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f70674899ebc8db54333aaf1b68ed2ec240672536549c29376b3191a75dbd03f | Text | 8,306 | 215 | # GenesisAeon Entropy Atlas — Packages 25 & 26
**Package 25: Apoptosis / Programmed Cell Death ATP Threshold**
**Package 26: Neuromorphic SNN Hardware Bridge (Intel Loihi 2)**
[](https://github.com/GenesisAeon/cellular-genesis/ac... |
c19b6533eb100169efbdaeb9a646945e6b35677c66e64f0b65f73cbf056de4b5 | Text | 8,408 | 170 | # MaGeZ contribution to the PETRIC reconstruction challenge
This repository contains algorithms developed by the MaGeZ team submitted to
the [2024 PETRIC reconstruction challenge](https://github.com/SyneRBI/PETRIC) and
published in the preprint [Fast PET Reconstruction with Variance Reduction and Prior-Aware Precondit... |
6300b9e6fc534f9b0a4e6e8ed648d91d81b2773e0b926800a76fe6de38327bf0 | Text | 8,418 | 127 | # Guide for the reproducible run
**Manuscript: _Spontaneous activity of astrocytes is a stochastic yet functional signal for memory consolidation_**.
## 1 Introduction
This repository contains the MATLAB code used for microdomain extraction and cross-correlation analysis used for the manuscript _Spontaneous activity ... |
e5f7a1a4942078653876ba378bd5e9ba001cce38f90b44415621d780c0d3b719 | Text | 8,430 | 182 | # DABEST-Python
<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
[](https://www.anaconda.com/distribution/)
[](https://badge.fury.io/py/dabest)
[**
[](https://github.com/GenesisAeon/diamond-setup/actions/... |
c65045339b50233c93697aeeb01799ae1d88a3b31b76d9efa819e7b2e84ff6c8 | Text | 8,451 | 148 | # Preprocessing of Paired-Tag/Paired-seq datasets
#### For latest protocol, please refer to [Paired-Tag protocol & FAQs](https://github.com/cxzhu/Paired-Tag/tree/master/protocol).
#### Please have the following softwares installed first:
- bowtie, http://bowtie-bio.sourceforge.net/index.shtml
For bowtie versi... |
b0630e07011f5a2cfe7660c374a44334fe913bae9127c08aa2acc96503bf4ac4 | Text | 8,511 | 90 | # DBS-VTA-optimisation
## Requirements
To successfully run the DBS-VTA-optimisation project, ensure you have the following software and libraries installed:
Python: Ensure you have a compatible version of Python installed (preferably Python 3.6 or later).
OSS-DBSv2: Install the OSS-DBSv2 package from https://github.... |
29a4e32cb4a190f7eba109ede69acda9678962989d02da170d862b56d12273b5 | Text | 8,522 | 142 | # Neurobiology and MIND in schizophrenia spectrum disorders (SSD)
This repository contains code and data created in support of the project García-San-Martín, N.; Bethlehem, R. AI; Segura, P. et al. *"Reduced brain structural similarity links to maturation and clinical outcomes in schizophrenia"* Nat Commun (2025). All... |
2473e594fc89d1426bf1d34abc4058a2682673fb1cf1f53231a6d22f615099c2 | Text | 8,538 | 183 | # line scanning repository
[](https://linescanning.readthedocs.io/en/latest/?badge=latest)
This repository contains all of the tool... |
6aa24483c426bf5d3ea95a16a13fff759963f9e8c873c1c4ae293971a792ca88 | Text | 8,590 | 99 | # scDblFinder <img align="right" style="margin-left: 20px; margin-bottom: 10px;" src="https://raw.githubusercontent.com/plger/scDblFinder/devel/inst/docs/sticker.svg"/>
[](https://github.com/plger/scDblFinder/actions)
The `scDblFin... |
d570b0e765628de274c45fc2679999cf623d7a4acd2ab79049a423d421d9126f | Text | 8,610 | 233 | FactorAnalyzer
--------------
.. image:: https://gitlab.com/EducationalTestingService/factor_analyzer/badges/main/pipeline.svg
:target: https://gitlab.com/EducationalTestingService/factor_analyzer/-/pipelines
:alt: Build status
.. image:: https://codecov.io/gh/EducationalTestingService/factor_analyzer/branch/ma... |
09f977ccb5f5927ea69c05af4cef3a8746db259b02f96d34d1ee1b206a80cce0 | Text | 8,650 | 105 | [](https://doi.org/10.5281/zenodo.16840270)
# MC-prediction
Predicting microbial community dynamics from time series of environmental samples using graph neural network models. Community abundance data is all that's needed, but supplementing it with envir... |
a05b1912fafcdc919fbd2b43f0a38d1911e2bb8d173069650dd5d03dfcb591ab | Text | 8,657 | 107 | # K_operator_Jupyter_eigenavalues
## Folder section3_1:
Here we consider 4 lobes, each one has 4 nodes, so 4 matrices 4x4. We generate four 4x4 random matrices with elements between 0 and 1 included and a K operator composed of four different parts.
