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280bc45e08621af97c66d00e6da4eb37a27314e961152af42fdfd11d728f1a45 | Text | 4,222 | 122 | # Learning spatial hearing via innate mechanisms
[](https://opensource.org/licenses/MIT)
This repository contains the implementation of the bootstrapping-based approach to learning sound source localization (SSL) presented in our paper: "Learning spatial he... |
eb22bfa2d778d0109dd44dd454a997baf0a72ae7c432cfa172ec472a06864f3c | Text | 4,226 | 95 | # About
This repository supplements the original [SINDy-RL code](https://github.com/nzolman/sindy-rl) for use with the [m-AIA (multiphysics - Aerodynamisches Institut Aachen) solver](https://www.tandfonline.com/doi/full/10.1080/10618562.2020.1742328); in particular, for training an agent to perform gust mitigation for ... |
6c99d8d3903bc8a7d396bd7b26f589d78a95df1f926f5eafc7f60cc51ffe809b | Text | 4,259 | 65 | # In Silico Purification for Methylation-Based Tumor Classification
This repository accompanies our manuscript, *"In silico purification improves DNA methylation-based classification rates of pediatric low-grade gliomas"*.
## Background
DNA methylation-based classification has transformed diagnostics for CNS tumors, ... |
e7c1f7b2e6b8dc63e04a30f54a7836de434d17ced40f2595e15999ab15e4238b | Text | 4,270 | 182 | JS Segment Annotator
====================
Javascript image annotation tool based on image segmentation.
* Label image regions with mouse.
* Written in vanilla Javascript, with require.js dependency (packaged).
* Pure client-side implementation of image segmentation.
A browser must support HTML canvas to use this ... |
2943bd23ed854f3d90170f0d5e2123e8e7e7783042af6c9cfed60b75f1d2891f | Text | 4,297 | 94 | # _seismic_: Single-cell Expression Integration System for Mapping genetically Implicated Cell types
This repository contains code for the R package [_seismicGWAS_](https://github.com/ylaboratory/seismic), an implementation of the
_seismic_ computational framework for mapping genetically implicated cell types
and the... |
ab55479a216425ac9e70e4e2aa036fbe0ebcbe6e3fa0127c01d4256be307bf2f | Text | 4,306 | 76 | # Simple snakemake pipelines for common/standard bioinformatics analyses
This repo contains a collection of ad-hoc and flexible pipelines for running common bioinformatics tools on a directory of input files.
See [Available Pipelines](#Available-pipelines) section for a list & description of available workflows. Wel... |
479ca7819ebc7d214d0465c7a8c5a1fd86b71c57e331ddf37f9a2dd495c49183 | Text | 4,312 | 97 | []()
[]()
# Context Representative Interpretable Model Explanations (CRIME)
`CRIME` is a Python package that integrates with LIME (Loc... |
653d73187c3c823fee988e27feb575e0771d70fe1fec8b406c6c6f85c0415453 | Text | 4,317 | 99 | # Vicarious_somatotopy
<img src="https://i.imgur.com/1Zy21Hf.png" alt="Image description" height="200"/>
## Overview
This repository contains the scripts for performing multi-source spectral connective field model fitting as described in this [preprint](https://www.biorxiv.org/content/10.1101/2024.10.21.619382v1). B... |
d840b607b47c5b4687b429d1e65be9edcd247eee843cad8b021a8bd7082ab1ea | Text | 4,348 | 91 | # Franken
[](https://github.com/CSML-IIT-UCL/franken/actions/workflows/CI.yaml)
[](https://franken.readthedocs.io/)
## Introduction
F... |
cd62132588a454c7e9233a0864a146cb3f49fbd333b0bef92f67f27b6e31f6b4 | Text | 4,355 | 44 | # IDENT study analysis scripts
This repo contains fMRI preprocessing/analysis scripts for the IDENT study, in which participants performed a variety of tasks engaging reasoning and memory about close familiar people and places (IDENT = identification).
Links to data and further information:
* [Methods](https://osf.io... |
0bb3ca8d0f8de1d552d36f3cbd7231129e05a6e43b70cd7575bead47710a2d9f | Text | 4,375 | 86 | # Marmoset_Cortex_Model
# README
## Overview
This repository provides the source code and data associated with our manuscript "*A hierarchy of time constants and reliable signal propagation in the marmoset cerebral cortex*". It includes executable Jupyter notebooks and auxiliary Python functions necessary for reprod... |
f32028c0bba5ef346462f30b9bc7fd5818fb19b1b0d3410028860780f79615f6 | Text | 4,376 | 90 | Code Supplement for:
Unsupervised feature extraction using deep learning empowers discovery of genetic determinants of the electrocardiogram
Authors: Ewa Sieliwonczyk et al.
==================================================================================
FOLDER STRUCTURE
This repository contains all scripts used i... |
bf0f622872877ad3fcc73ec945c4b609747ed226627126b50bfbaa4c54132f77 | Text | 4,396 | 77 | # Simple snakemake pipelines for common/standard bioinformatics analyses
[](https://doi.org/10.5281/zenodo.15210437)
This repo contains a collection of ad-hoc and flexible pipelines for running common bioinformatics tools on a directory of input files.
