain meso-vein imaging in living humans using fast 7 T MRI** manuscript (Gulban et al. 2025).
## Citation
- Gulban, O.F., Stirnberg, R., Tse, D.H.Y., Pizzuti, A., Koiso, K., Archila-Melendez, M.E., Huber, L., Bollmann, S., Kay, K.,... |
c35309f0c8fd4a1ef6fbff6863de3536c39212123285f2a50067fe1aa3b07b83 | Text | 1,593 | 45 | # Flexible Ultrasound Array Simulation
Simulation code for: **Flexible ultrasound array for subcortical brain stimulation in humans: a simulation study**
DOI: [10.1038/s44384-026-00046-9](https://doi.org/10.1038/s44384-026-00046-9)
k-Wave-based 3D elastic wave simulation of a skull-conforming flexible ultrasound ar... |
d9a0f708e55ce52b0fde5d77a09bfa0dfaec72718f4b095f6a678e637f998184 | Text | 1,617 | 21 | # Language task battery dataset for Functional Fusion
Language task battery dataset. Contrast estimates for 18 task conditions collected over 8 imaging runs for 17 participants.
Resting state data and time series are not included in public release due to size restrictions.
### Installation and use:
The dataset is ... |
65441b9b21f800e970a572b88ac438d150d6db909b28589839f1ca78ac8c492c | Text | 1,627 | 29 | # Meso-MRI with 3DEPI
This repository contains the data processing scripts for **hole-brain meso-vein imaging in living humans using fast 7-T MRI** manuscript (Gulban et al. 2026).
## Citation
- Gulban, O.F., Stirnberg, R., Tse, D.H.Y., Pizzuti, A., Koiso, K., Archila-Melendez, M.E., Bollmann, S., Goebel, R., Kay, K.,... |
3aae3ff933c24bff472ea3edff1dd458835dbd64339d6cea93211c3e236c7653 | Text | 1,630 | 44 | This package contains data and code for the manuscript "Electrophysiological effects of psilocybin co-administered with midazolam"
by Michael H. Sutherland, Christopher R. Nicholas, Richard L. Lennertz, Cody J. Wenthur, Bryan M. Krause, Christina J. Sauder, Brady A. Riedner, Richard F. Smith, Paul R. Hutson, Charles L... |
b628557dc05adbdf9b04be656fb4799a71e5eb4c5f07d98862ba2cbf10239ee2 | Text | 1,631 | 35 | # Object Detection Pipeline for Nigral Neurons
## Installation
Clone the Countnigra GitHub repository:
```bash
git clone https://github.com/onnonuro/countnigra.git
```
## Tutorial with Google Colab
Google Colab is the easiest way to try this software with GPU support... |
5fd1fbe0e9bfdd0b6695bfe0bc5e80b596e12a85009328ecc8025d25afc676bc | Text | 1,632 | 33 | # Hyperbaric oxygen intervention, cooperation, and inter-brain synchrony
This repository contains analysis code and example data for the manuscript:
**Hyperbaric oxygen intervention enhances cooperative gains in high-trust people at high altitude: the role of medial prefrontal inter-brain synchrony**
## Overview
Th... |
482f53da0b44e46fe2db63e3d5d7534d03e5380dd02b12ad461711bb99127add | Text | 1,634 | 35 | # The E-H PhaseSync Model
The model was built to simulate the 3-fold periodicity of Hippocampal activity, which was found in the manuscript entitled "The spatial periodic computation of hippocampus-entorhinal circuit in navigation", DOI: https://doi.org/10.1101/2022.01.29.478346.
<br />
The main finding of this pap... |
b26c19b609ee7bcf05ecb8e7f55a1288e0988bbbd3ab70e1b0edefc6065d4b7b | Text | 1,639 | 72 | # 3DTCMPE and CINR - Medical Image Processing Tools
This repository contains two main components:
1. 3DTCMPE for texture encoding
2. Cycle INR (CINR) for shape encoding
## Installation and Setup
Both tools can be installed in separate conda environments:
### 3DTCMPE Installation
```bash
# Create and a... |
4b329ee17a72f40e078cdc13fa817cb1a96a5bdda5f6630331a47ef189314265 | Text | 1,641 | 18 | # Emergent Reservoirs
This repository contains code for replicating all analyses and figures of the corresponding preprint *Evolving reservoir computers reveals bidirectional coupling between predictive power and emergent dynamics* by Tolle et al., 2024.
# Installation
The code depends on the following external MATLAB... |
cea57ff79609b7ca35ce7e17534e18ea451f59da6e83aab17a7a2da34f5b4790 | Text | 1,643 | 38 | # NetworkFlowTracker
## Overview
*NetworkFlowTracker* (NFT) is a Python package for particle tracking in spatial networks. It is developed for tracking red blood cells (RBCs) circulating in 3D vascular networks, where RBC densities and flow speeds vary by orders of magnitude across vessels. NFT utilizes a spatial grap... |
752fd25b5d2491ae19de17c53da88fa601c8b0940719c20c2a5ba7329af8ab03 | Text | 1,649 | 9 | VeloVAE - Variational Mixtures of ODEs for Inferring Cellular Gene Expression Dynamics
The rapid growth of scRNA-seq data has spurred many advances in single-cell analysis. A key problem is to understand how gene expression changes during cell development. Recently, RNA velocity provided a new way to study gene expres... |
9644e09902b87f88fdbb8bfffdbceb3fe4877d7c451d44797d6c6c5311e7bda7 | Text | 1,660 | 25 | This folder contains all the data used for the paper: "Physics-informed Hamiltonian learning for
large-scale optoelectronic property prediction"
Each subfolder contains the data for the respective material. For GaAs, the first-principles data
is already published in 10.5281/zenodo.10089542.
Input files for calculati... |
dd9009c354f53f3c1b3ae3da417c8e23d861ff1faa6d56f104db43c8f1eba0d5 | Text | 1,668 | 44 | # Official Source Code for IgPose
This project is licensed under the **CC-BY-NC-ND-4.0** license.
## Environment Setup
- **Create a conda environment:** `conda create -y -n <env_name> python=3.12`
- **Install dependencies:** Execute the setup script to install all required packages:
`bash scripts/setup.sh`
---
... |
8dd639e16adbb5aecc70b8d7649b2e1518c8026ff2ed335c2ce3196dc99a9bde | Text | 1,680 | 35 | 
[](https://bx-python.readthedocs.io/)
# bx-python
The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains ... |
d3552db3500c698afa63d56a7dac84356d183071a423baf429a3b3ab34d66dcc | Text | 1,691 | 59 | # nsdcode
This repository contains nsd_mapdata.{m,py}, a light-weight utility that
allows the user to map data between different reference spaces
(e.g. anatomical, functional, volume-based, surface-based) in the NSD dataset.
Both MATLAB and Python versions of the utility are provided.
For more information on the NSD ... |
9db66b3237de504973e3c711b7fba55dc0cde3bcf83b6d25895ba6c663c9019b | Text | 1,693 | 38 | # pruningComparisons
## Overview
This repository contains scripts for fNIRS data pruning using different methods and parameters, plus analysis of the effects on data quality and retention.
- **MATLAB (`pruningComparisonsMatlab/`)**: Processes raw data and generates output tables.
- **R (`pruningComparisonsMatlab/`)**... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.