In the cript we have:
- for the healthy brain, namely G_matrices: 4 ... |
d01e870e1f56ded5d3616fd252935990600f7b324c678a6f37797f385457f36a | Text | 8,657 | 185 | # WinnowNet
This algorithm was implemented and tested on Ubuntu 20.04.6 LTS (GNU/Linux 5.15.0-84-generic, x86_64).
## Note:
This repository contains the development version of WinnowNet. For the code used to reproduce the experiments in the paper, please refer to the following repository: https://github.com/Biocomputi... |
3d181397374d0e6382bd1afaa7d0483235f3fa3f7839014573bce4bd202c5dd6 | Text | 8,674 | 131 | <img src="data/logo.jpg" width=25% align="right" /> [](https://travis-ci.org/erlerobot/gym-gazebo)
**THIS REPOSITORY IS DEPRECATED, REFER TO https://github.com/AcutronicRobotics/gym-gazebo2 FOR THE NEW VERSION.**
# An OpenAI gym extension f... |
4998c63c09459aea0943132a6fc8a888eb22054415a3c113c75f21daf1b4a335 | Text | 8,705 | 116 | # MIMIC Code Repository [](https://doi.org/10.5281/zenodo.6818823)
The MIMIC Code Repository is intended to be a central hub for sharing, refining, and reusing code used for analysis of the [MIMIC critical care database](https://mimic.mit.edu). To find out... |
641b2d4695ee7caed9e0efee7cedc060371a0d24554f6996c94df393e5dad8ff | Text | 8,711 | 92 | # DBS-VTA-optimisation
## Requirements
To successfully run the DBS-VTA-optimisation project, ensure you have the following software and libraries installed:
Python: Ensure you have a compatible version of Python installed (preferably Python 3.6 or later).
OSS-DBSv2: Install the OSS-DBSv2 package from https://github.... |
3fcb15d3f880ab1f159343f1c536e2e29de91ccab9d2bb1b76a106b03cbf0053 | Text | 8,724 | 100 | # sync_osc_MSTMs
Code used for the article "Synchrony, oscillations, and phase relationships in collective neuronal activity: a highly-comparative overview of methods" by F. Baroni and B.D. Fulcher (2025).
Our original code is licensed under the [GNU GPL v3 license](http://www.gnu.org/licenses/gpl-3.0.html) (or later).... |
3b19afdcd6d0979519729b3c39c3220b7948c68f9586a1d898a4c5bb9067ab84 | Text | 8,765 | 108 | 
### A list of R scripts for the analysis of microbial profiles
## Introduction
The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge ... |
af3e0f477df85d5db8e782b3c0ef4dc1e64e59bf7d1ae52a4cfd13e5717cfba3 | Text | 8,873 | 146 | Authors: Mallia Geiger, Victoria Meslier, Mathieu Almeida
Date : 2025-05-07
I. General informations
The analysis focuses on microbiota data derived from two groups of mice (a total of 57 fecal samples) at 3 and 6 months:
- A group without any mutations.
- A group carrying a heterozygotous GBA1 gene muta... |
2ba35be9ffbe8406eec039e594d47c1b369da356aec46c24d507fd4fef4cb27e | Text | 8,876 | 55 | # INSight
Welcome to INSight, the open source infrared neural stimulation system! Here you will find design documents, code, and bill of materials to build your own INSight. Questions can be made in the Issues section of this respository.
# Citation
If you use INSight, we only ask that you cite our paper: and consult ... |
74217b94103a11c044d182819a36820451533473b0901a235e8282e50d7b3946 | Text | 8,907 | 105 | <div align="right">
Last update: 2025 September 8, 11:35 MT (by Wayne Lam)
</div>
<hr>
# :crystal_ball: Integrated Evolutionary Learning #
Integrated Evolutionary Learning (IEL) provides an automated method for simultaneously accomplishing principled feature selection and hyperparameter tuning while furnishing inter... |
81cc7d7897c36d3af692169dacb54d6b968d2c5d649c803d8352ced82643e55f | Text | 8,929 | 127 | # Cortical Column model of Predictive Coding (CoCo-PC)
Predictive coding (PC) is an influential theory in neuroscience, which gives rise to a perceptual architecture of the cortex by constantly generating and updating predictive representations of sensory inputs. While its computational goal is clearly defined as pred... |
ef56b3abc99c653ec959534290133e3cd4cc7c307f03d9ceb28db61a9e112a0c | Text | 8,968 | 112 | [](https://doi.org/10.5281/zenodo.15044567)
# Axon quantification algorithm
- Used in `Convergence and Segregation of Excitatory and Inhibitory Afferents in the Paraventricular Thalamic Nucleus` paper
## Requirements
Unzip the zip containing FIJI that is attached to the... |
b3ba56435ee177742e6612ee06e178148fa6fec55c40257e2e9067de7293b752 | Text | 8,998 | 159 | # Description
Training networks of LIF neurons including delays to classify patterns using `pytorch`, for explanations see publications below.