See [Available Pip... |
49c8a9b64320553c42ded2ab3509d973ee9731647a8ad3af3ee227886d8aab8d | Text | 4,402 | 62 | # GeNEsIS - GEnerator of Numerical ElementS Images Software
(Repository DOI: https://zenodo.org/badge/latestdoi/296050999)
This is a custom program written in Matlab (Matlab R2019a, The MathWorks Inc., Natick, Massachusetts, USA), using Appdesigner.
A supplemtary tool of this program uses also Psychtoolbox-3 (the Psy... |
c0f24f66cb5f52ade59b7b53f69d87c7df7e6ecc3f1751b6137ae89f2abad041 | Text | 4,404 | 83 | <p align="center">
<img src="https://i.postimg.cc/sxghVMck/figure-Oflv.png" alt="lv"/>
</p>
<h2> <b> LivelyVectors (lv) </h2> </b>
---
<li>
Can be used for EEG analyses and other multivariate data, can be used with videos, speech, data from sensors, etc.
</li>
<li> Can be given <b> custom-built </b> pipeline steps... |
056e4811aa4c0e6ca096b8d1ae5d33a5d91f3ba02d1aad1ebce0d779c67be425 | Text | 4,409 | 75 | # Prospective Validation of Machine Learning Algorithms for ADME Prediction: An Industrial Perspective
Absorption, distribution, metabolism and excretion (ADME), which collectively define the concentration profile of a drug at the site of action, is of critical importance to the success of a drug candidate. Recent adv... |
de646789f5d3ee7a66f2e018de5ee770e242acc1006c0666340eea8cb75cd92a | Text | 4,427 | 107 | # Benchmarking Scientific ML Models for Flow Prediction
This repository provides the source code and training scripts for **"Geometry Matters: Benchmarking Scientific ML Approaches for Flow Prediction around Complex Geometries."** The project evaluates state-of-the-art **neural operators** and **foundation models** fo... |
fd261a737b651d06b875273facf1bf9a23b0c1c3057201d7d0114cb1832c1f44 | Text | 4,445 | 97 | # Automatic Spinal Cord Segmentation on gradient-echo EPI Data
Repository for the project containing training information, model weights and inference instructions. The code is based on the [nnUNetv2 framework](https://github.com/MIC-DKFZ/nnUNet).
Dataset used for this project is open-sourced! Find it [here](https://op... |
bef18a4ae16872f83e074a75ca68e8823b2e2fb143697c1685264fa3905568dc | Text | 4,463 | 96 | # `Etho`: A Python framework for coordinating stimuli, data acquisition, and hardware control in neuroscience experiments
[](https://github.com/janclemenslab/etho/actions/workflows/python-package.yml)
[
**Authors**: Charlotte Bunne\*, Stefan G. Stark\*, Gabriele Gut\*, Jacobo Sarabia Del Castillo, Mitch Levesque, Kjong-Van Lehmann, Lucas Pelkmans, Andreas Krause, Gunnar Rätsch
The Nature... |
ea9fdd39c8a500db6521854fe58ca33eea60f9c6815123d9d22708ba564a0b2a | Text | 4,511 | 144 | .. -*- mode: rst -*-
|MNE|
MNE-Python
==========
MNE-Python is an open-source Python package for exploring,
visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG,
ECoG, and more. It includes modules for data input/output, preprocessing,
visualization, source estimation, time-frequency analy... |
2113f5766e33f4c8f1ead133f3eafd006a505e9cf5932a0728afc104b428fde9 | Text | 4,543 | 137 | # Nanotube Image Segmentation and Region Tracking: CNN-Based Patch Classifier for in situ HRTEM datasets
This repository contains code used to support the analysis of wetting dynamics inside nanotubes in the manuscript:
"Capturing atomic wetting dynamics in real time" by
George T. Tebbutt, Christopher S. Allen, Anna F... |
e365a4d7d2df46aabaf3f7ba8c5e14318dd2efcb4a608e5a4769e23e9ec12a47 | Text | 4,566 | 47 | # DeepInMiniscope: Learned Integrated Miniscope
Feng Tian, Ben Mattison, Weijian Yang "DeepInMiniscope: Deep learning–powered physics-informed integrated miniscope"
### Clone this repository:
```
git clone https://github.com/Fengshub/DeepLeMiN-Learned-Lensless-Miniscope
```
## [Paper link](https://www.science.org/doi/... |
48c0cda1c9d799ce85fcab1431a2861068dde0d97149043c8188a80bf5bf454d | Text | 4,568 | 122 | # Abstract
**Motivation:** Graph Neural Network models have emerged in many fields and notably for biological networks processing. Here, we introduce GNNenirch a novel graph neural network-based enrichment analysis method.
Through multiple levels of embedding that integrate protein sequence properties and interaction ... |
35bfedc765e8a5bef7c1a3a69c402e89ae94ee74eff2455518e01d4d5c4c69d5 | Text | 4,578 | 77 | # Faster Temporal Median
A rewritten version of the Fast Temporal Median Filter, enabling extra features like more bit-depth support and larger-than-ram datasets, as well as being slightly faster than previous versions.
## Installation
One can get the Plugin by using the download link below, or by subscribing to the H... |
10121682ebd5e8cbe5df5fe8372b1e5c7cac24642701013825907041def2d121 | Text | 4,586 | 104 | # Using single-cell perturbation screens to decode the regulatory architecture of splicing factor programs
Adapting splicing factor activity analysis to gene expression signatures to study the regulation of splicing factors from single-cell Perturb-seq screens.
This repository contains the workflows (from data downlo... |
4d4fa5f4e4219fa59a70e270862d963766bf9590cbb0f28b23460e1690e3be54 | Text | 4,587 | 104 | # Decoding the regulatory architecture of splicing factor programs through single-cell perturbation screens
Adapting splicing factor activity analysis to gene expression signatures to study the regulation of splicing factors from single-cell Perturb-seq screens.
This repository contains the workflows (from data downl... |
127d9da3b4bb90ca3c9f2df9afc50d4fd2f6bf23c2525cd0c9fb792fa51f4677 | Text | 4,636 | 78 | 
[](https://github.com/funkelab/daisy/actions/workflows/tests.yaml)
[](https://github.com/funkelab/daisy/actions/workfl... |
a94ec26a007b979061562fc8addc4c78e5e7b1616d8b34437b5b195976272b92 | Text | 4,651 | 118 | # INIF
This repo is the offical codebase for the manuscript 'Implicit Neural Image Field for Biological Microscopy Image Compression'.
## Introduction
**Implicit neural image field (INIF)** is a SOTA paradigm for microscopy image compression, characterized by its effectiveness and flexibility. It adopts a learned opti... |
f14cc7e521135ccc68dea968719fd66a8433d1dd68e0b76ca2b3e5125a0db941 | Text | 4,659 | 135 | # $\Psi$-NN Project Description
$\Psi$-NN adopts a three-step method of "distillation - structure extraction - network reconstruction", which can automatically discover and implicitly embed the physical properties of PDEs into the MLP network structure.
## Example Se... |
fb5e7ad3b5f6b6d452f9006070951eeb1af33a28c81c05c1327b67122393ad0c | Text | 4,664 | 52 | # Contribution of amygdala to dynamic model arbitration
## Overview
This repository contians custom MATLAB codes for generating analysis plots for the following manuscript: _Woo et al. (2024) Contribution of amygdala to dynamic model arbitration._
Requires installation of MATLAB 2021b or higher. Some functionality mi... |
5ce59236a431e5757d46d1478b4a1fa5c4886f0561d86e12b74e4650aa85fad3 | Text | 4,671 | 98 | # <img src="https://raw.githubusercontent.com/ezmsg-org/ezmsg/main/docs/source/_static/_images/ezmsg_logo.png" width="50" alt="ezmsg logo" /> ezmsg
Messaging and Multiprocessing.
`ezmsg` is a pure-Python implementation of a directed acyclic graph (DAG) pub/sub messaging pattern based on [`labgraph`](https://github.co... |
d8dbcf8af7055780ee0021f945013d3fb843e22f69bed315ce0e5ecdb3c2af94 | Text | 4,694 | 80 | # brainconn (brain connectivity) library
The `brainconn` Python library is a fork of `bctpy`, which in turn is a Python implementation of the `BCT` MATLAB toolbox. `bctpy` was written by [Roan LaPlante](https://github.com/aestrivex) and is a wonderful tool. However, there were certain elements of the implementation th... |
b21209a195b199ffdbe048d723dec741146cb5e88152e70bbe2012360ef25c4e | Text | 4,707 | 23 | # snmCAT-seq_integration
This repo is associated with the cross-modality integration comparison part of our [manuscript](http://dx.doi.org/10.1101/2019.12.11.873398)
We tested five data integration tools: 1) Scanorama(Hie et al., 2019); 2) Harmony(Korsunsky et al., 2019); 3) Seurat(Stuart et al., 2020), as well as 4)... |
993be501779434bbeaed1e3309a73379059daea14e4d540ca8e4372408bf41b0 | Text | 4,732 | 135 | # iGCPs: Generalized Neurocytoskeletal-PDEs Model
We introduce the iGCPs (Generalized Neurocytoskeletal-PDEs) model, incorporating regulatory protein interaction networks for quantitative spatiotemporal simulations in neurocytoskeleton dynamics.
## Key Components and Scripts:
1. **2D_to_initialswc.py**
Used for... |
b052a3ec16ed0a150508e327fe63cac8104c61bcc71b3c2c835ea55ae0545276 | Text | 4,740 | 46 | # brain-mri-nlp
This repository contains a project files, scripts and configs written during the development of a spaCy span categorisation NLP project for the automated extraction of mentions of volumetric assessment from brain MRI reports in a memory clinic context.