## References
* Fast and deep: energy-efficient neuromorphic learning with first-spike times; **Julian Göltz∗, Laura Kriener∗**, *Andreas Baumbach, Sebastian Billaudelle, Olive... |
c97e7fb131e9ced66ac39f17eb3f9619714e4844b0d340dc0a3e7e7cb10f001f | Text | 9,004 | 280 | # Moment Neural Network
Moment Neural Network (MNN) is a PyTorch-based framework for building,
training, and simulating neural networks that propagate second-order
statistics. Instead of tracking only mean neural activity, an MNN tracks
both mean activity and covariance, making it suitable for studying
correlated neur... |
66f1242c48d1d35e8b4f3412fb84f947409b14bbf2c796143f5bea9e517a607f | Text | 9,008 | 116 | # 1. deTS introduction (v1.0)
Genome-wide association studies (GWAS) and next-generation sequencing technologies have identified hundreds of thousands of disease-associated variants and genes. Interpretation of these variants could be greatly enhanced in tissue-specific systems. However, there are many diseases or trai... |
cab2bf5b617600db0758d8db75c82ed202f4e33e52abb803e812d86da986c891 | Text | 9,050 | 140 | # GNN_PPI
Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction".
> [Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction](https://arxiv.org/abs/2105.06709) \
> Authors: Guofeng Lv, Zh... |
b9fd218d0683c97f5aaaf911692c930c1bc2a6bf16fae85210b3e922821ec18e | Text | 9,144 | 214 | <img src="docs/source/_static/icon.png" alt="SCORE logo" width="128"/>
# ***SCORE***: Single-cell Chromatin Organization Representation and Embedding
A Python package developed by the Jin Lab for combining, benchmarking, and extending methods of embedding, clustering, and visualizing single-cell Hi-C data.
## Inst... |
1ee45e063dbfb5d3583d2b3fb03b8bab8e3741309c764de599d582545f2fc897 | Text | 9,258 | 181 | # MRS Digital Brain Phantom Framework
## Overview
This repository contains the code for the **MRS Digital Brain Phantom Framework**, a tool for simulating Magnetic Resonance Spectroscopy (MRS) data. The framework is designed to be comprehensive and flexible, allowing researchers to generate MRS data efficiently for th... |
250b6efc6238318ae5e7476c1c6930c50ba4ff6f6a1b48bb16c80dce8c58ff93 | Text | 9,287 | 210 | VSN-Pipelines
==============
A repository of pipelines for single-cell data analysis in Nextflow DSL2.
|VSN-Pipelines| |ReadTheDocs| |Zenodo| |Gitter| |Nextflow|
**Full documentation** is available on `Read the Docs <https://vsn-pipelines.readthedocs.io/en/latest/>`_, or take a look at the `Quick Start <https://vsn... |
2f6617deab9cc62506d1f1f687670f5225385ac131b2a5a2b54d5629f4788a2b | Text | 9,411 | 154 | # Large Language Models Enable Textual Interpretation of Image-Based Astronomical Transient Classifications - Code Repository
[](https://opensource.org/licenses/Apache-2.0)
[](... |
c534f398769f734ecff1b0e1da87d9bbede2def137325b0d39c67b9b044421c9 | Text | 9,460 | 130 | # Domain Shifts in White Matter Fiber Estimation
[](https://github.com/Medical-Image-Analysis-Laboratory/dl_fiber_domain_shift)
[](https://doi.org/10.1002/hb... |
a1465bb7361044217a8d5c6e05671f93dd85f5c08565f2d830e95f8ff662f28c | Text | 9,527 | 167 | ---
<div align="center">
# ITsFlexible: Predicting the conformational flexibility of antibody and TCR CDRs
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
<a href="https://pytorchlightning.ai/"><img alt="Li... |
3b3cc3d43dbf372e7d0f34f10e358e8f55634d29faddd4b5dded503c50bf143d | Text | 9,538 | 215 | VSN-Pipelines
==============
VSN-Pipelines has now been archived
-----------------------------
**2023-04-19 - Unfortunately due to lack of developers, VSN-pipelines is no longer being worked on and has been archived. The repo will remain in read-only mode from this point on.**
A repository of pipelines for single-ce... |
065e534ddd0e6e3e626c457140810d535b2f6c765f431680638c871c2f0a4dc6 | Text | 9,590 | 239 | # IsoLamp: isoform identification and quantification from long-read amplicon sequencing data
[](#installation)
[](https://shields.io/)
[
[](https://github.com/psf/black)
[. ##
# Fast spike sorting for hundreds of channels #
Implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings. Very fast when a GP... |
14922087a3efa615b0eab2ffba8d36180256cb2906e73b789302f32c6090b005 | Text | 9,853 | 140 | # Measuring Multimodal Mathematical Reasoning with the MATH-Vision🔥 Dataset
[](https://github.com/python/black)
[![codecov]... |
fbb9d3dae084e80f2e0f631f609ee7a2e484017a211a57c4ab59d6d5c246afb7 | Text | 9,885 | 244 | # IsoLamp: isoform identification and quantification from long-read amplicon sequencing data
[](#installation)
[](https://shields.io/)
[
--------------------------------------------------------------------------------
kMoL is a machine learning library for drug discovery and life sciences, with federated learning capabilities.