This includes scripts and project.yml options for c... |
5cd8aaa14b918c39092dac919fbadf1097243d107bb0c1616f83bcd8a31babaa | Text | 4,749 | 99 | # Extract reads with soft-clipped polyA tails from bulk RNA-seq
Snakemake pipeline to extract polyA-tail containiing reads (PATRs) from aligned bulk RNA-seq datasets and identify poly(A) site clusters. Broadly mimics workflow reported by [Vlasenok et al. 2023](https://doi.org/10.1093/nargab/lqad051) with more customis... |
465e4598095b47f4db7aa35caa453385e351ff172e3407b97617d98dbeb1e7b2 | Text | 4,755 | 96 | # DeuteMetCon
This MATLAB software repository is part of a human brain 3D deuterium metabolic imaging (DMI) work to investigate SNR improvement of bSSFP acquistion when using spectral-spatial CSI and multi-echo encoding schemes.
What can it do:
- reconstruct CSI and multi-echo raw data in SNR units
- multiple ways o... |
28d0b509a6d68e49ab72f1d5de5e3ae2140a41a4f7035ffdd9713d35bd79ce5f | Text | 4,760 | 208 | # SegClarity
**Semantic Segmentation & Explainable AI Framework for Documents and Urban Scenes**
[]()
[]()
[]()
[![Paper... |
f4877cdc763d6c7b68ebf71df3291bc7a52733aafce168d847f77e6b1e2414eb | Text | 4,771 | 171 | # PROTRACK3D
----------------------------
System requirements: 8 GB RAM
HDD/SSD space: 200 GB
CUDA compatible NVIDIA GPU
----------------------------------------------------
## Video Guide
https://drive.google.com/drive/folders/1P1xnie3QyOVtE7kxuKFWwB8wfDo5jfoI?usp=sharing
## Install Python
[Download Python] ... |
8f4c4759e834eb788a777b72023b5ae75b7dbce5df0e1ec4cc65eaeda054aa5f | Text | 4,774 | 96 | # DeuteMetCon
This MATLAB software repository is part of a human brain 3D deuterium metabolic imaging (DMI) work to investigate SNR improvement of bSSFP acquistion when using spectral-spatial CSI and multi-echo encoding schemes.
What can it do:
- reconstruct CSI and multi-echo raw data in SNR units
- multiple ways o... |
6be5401dbd9b26014e1f873a3cbc3329bcbd7e12b479aa3b730a7464132473a2 | Text | 4,848 | 82 | ---
license: apache-2.0
license_link: LICENSE
tags:
- chemistry
- molecular simulations
- machine learning potentials
- neural network potentials
- drug discovery
---
# Acellera AceFF 1.0 (OLD)
**Organization(s):** Acellera Therapeutics, inc
**Contact:** info@acellera.com
**License:** Apache 2.0
---
## Overview... |
9ac0efdb6a061b640648ef63a20b4d9a6ffa36e2cf4563e59a68148affd92c61 | Text | 4,854 | 76 | # Premethyst
Premethyst is a pre-processing pipeline for single-cell DNA methylaiton data generated using sciMET workflows. It starts with demultiplexed fastq files and proceeds through alignment, methylation call extraction, and produces a compressed h5 file containing all base-level methylaiton calls for each cell wi... |
f629fb0de303cfb859a8092c0c1183080fd48d1960854ffbdaaa350a68405674 | Text | 4,866 | 89 |  OrganoidTracker
================================================
[Publication of OrganoidTracker 1](https://doi.org/10.1371/journal.pone.0240802) / [Publication of OrganoidTracker 2](https://doi.org/10.1038/s41592-025-02845-6)
Program for tracking cell nuclei in (intestinal) organoids... |
f1d52bb10bd6d33e21bbb350995f02419434e4fa9b81533f83600edb3fae7ab4 | Text | 4,882 | 94 | # AOTools: A microscope add-on for adaptive optics
A composite device for controlling and using deformable mirror adaptive
optic elements. This composite device can be constructed from any
python-microscope compatible adaptive optics elements and cameras (see
python-microscope compatibility list) as well as certain s... |
0ea4801b1f872df206b1dc4f91137d5d9646d1f8025a119f289aeae9be450d4c | Text | 4,903 | 101 | # A-to-I editing regulates splicing and circRNAs in the brain
This repository contains the code associated with the article titled "A-to-I editing regulates splicing and circRNAs in the brain". The code provided here was used for the analysis and generation of results presented in the article.
## Introduction
The co... |
0fa7870bfe422b6f4c90d13b5346c1e7b56ab7ee0c999c872d2511a47563a4e9 | Text | 4,908 | 85 | # MATLAB code to replicate main results from "Functional ultrasound neuroimaging reveals mesoscopic organization of saccades in the lateral intraparietal area"
## Project Organization
------------
├── LICENSE <- license
├── LICENSE.md <- license
├── main_a... |
7c2846029b5fb073ae6c6f2d65729d202f138bab3dd7d96376f2e09e9c49ffd2 | Text | 4,911 | 116 | # Dataset and code of our EMNLP 2019 Paper (Multilingual and Multi-Aspect Hate Speech Analysis)
If you use our dataset or our guidelines please cite this paper:
@inproceedings{ousidhoum-etal-multilingual-hate-speech-2019,
title = "Multilingual and Multi-Aspect Hate Speech Analysis",
author = "Ousidho... |
7a089d21cfacdda2366b8bd03d2ec625db700642f31f20b6b3e94b6a723f3ce9 | Text | 4,912 | 126 | # KGG
Knowledge-Guided Graph Self-Supervised Learning for Molecular Property Predictions [(ChemRxiv)](https://chemrxiv.org/engage/chemrxiv/article-details/68088e84e561f77ed461ef2d)
## Overview
**Knowledge‑Guided Graph (KGG)** is a lightweight, self‑supervised pre‑training framework that injects orbital‑level che... |
ec8dc7f37cb76417c86fbf3bcdf2e5dcd4b6fb2e732c24efb9f0961ba969e0ad | Text | 4,915 | 141 | # $\Psi$-NN Project Description
> 🟢 Published in Nature Communications (2025): [DOI: 10.1038/s41467-025-64624-3](https://doi.org/10.1038/s41467-025-64624-3)
$\Psi$-NN adopts a three-step method of "distillation - structure extraction - network reconstruction", which can automatically discover and implicitly embed th... |
2c207bcd554414609b7017a95c26732f78397ad25a70c4a4130b6e801e047ef4 | Text | 4,933 | 95 | # NiMARE: Neuroimaging Meta-Analysis Research Environment
A Python library for coordinate- and image-based meta-analysis.
[](https://pypi.python.org/pypi/nimare/)
[](https://pypi.python... |
cae8ce47bf0e203b7d91294373c0c418eebc9428ca4c277a9d4ead071a558ed1 | Text | 4,944 | 94 | # SpateCV
SpateCV is a unified framework for the joint analysis of scRNA and scST data, enabling the imputation of unmeasured genes and data integration.
## Installation
This implementation is written in Python3 and relies on jax, flax, sklear... |
634e7846b4336e5d4a80b125d94542d6269e8fea27bea9e807cf78d02db0cfa8 | Text | 4,962 | 88 |
# MAP: Modular Agentic Planner
Official repository for the paper - "[Improving Planning With Large Language Models: A Modular Agentic Architecture](https://arxiv.org/pdf/2310.00194)."
## Requirements
- python 3.9.17
- numpy==1.24.3
- tqdm==4.65.0
- json==2.0.9
- openai==1.24.1
## Tower of Hanoi (ToH)
For ToH tas... |
ed270353dd0ba4ba977f33914b7b1879685ae84564b8f8a1bc84e486c8f804b3 | Text | 4,991 | 138 | # Microneurography Spike Sorting Pipeline
This repository provides a reproducible pipeline for preprocessing, sorting, and analyzing spikes based on different feature sets (amplitude and width, features from the SS-SPDF method [Caro-Martín et al., 2018](https://pubmed.ncbi.nlm.nih.gov/30542106/), raw waveform) via *... |
78f61c012ff1f42b8b7b4f384d645154486c05fbd11694ed1e52b915278b9bf2 | Text | 4,999 | 73 | # (QTAIM) Generator
<img src="https://github.com/santi921/qtaim_generator/blob/main/qtaim_gen/notebooks/TOC.png" width=50% height=50%>
A simple package to perform QTAIM on molecules, reactions, and (soon) periodic systems. Uses QTAIM to define bonds in a system as well as define a rich set of descriptors for machine ... |
265eba8def1c51c6340ec0bcdc6fd4dc9bed5f4cb36aaac6cd6e8ca66fa63a51 | Text | 5,045 | 107 | # Node2Vec
[](http://pepy.tech/project/node2vec)
Python3 implementation of the node2vec algorithm Aditya Grover, Jure Leskovec and Vid Kocijan.