Some of its features include state-of-the-art graph-based predictive models, explainable AI components, and ... |
c617759059862746bebdbb18bc54d8abce3acc53091c0664e3a42861e98f5177 | Text | 9,917 | 121 | # SINDy-RL
This repository houses the code associated with the paper [**"SINDy-RL: Interpretable and Efficient Model-Based Reinforcement Learning"**](https://arxiv.org/abs/2403.09110). A video abstract of the work [can be found here](https://youtu.be/7Q8oNNsZGcA).
While we do provide some amount of documentation, the... |
246a596f77d7c791a63361b95ff09fe0b404812240c2781efadb399ccaba6443 | Text | 9,933 | 247 | # FractalDB
## Summary
The repository contains a Fractal Category Search, FractalDB Construction, Pre-training, and Fine-tuning in Python/PyTorch.
The repository is based on the paper:
Hirokatsu Kataoka, Kazushige Okayasu, Asato Matsumoto, Eisuke Yamagata, Ryosuke Yamada, Nakamasa Inoue, Akio Nakamura and Yutaka Sat... |
a826ec662f5fffa47e8f3f1ca1b9cd8b175866c0ab24fd895eef6673dc5bf16b | Text | 10,006 | 251 | # AI Fairness 360 (AIF360)
[](https://github.com/Trusted-AI/AIF360/actions/workflows/ci.yml)
[](https://aif360.readthedocs.io/en/latest/?badge... |
cbada180309ddaafd225dda03f520bfff8bb132884bbcaa02249453d9b34c788 | Text | 10,029 | 89 | # instance-loss
Official implementation of **instance loss functions**, a family of instance-level segmentation and detection loss functions, to improve semantic segmentation and detection of multiple instances in biomedical images. Please cite our publications below if our proposed loss functions are beneficial to you... |
7b7dc13d7b2f3d252c636064e422b0d23a657391954e12d82ef805f82c0fb1bb | Text | 10,077 | 33 | # pan-exm-t_paper
This code repository accompanies the publication "All-optical visualization of specific molecules in the ultrastructural context of brain tissue" by O. M'Saad, A. Cairns,... A.T. Kuan, J. Bewersdorf, et al.
Here we provide links to access image data associated with the paper, and data processing and ... |
06f87f1184a3fb65ba867165f7bccb280b216580530d866648946db7134fb360 | Text | 10,415 | 214 | <p align="center">
<img alt="AnyLabeling" style="width: 128px; height: 128px; height: auto;" src="https://github.com/user-attachments/assets/847e47e6-acf0-4f96-9ed9-5485ab405ae0"/>
<h1 align="center">🌟 AnyLabeling 🌟</h1>
<p align="center">Effortless data labeling with AI support from <b>YOLO</b> and <b>Segment ... |
f700b894e5797397b65dfbe42bd250bab9fd8e33291a3234bc7351e31aae4664 | Text | 10,540 | 184 | # DeepLION2<img align="left" src="Figures/Lion.png" width="45" height="45" >
Deep Multi-Instance Contrastive Learning Framework Enhancing the Prediction of Cancer-Associated T Cell Receptors by Attention Strategy on Motifs
------------------------------
DeepLION2 is an innovative deep multi-instance contrastive lea... |
57c080cc0604eb890d698efed4ccafc20cfa42126d91fc72de66d55939a92000 | Text | 10,607 | 131 | > [!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/BlueRecording
# BlueRecording
BlueRecording is used to produce an input file (also refered to as an electr... |
92d33b35f70a9ff824ba63309db11868106d07bbf840dc0c8790aa38aebd8146 | Text | 10,632 | 135 |