[node2vec: Scalable Feature Learning for Networks. A. Grover, J. Leskovec. ACM SIGKDD International Conference on Knowledge Discov... |
12e32ba3919fba47727defb63a5ad427acb8de54e0fac8bb44eeac41eef324df | Text | 5,046 | 129 | # The Brain Scaffold Builder
[](https://codecov.io/gh/dbbs-lab/bsb)
[offensive (OFF vs NOT_OFF) language tags for Arabic social media comments collected from three differen... |
a6987cf61cd48c8ac50f2bdd17c4c93edff699011b8eda911cd8e2435e928026 | Text | 5,117 | 119 | ========================================================
NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
========================================================
.. image:: https://travis-ci.org/nipy/nipype.svg?branch=master
:target: https://travis-ci.org/nipy/nipype
.. image:: https://circleci.com/gh/nipy... |
c4cf5a81fe32e6d615ecc0d8747dc247ede23f0314c0efbdc7a179b280e3507b | Text | 5,120 | 83 | # Code associated with the article *Assessing radiofrequency safety of active implants by measuring induced radiofrequency currents using MRI*
The context of use of this code is in the area of MRI safety for active implants. This code corresponds to the data processing of a proposed method to better individualize MRI e... |
62d03ca190d8782cb78020cf4c42922a014a16e50567fbee82df043d6177b0e5 | Text | 5,155 | 132 | # Compound-protein interaction (CPI) prediction using a GNN for compounds and a CNN for proteins
### _**Important: this repository will not be further developed and maintained because we have shown and believe that graph neural networks or graph convolutional networks are incorrect and useless for modeling molecules ... |
6d6795c57ca6b7677c0152b87cff4cb09a0131cced49e95da0850f7ca84560b0 | Text | 5,166 | 71 | # Scripts for data processing for “Enhancing Transcranial Ultrasound Stimulation Planning with MRI-Derived Skull Masks: A Comparative Analysis with CT-based processing”
This collection includes the scripts and steps required to reproduce the analyses presented in the publication Zadeh *et al.* 2024, *Enhancing Transcr... |
7b738c35f80f7eb62519d79ffd904e38d3e73dfee681680c3527423bfc9dd63b | Text | 5,194 | 80 | [](https://colab.research.google.com/github/abbasilab/celltransformer/blob/main/notebooks/demo_celltransformer_onesection.ipynb)
# Contents of Repo
This repo contains several items necessary to reproduce the paper
"Data-driven fine-grained regi... |
49a4adc0c987bb24d468a1d86f0ebf247c92b89c72322e250cf2aa67b45c30db | Text | 5,198 | 115 | # CLRIA
CLRIA: connectome-constrained ligand-receptor interaction analysis for understanding brain network communication
<img src="./img/Fig1.png" alt="Fig1" style="zoom: 45%;" />
## Installation
* Install from PyPI: `pip install clria`
* install from source:
```bash
git clone git@github.com:duzc-Re... |
1571d30e9c1caa06be898a2351486d428fc2f1446f1a0e792fdd140ffc86e449 | Text | 5,217 | 111 | 
# Tools for mini-ImageNet Dataset
[](https://github.com/y2l/meta-transfer-learning-tensorflow/blob/master/LICENSE)
[ - R
## Install all needed packages following the instructions detailed here: https://satijalab.github.io/azimuth/index.html
## To see some examples how to use the tool and visualize the results, please visit: https://satijalab.github.io/azimuth/articles/run_azimuth_tutorial.h... |
970a2e49439baa67e5eac5b364d1ad2a194278a4dc805e2380de0ca97efe1b21 | Text | 5,269 | 48 | # Synaptic-Proteome-Diversity
This repository includes the code develop for the scientifc article entiteled 'Synaptic proteome diversity is primarily driven by gene regulation of glutamate receptors and their regulatory proteins'. This work is freely available at the preprint repository bioRxiv, which can be downloaded... |
34fd9567086fbcc6b42d7e57ea07ee03840df620a9ea4595e50319f20c0cad0c | Text | 5,296 | 80 | [](https://github.com/microsoft/aoc/actions/workflows/install-test.yaml)
[](https://github.com/microsoft/aoc/act... |
4818e96eaa57c16b5ae2e296d998f2dde7e0f6feb57f7a29aac01deeff157afa | Text | 5,331 | 128 | 
[](https://github.com/activityMonitoring/bioban... |
cf2d1f7c1d083e16cb93ddca7059440171a79d9e99e7dd282b4692e7c650adf2 | Text | 5,338 | 117 | # MRIPreprocessor
This repository provides a simple pipeline to co-register different imaging modalities and skull strip them.
This package uses HD-BET (https://github.com/MIC-DKFZ/HD-BET) and ANTsPy (https://github.com/ANTsX/ANTsPy).
For example, this pipeline is designed for the BraTS dataset.
If you find this c... |
e11bbdca0b76ef327e6dfbbf221afaaa5e7ab28e37a8b293e081cca480716abb | Text | 5,340 | 82 | # Note that this package is obsolete. Active development has moved to [s3pipe](https://github.com/BRAIN-Lab-UNC/s3pipe).
# [Spherical U-Net package](https://pypi.org/project/sphericalunet/)
Python-based spherical cortical surface processing tools, including spherical resampling, interpolation, parcellation, registratio... |
bcac00f5245daf4b644a37d8b831b276c045714b65e1cb37f0c530d547f06ddd | Text | 5,363 | 151 | # Physics-informed Transformer for Electronic Quantum States
<p align="center">
<img src="log.png" width="40%">
</p>
---
This repository contains all the scripts used to generate and analyze the data in the paper "Physics-informed Transformer for Electronic Quantum States".
**Authors:** João Augusto Sobral (Univer... |
385d106069f5fb7808a16b8207f91333ecc82e37c30befa2a3873ec01e3d7cd4 | Text | 5,382 | 119 | ## Introduction
JUMP (JUmbo Mass spectrometry-based Proteomics tool) is a software suite for
processing mass spectrometry-based proteomics data including peptide/protein identification,
filtering of identified peptide-spectrum matches (PSMs), quantification of peptides/proteins and so forth.