# CORnet: Modeling the Neural Mechanisms of Core Object Recognition
## What is this?
A family of simple yet powerful deep neural networks for visual neuroscience. What makes CORnets useful:
- Simple
- Lightweight
- Recurrent
- State-of-the-art on predicting primate neural and behavioral responses [Brain-S... |
9f3e142293b3fda43c44c0e2a90625f1d282bc4963b7fb4cc3657ccbcd5a30a2 | Text | 10,667 | 170 | This algorithm was developed by Y. Zhang, Sina David, Sjoerd M. Bruijn, Michiel Punt, Jorunn L. Helbostad and Mirjam Pijnappels from Vrije Universiteit Amsterdam, the Utrecht University of Applied Sciences, and Norwegian University of Science and Technology.
# Recognize real-life gait episodes using lower back IMU ... |
7fe78bf97eeb75eae7b83281ab98b2b0336107c4f6ca5f79b608a3f63fa32ee1 | Text | 10,671 | 97 | # EMBA: using the Bayesian Brain to investigate the specificity of emotion recognition differences in autism and ADHD
Mutual social interactions require people to be aware of the affective state of their counterpart. An important source for this is facial expressions, which can be indicative of the emotions experience... |
4be0d4adad6e9b26634082a9bce2fe8e98946716e05e671e1bf7cc58054ca85d | Text | 10,693 | 150 | # PAPA - Pipeline Alternative polyadenylation (APA)
Snakemake pipeline for detection & quantification of novel last exons/polyadenylation events from bulk RNA-sequencing data
The workflow (in brief) is as follows, but can be toggled depending on your use case:
- Use [StringTie](https://github.com/gpertea/stringtie) ... |
472a71656ac1cfb4fa8a10ea52aa38f822c9b134673ebf95bb3f5880ae1fcae5 | Text | 10,772 | 320 | [](https://github.com/e11bio/volara/actions/workflows/tests.yaml)
[](https://github.com/e11bio/volara/actions/workflows/ruff.yaml)
[
[](https://doi.org/10.5281/zenodo.15210360)
Snakemake pipeline for detection & quantification of novel last exons/polyadenylation events from bulk RNA-sequencing data
The workflow (in brief) is as follows, but can be t... |
ff669545bdec329c452eb51e6ddb569c60caee247bce3692b59c2d2ed1b24974 | Text | 10,811 | 273 | # Revealing emergent human-like conceptual representations from language prediction
## Setup
To set up the project, follow these steps to organize the necessary directories and environment:
### Prerequisite
Before running this project, ensure that you have Conda installed on your machine. Conda is used for managing... |
f19ed5fe5575439d39675bb0ccd1fea380e4fecdf8d4f60d4986e7d9f7b03bb9 | Text | 10,878 | 194 | # deepSTRF
*A PyTorch library for fitting sensory neural responses with deep neural network models*
[](https://deepstrf.readthedocs.io/en/latest/)
[![CI](https://github.com/urancon/deepSTRF/actions/workflows/ci.yml/badge.svg?branch... |
487b1f6d0177ba0a92e98fe1a79142263fc0a4b4295f427e79ed200a7d4d8f77 | Text | 10,948 | 121 |
<p align="center">
<img src="https://kaapana.ai/kaapana-downloads/kaapana-docs/stable/img/kaapana_logo_2.png" height=170 alt="kaapana" border="0" />
</p>
[](https://kaapana.readthedocs.io/en/latest/?badge=latest)
<a href="https://... |
fc1976a32f99edb5348e31a28e73cc9ebf0f655cad8ee998c2aab50ba75be59c | Text | 11,099 | 258 | # GetContacts
[](https://opensource.org/licenses/Apache-2.0)
[](https://travis-ci.com/getcontacts/getcontacts)
Application for efficiently computing non-covalent contac... |
033a6664df6844266112253f8754223ba4449fcb4834bacca75b489d1a8efaf3 | Text | 11,114 | 249 | # Depth to Pressure Translation Repository
This repository contains code, data, and models for research on body pressure estimation using deep learning. The repository is organized into several directories containing data sets, trained models, and supporting documentation.
```bash
AttnFnet
├── assets
│ ├── test_pr... |
7e96ee4e8282e59f7a09a551032a75390e81397e96ab852c5bb39b5d6f436d13 | Text | 11,197 | 306 | # DirectRM
## 0 Brief introduction
DirectRM allows simultaneous detection of the six most abundant modifications, namely ac4C, m1A, m5C, m7G, m6A and pseudourdine, from nanopore direct RNA sequencing data. It employs a two-stage detection framework:
- De novo detection: identification of potential modified kmers re... |
43907f37fbc518e32643bac0a52049badbaa68388939e2a93f4d2d9581d2d825 | Text | 11,201 | 145 | # Human_DLPFC_Deconvolution
[](https://zenodo.org/doi/10.5281/zenodo.10616687)
This is an integrative, multi-assay project including individual-matched data generated from human dorsolateral prefrontal cortex (DLPFC) using spatially-resolved transcriptomics with Visium (1... |
632b36a2e1609b66547ac4fc829a24bc16fdf36a38ba06e3a49c3d3f41629d13 | Text | 11,255 | 72 | # NeuroProcImager-Pro
#### Yun Zhao (Monash University, Australia), Levin Kuhlmann (Monash University, Australia), David Grayden (The University of Melbourne, Australia)
Contact Email: yun.zhao@monash.edu
**NeuroProcImager-Pro** was used in the below manuscripts
1. *Cortical connectivity, local dynamics and stabili... |
15cea89723669de95f1b0d3a1a34c171d457585ed30514b84f111dbac4a7f622 | Text | 11,273 | 248 | # CELLECT
# CELLECT (Contrastive Embedding Learning for Large-scale Efficient Cell Tracking)
The CELLECT tracking framework — officially published in *Nature Methods* (<https://www.nature.com/articles/s41592-025-02886-x>)
The CELLECT tracking framework is designed to extract cell center points from images along with ... |
6d5ca631ac0d49c3275dfa78df25f1efb590a06bc2002fda6f51481546782d45 | Text | 11,279 | 128 | # Discovery of novel obesity genes through cross-ancestry analysis
Codebase for manuscript titled "Discovery of novel obesity genes through cross-ancestry analysis"
[DOI](https://doi.org/10.1101/2024.10.13.24315422) | [Supplementary Tables](https://www.medrxiv.org/content/medrxiv/early/2025/02/28/2024.10.13.24315422/... |
9f97266986928db491211cd39e2726b2012f7ccffd64ac9d4e369f534828380b | Text | 11,348 | 223 | [](https://dev.azure.com/guocheng672/sequential-recommendation-datasets/_build/latest?definitionId=1&branchName=master)
[ usage. This guide covers the steps necessary to set up and run APA-Net.
## Requirements
- Python 3.8 or higher
- PyTorch 1.8.0 or higher
- NumPy
- Pandas
- SciPy
- tqdm
- wandb (optional, for experimen... |
a62e64d7d98c1932c1e14205043d1e462a565b21b685e110122cd942df54ccad | Text | 11,408 | 218 | ## Analysing dynamics, trajectories, neural tuning, and behavior of continuous-time RNNs with different architectural choices
This repository contains the code for running analysis on how the seemingly inconsequential RNN design-choices affect the dynamics, trajectories, neural tuning and, finally, behavior.
### Sett... |
95be2b61c872cd7e15551b91e7f15b70563dc078b85c5ab81833982d166bf84c | Text | 11,532 | 191 |
# Single-cell sequencing analysis of melanoma brain and extracranial metastasis
* This repository belongs to the publication
* ***Single-cell transcriptome analysis suggests cells of the tumor microenvironment as a major discriminator between brain and extracranial melanoma metastases***
* Konrad Grützmann ... |
bee340867b05c14b5487912d5282c66e55b84193e8b18fc8f0ebed6ec7201d00 | Text | 11,555 | 88 | **Custom scripts used for analyzing mouse embryonic cortex single-cell RNA-sequencing (scRNA-seq) data, published human fetal cortex scRNA-seq data, and mouse juvenile cortex single-nucleus RNA-sequencing data, alongside scripts for quantifying CHD8-to-nuclear stain signal ratio, as reported in:**
Kristina M Yim*, Mar... |
b0d33500ad088b268e83ca75e6a1e5168e580a91305219143440d0a9c5933a8a | Text | 11,569 | 227 | # ukbrapR <a href="https://lcpilling.github.io/ukbrapR/"><img src="man/figures/ukbrapR.png" align="right" width="150" /></a>
<!-- badges: start -->
[](https://github.com/lcpilling/ukbrapR)