## Basic installation
A b... |
2ce34f425652ddd2c9b66b30173604b19f380108755d601c8c4e725ed5798a5a | Text | 5,404 | 98 | # GLMsingle
-------------------------------------------------------------------------------------------
GLMsingle is a toolbox for obtaining accurate single-trial estimates
in fMRI time-series data. We pro... |
9e9dffcd0f9d7ef607ae07272a47525891801f8ca6418aad2b43dbcf63b6c5b2 | Text | 5,417 | 50 | # RS-FetMRI
RS-FetfMRI for processing Fetal resting-state functional MRI scans
### Introduction
Resting-state functional magnetic resonance imaging (rs-fMRI) has most recently proved to open a measureless window on functional neurodevelopment in utero. We focused the Fetal resting state functional MRI processing pipe... |
90c22be1e303bc9c89c538188eb6074b3ad3c7cf3349efd7016eed1628721eb8 | Text | 5,438 | 93 | # 3D Point Clouds
Files in this repository were used for the manuscript "Spatially integrated cortico-subcortical tracing data for analyses of rodent brain topographical organization"
## How to use this repository
There are a few ways to use this repository:
**1. Download the zip file:** Click on the green "C... |
ced0e4d23578d24ff8268f5175256b6d439e7512f9a74329e6fd01941bed2634 | Text | 5,465 | 121 | TIGER: Tools for Intensive Genome alignment of Extracellular small RNA
==
* [Introduction](#Introduction)
* [Installation](#Installation)
* [Example](#Example)
<a name="Introduction"/>
# Introduction
Recent advances in high-throughput small RNA (sRNA) sequencing and the ever expanding transcriptome have opened incre... |
feae5622c2b6f02789d998d4bdc89c7edc11429e7f00bb339c5e6ece437354f3 | Text | 5,484 | 101 | # naturalsoundmixtures
## Overview
This repository contains the Matlab code used for the analysis and figure generation presented in:
Landemard A, Bimbard C, Boubenec Y. **Hierarchical encoding of natural sound mixtures in ferret auditory cortex**. _eLife_. 2025. 14:RP106628, doi: [10.7554/eLife.106628](https://doi.o... |
933d0b56962198ac6bc8f9ed7cc689300c2196fd56fa3c348e754d8da5c9adcb | Text | 5,487 | 159 | # spiking-aeon — Package 26
**Neuromorphic SNN Hardware Bridge (Intel Loihi 2)** — GenesisAeon Entropy Atlas Package 26
[](https://github.com/GenesisAeon/spiking-aeon/actions/workflows/ci.yml)
[![Python 3.11+](https://img.shields.io/... |
666d931790422d1699e92340062c06e13f7c4edff595888cc215cc21ead83e7f | Text | 5,494 | 127 | .. warning::
The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
Future development will take place at: https://github.com/openbraininstitute/neurodamus
|banner|
=============
Neurodamus
=============
.. image:: https://zenodo.org/badge/640796304... |
62500bbb3107f14216a4e8174d5bfbec8643e4a1307f74b90ece3b32db068448 | Text | 5,507 | 93 | # Kikhia et al 2025
This repository hosts the code used in the manuscript: "Multicolor fate mapping of microglia reveals polyclonal expansion, heterogeneity, and cell-cell interactions after ischemic stroke"
# Content
* Each subdirectory contains the code files necessary to run the analysis indicated in the subdirecto... |
77410249ad97892d299327b9dba8dc4e8023cfc04b81d80ce1244de912098344 | Text | 5,514 | 155 | .. image:: https://raw.githubusercontent.com/giotto-ai/giotto-tda/master/doc/images/tda_logo.svg
:width: 850
|Version|_ |Azure-build|_ |Azure-cov|_ |Azure-test|_ |Twitter-follow|_ |Slack-join|_
.. |Version| image:: https://img.shields.io/pypi/v/giotto-tda
.. _Version:
.. |Azure-build| image:: https://dev.azure.co... |
073ec26107c46b38fba11f6c52662c0285d5829a971d247b6adaa6891780fc3d | Text | 5,522 | 112 | # Biophysically inspired mean-field model of neuronal populations driven by ion exchange mechanisms
Code and data accompanying
> Rabuffo G, Bandyopadhyay A, Calabrese C, Gudibanda K, Depannemaecker D,
> Mitiko Takarabe L, Chatterjee S, Saggio ML, Desroches M, Ivanov A, Linne M-L,
> Bernard C, Petkoski S, Jirsa VK. *B... |
011a8098d9262995214572d4d2845493d42ec37f7242165747ebd4f6e24fb0b3 | Text | 5,529 | 60 | # 2D brain plot
Create two-dimensional plots on a picture template using the example of a 2D brain map.<br/>
<br/>
The figure shows randomly colored brain regions in coronal view on template slices of the gyral Allen Human Brain Atlas. Allen Reference Atlas – Human Brain ... |
0ac745d9bee695adcfc52f6f6a63960642251ea1ef13d84ad3a31fa14ddfc8f8 | Text | 5,533 | 105 | # NiMARE: Neuroimaging Meta-Analysis Research Environment
A Python library for coordinate- and image-based meta-analysis.