[
[ for closed-loop control of neural activity.<br/>
The software integrates a calcium imaging analysis toolbox (CaImAn, Giovannucci et al., 2019, https://github.com/flatironinstitute/CaImAn), a custom hologram control software (HoloBli... |
9c831e5670ec9ac8e6f7ea161b3ea6f451206679f0e0ecc6292c1a07c8024a8f | Text | 11,713 | 229 | # scGALA
scGALA advances graph link prediction–based cell alignment for comprehensive data integration and harmonization
For detailed instructions, comprehensive documentation, and helpful tutorials, please visit:
- https://scgala.readthedocs.io/en/latest/intro.html
## Overview
<img title="scGALA Overview" alt="Alt t... |
706e2ef4e4b5e0c9c759b45caa0d05decc0c2a85844b8831fd2453f95408e535 | Text | 11,768 | 113 | # <a name="top"></a>Heterogeneous, temporally consistent, and plastic brain development after preterm birth
This repository accompanies the paper:
Melissa Thalhammer, Jakob Seidlitz, Antonia Neubauer, Aurore Menegaux, Benita Schmitz-Koep, Maria A. Di Biase, Julia Schulz, Lena Dorfschmidt, Richard A. I. Bethlehem, Aar... |
a4f9e8d64d9b25a962c4c494c65626a99bcee7d1baa592aac4cbece9e922b4fe | Text | 11,860 | 227 | # scVI-3D: Normalization and De-noising of Single-cell Hi-C Data
[Ye Zheng\*, Siqi Shen\* and Sündüz Keleş. Normalization and De-noising of Single-cell Hi-C Data with BandNorm and scVI-3D. bioRxiv (2021). * contribute equally.](https://www.biorxiv.org/content/10.1101/2021.03.10.434870v1)
## What is scVI-3D?
The adv... |
fe2e47a39c728d24669fd7060fa582a794f78e1962daed6ff24700d68932f167 | Text | 11,881 | 317 | .. image:: /readme/images/labelimg.png
:target: https://github.com/heartexlabs/label-studio
Label Studio is a modern, multi-modal data annotation tool
=======
LabelImg, the popular image annotation tool created by Tzutalin with the help of dozens contributors, is no longer actively being developed and has bec... |
7a785b3c05c0821b8e1f0506af5f528be1bd25a95ff9bb671b0e787b4f4f1881 | Text | 11,907 | 178 | ## [A Hierarchical Deep Temporal Model for Group Activity Recognition. Mostafa S. Ibrahim, Srikanth Muralidharan, Zhiwei Deng, Arash Vahdat, Greg Mori. IEEE Computer Vision and Pattern Recognition 2016](http://www.cs.sfu.ca/~mori/research/papers/ibrahim-cvpr16.pdf)
## Contents
0. [History](#history)
0. [Abstract](abs... |
79501800e2af7e446c3823e44a721a229e8754ba430fa80af976582259166c8f | Text | 12,058 | 172 | # CI-beNNch
[](https://www.gnu.org/licenses/gpl-3.0)
[](CITATION.cff)
**A modular framework for performance benchmarking of neuronal network simulations.** CI-beN... |
5da2e1df7e00442570ed4678064af1400074dcd90cf4e097ddff38f5b4935410 | Text | 12,240 | 268 | [](https://opensource.org/license/mit) [](https://doi.org/10.5281/zenodo.15174067)
# Depth to Pressure Translation Repository
This repository contains code, data, and models for research on bo... |
577ee4ef32be8f6c3133ece8e0837625882d4cfb8c5071bd1cd8fac8aa733bd5 | Text | 12,261 | 251 | # Pretrained METL models
[](https://github.com/gitter-lab/metl-pretrained/actions/workflows/test.yml)
This repository contains pretrained METL models with minimal dependencies.
For more information, please see the [met... |
ce2788f18d334c00359ed29aa2024a413b7a9aac65fcb151cf82c5045ec9baaf | Text | 12,313 | 198 | ReduXis
============
<p align="center">
<img width="500" alt="ReduXis Logo" src="https://github.com/user-attachments/assets/d7884817-0981-4f0c-bde8-302db365b187"/>
</p>
**Redu**ced-dimensional **X**-modality **I**ntegrated **S**tage and Subtype Inference, or ReduXis, is a lightweight and powerful
preprocessing and wr... |
90118263470c85d97db3060514d8f7465a7969520da775b9bb0ca48ab06cfd2a | Text | 12,334 | 280 | Code used for the article "Synchrony, oscillations, and phase relationships in collective neuronal activity: a highly-comparative overview of methods" by F. Baroni and B.D. Fulcher (2024).
All code written by F. Baroni unless indicated otherwise, apart from what's included in ./third-party/.
%%%%%%%%%%%%%%%%%%%%%%%%%... |
03610540353c18b67e3db104140fc6c19bcdd0aeb9c7c57a09d61e93eba73e9b | Text | 12,336 | 348 | # DirectRM
## 0 Brief introduction
DirectRM allows simultaneous detection of the six most abundant modifications, namely ac4C, m1A, m5C, m7G, m6A and pseudourdine, from nanopore direct RNA sequencing data. It employs a two-stage detection framework:
- De novo detection: identification of potential modified kmers re... |
0d67a0397ef1386aff67d63383fccdb66eafdf73cf7f99a9be08d83a0b36f547 | Text | 12,346 | 169 | epDevAtlas: Early Postnatal Developmental Mouse Brain Atlas (RRID:SCR_024725)
- Version 1.0
- Created by the Yongsoo Kim Lab (https://kimlab.io/) at Penn State College of Medicine, Hershey, PA, USA
- Data visualization resource URL: https://kimlab.io/brain-map/epDevAtlas/
Reference:
1) epDevAtlas: Mapping GAB... |
4860b2e987991dd0a44e58784c38ea1f5b9b29bb2bb0855acb14fac7c2870f22 | Text | 12,493 | 192 | ## This is the GitHub repository for the publication:
# GEMS: Resolving data bias improves generalization in binding affinity prediction
[](https://opensource.org/licenses/MIT)
[](http... |
395c1e51a36717688fa2b989c4d3870fc7e224023539d0ee170348b39cc7f025 | Text | 12,587 | 229 | ProteinLigandBenchmarks
==============================
[//]: # (Badges)
[](https://github.com/openforcefield/protein-ligand-benchmark/actions/workflows/ci.yaml)
[
](https://opensource.org/licenses/MIT)
[](https://github.com/HFooladi/ALineMol/... |
de83665f0eeea98d0656e7bd3d324448ed90206001701ab6d99dd63d6b6edb33 | Text | 12,783 | 298 | # TCFormer: Temporal Convolutional Transformer
> Official code for the paper **“Temporal convolutional transformer for EEG based motor imagery decoding.”**
> Paper: https://www.nature.com/articles/s41598-025-16219-7 (Nature Scientific Reports, 2025)
- Built upon ideas/code from [**EEG-ATCNet**](https://github.com/Al... |
ea67d1e504bf497daf54305af990b5284d0d6507d1453355a2ab55a4bcfb93fb | Text | 12,792 | 328 | .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4007376.svg
:target: https://doi.org/10.5281/zenodo.4007376
What is sc2reader?
====================
sc2reader is a Python 3 library for extracting information from various different Starcraft II resources. These resources currently include Replays, Maps, and G... |
4b434c6fe6fc4a4413b6d8807942d23cce03933e7d66b4ad663c77dd0c7f8cbc | Text | 12,805 | 71 | ### Description of the setup:
This set of codes was designed for a project where trout were filmed as behavioural tests. There were up to four trout in each video, all kept in separate boxes. The trout were tested through an open field test, barrier navigation, and reaction to colourful objects (in the form of red and ... |
040db67701a1179a2ad590b44b1ea4444c38edbe6584bad11867370296fe1678 | Text | 12,981 | 216 | # GOUHFI: novel contrast- and resolution-agnostic segmentation tool for Ultra-High Field MRI
[](https://doi.org/10.1162/IMAG.a.960)
[](https://arxiv.org/abs/2601.09006)
[![Zenodo](http... |
6be509af63cb5336c01c0ce6db48177ed393fe3d1c6a7dd282da6d9f814b079a | Text | 13,021 | 211 | [<img src="logo.png">](https://github.com/ETHZ-EDAC/STAMP)
## Short Description
Unified modeling and inverse material design framework for stochastically mixed voxelated polymer structures developed by the Engineering Design and Computing Laboratory (EDAC) at ETH Zurich.
## Introduction
Polymer material jet... |
78b829c8bcbe9836b6171c0415375af501eb5861a6994627abe57faa85eef68c | Text | 13,055 | 175 | # RESPAN: Restoration Enhanced SPine And Neuron Analysis.
<p align="center">
<img src="images/Panel 1.jpg" alt="RESPAN" width="600">
</p>
RESPAN is an end‑to‑end, GPU‑accelerated pipeline that restores, segments, and quantifies dendrites and dendritic spines in fluorescent microscopy images in a robust, accurate, and... |
de90727d84f3d3e3648823c03015a0435f47dc9d3521ee88b6995a7f79685ec7 | Text | 13,094 | 211 | [<img src="logo.png">](https://github.com/ETHZ-EDAC/STAMP)
## Short Description
Unified modeling and inverse material design framework for stochastically mixed voxelated polymer structures developed by the Engineering Design and Computing Laboratory (EDAC) at ETH Zurich.
## Introduction
Polymer material jet... |
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