[](https://pypi.python.org/pypi/nimare/)
[](https://pypi.pytho... |
1e47c9a0aae154a6d35c21ad12db4d7e0ce19250f1eeb6a6cf92fc433794aac1 | Text | 5,534 | 122 | # kymopy
generate kymographs with ease!
## install
first create a fresh virtual environment of your choice then follow the command below:
```bash
pip install -e .
```
## usage
Dataset directory typically has a threshold spreadsheet and folders for images
```bash
kymopy /PATH/TO/DATASET
```
#... |
13d461610140c1ff74648d3d0fb9b9fc56d750115bc427df73e333ec22b4aec3 | Text | 5,543 | 135 | # MINC - TOOLKIT (Medical Imaging NetCDF Toolkit)
## Introduction
This metaproject bundles multiple MINC-based packages that historically have been developed somewhat independently.
Here is a list of bundled packages:
* zlib - data compression library
* NetCDF - file format library ( used for MINC1)
* HDF5 ... |
13654f02d679f098a9885a8ab638967437482910b8a5da4c50a0227647428424 | Text | 5,588 | 119 | # NeuroSC & PromoterDB
NeuroSC is an accessible and interactive tool for streamlined observation of neuronal morphology, membrane contact, and synaptic connectivity across developmental stages in the nematode C. elegans. Details can be found [here](https://elifesciences.org/reviewed-preprints/103977v1).
This reposito... |
794400d741d49bce12ee807dda8235a53925fd78f8977441ad1acce430da35dd | Text | 5,621 | 121 | # Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks
[](https://zitniklab.hms.harvard.edu/projects/PDGrapher/) [](https://github.com/mims-harvard/PDGra... |
6bf781be67af9d9e428f067670cbf81c1b27107df20ece19dbf7fc9c190e2065 | Text | 5,624 | 97 | # CU Cilia: Nuclei and cilia detection
## Running on Constructor Platform (CP)
1. Inside the `data` folder, create a new folder and upload your images there. **Only `tiff` and `tif` image formats are supported**. You can also upload images within a nested folder structure if necessary.
](https://github.com/srikash/MPRAGEise/releases/tag/v1.9.2) [](LICENSE) [](https://github... |
9c646c3eed973812542b4a0e6e1b7e6ffdf551dbd0276df7f8370b0ffb08611b | Text | 5,663 | 149 | MaPPeRTrac
===========
[](https://github.com/LLNL/mappertrac/actions/workflows/build.yml
) [](https://badge.fury.io/py/mappertrac
) [](h... |
82ea91136c8cc61c44fb2c04b55ae21ebbb9f4e51f0f3e3e54e2f5ccf45ffc67 | Text | 5,666 | 75 | # Cartan: Neural Symmetry Detector with Lie Algebras
Cartan is a framework for unsupervised neural symmetry detection using PyTorch. It leverages an encoder–decoder style architecture to (1) determine a symmetry generator and (2) estimate transformation magnitude distributions in order to find geometric relationships ... |
10ef1a5baedc6d65a2cf1cb352f51cb0b9303ff102be897dea9e612c85a1ab5b | Text | 5,679 | 97 | EchoNet-Dynamic:<br/>Interpretable AI for beat-to-beat cardiac function assessment
------------------------------------------------------------------------------
EchoNet-Dynamic is a end-to-end beat-to-beat deep learning model for
1) semantic segmentation of the left ventricle
2) prediction of ejection fracti... |
53368c86b844f521e9d0a85e5d388a3f59b1826a666a5d99a22915285269108b | Text | 5,739 | 60 | <p align="center"><img src="img/catch22_logo_square.png" alt="catch22 logo" height="220"/></p>
<h1 align="center"><em>catch22</em>: CAnonical Time-series CHaracteristics</h1>
<p align="center">
<a href="https://doi.org/10.5281/zenodo.4431165"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4431165.svg" height... |
c5ddd13b57252f6e059f609670c0d824e1eb12d319afb1cd2c307a898494dc1d | Text | 5,742 | 69 | <div align="center">
<a href="https://vldgroup.github.io/graph-pes/">
<img src="docs/source/_static/logo-text.svg" width="90%"/>
</a>
`graph-pes` is a framework built to accelerate the development of machine-learned potential energy surface (PES) models that act on graph representations of atomic struc... |
48603150b67c679491f982ecd72236686733682d626adb92561c0a16f934c038 | Text | 5,787 | 96 | [](https://doi.org/10.5281/zenodo.16891418)
# Kikhia et al 2025
This repository hosts the code used in the manuscript: "Multicolor fate mapping of microglia reveals polyclonal expansion, heterogeneity, and cell-cell interactions after ischemic stroke in mice"
https://doi.... |
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