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eeb6954a5792330007273fcfc08197566446be6aaabb1f89b2ab1ef0caae9338 | Text | 4,299 | 120 | [](https://arxiv.org/abs/2402.08708) [](https://zenodo.org/badge/latestdoi/593278428)
# Similarity based Molecular Generation (SiMGen)
<a href="https://zndraw.icp.uni-stuttgart.de">
<img src="banner_animation.gi... |
8aa42e6c844e8b475157101e03b9cc9af38c8f296734fe2e3c3bd389fa6820ea | Text | 4,334 | 69 | # AutoHotkey #
AutoHotkey is a free, open source macro-creation and automation software utility that allows users to automate repetitive tasks. It is driven by a custom scripting language that has special provision for defining keyboard shortcuts, otherwise known as hotkeys.
https://www.autohotkey.com/
## Support #... |
a2225a261fac0651237f0077cfcff0c2e690fc6cb3d074ea839b4c6e95a12d97 | Text | 4,349 | 58 | <img src="https://xgboost.ai/images/logo/xgboost-logo-trimmed.png" width=200/> eXtreme Gradient Boosting
===========
[](https://buildkite.com/xgboost/xgboost-ci)
[ for robot pose prediction.
**Author:** Alexander (Aleks) E. Siemenn <asiemenn@mit.edu>
## Overview
Integrating autonomous contact-based robotic characterization into self-driving laboratories can ... |
51ae5a78dec91f6b37cf1147aae7f526ae81d051856a9f548cefdfa90c568c09 | Text | 4,456 | 101 | # Spine Generic Public Database (Multi-Subject)
[](https://doi.org/10.5281/zenodo.4299140)
[](https://github.com/spine-generic/data-multi-subject/acti... |
508a625a4d578f93521b0a1cbd30f8f2e59553e4c369159848e9aefb5a089fcb | Text | 4,475 | 52 | # Path-MGCN
## Path-MGCN: a pathway activity-based multi-view graph convolutional network for determining spatial domains
Spatial transcriptomics (ST) comprehensively measure the gene expression profiles while preserving the spatial information. Accumulated computational frameworks have been proposed to identify spati... |
2241f3660fa1f87ece7a3e6c150758c0d9ae5f99a90d585c1eeb5d9035cce742 | Text | 4,482 | 113 | |PyPI| |Docs| |Build Status|
.. |PyPI| image:: https://img.shields.io/pypi/v/brie.svg
:target: https://pypi.org/project/brie
.. |Docs| image:: https://readthedocs.org/projects/brie/badge/?version=latest
:target: https://brie.readthedocs.io
.. |Build Status| image:: https://travis-ci.org/huangyh09/brie.svg?branc... |
a2e1f4eca0bdb8f5c886cc1f108e745d2d062755b792625d1a102183f314e9a2 | Text | 4,505 | 86 |
#
# 
<div ... |
f3f08278ba6bc2be4070158a7db61635abb5c5625de6318ed350e2973e9fb449 | Text | 4,531 | 93 |
# <sup>:notes:</sup>:saxophone: Sol*pH*<sup>edge</sup>
pH-dependent solubility predictions for small molecules
[](https://opensource.org/licenses/MIT)
## Use in the browser
Try it without any local installation by clicking the badge below!
⏬⏬⏬⏬⏬... |
8566dd350f9a7de836042b564ea688978bed005300a96ebb86acbb9b9df6e052 | Text | 4,535 | 117 | # Frag_MD/GD and MD/GD
Effective Generation of Heavy-Atom-Free Triplet Photosensitizers Containing Multiple Intersystem Crossing Mechanisms Based on Machine Learning
### 📦 Download Data
The dataset used in this project is publicly available via Zenodo:
🔗 [Download from Zenodo (DOI: 10.5281/zenodo.15638748)](http... |
0be6b313c05cccfe9dec9bb69824c33292fe501068089ed9b6b08eba5ce6253b | Text | 4,641 | 98 | # nnn_paper
Code for the paper "High-Throughput DNA melt measurements enable improved models of DNA folding thermodynamics" https://doi.org/10.1101/2024.01.08.574731.
"NNN" stands for "Not-Nearest-Neighbor"
## Figures
Jupyter notebooks 01.1 to 01.5 correspond to the 5 main figures.
Notebook `01.0_DataPrep.ipynb` per... |
67911a5af0a333e20403c80460e34bfab9d45e94533db335bb2d7ba5907a591a | Text | 4,643 | 84 | # Garcia_et_al_2025
Data analysis codes for the paper:
"Noncanonical Short-Latency Auditory Pathway Directly Activates Deep Cortical Layers."
Michellee M. Garcia, Amber M Kline, Koun Onodera, Hiroaki Tsukano, Pranathi R. Dandu, Hailey C. Acosta, Michael R. Kasten, Paul B. Manis, Hiroyuki K. Kato.
Nature Communications... |
78f76a04f97cdef50cd5ac39ee4ddb4ceb41bb0e89f24bc3fdc396783db90958 | Text | 4,675 | 130 | # KinderSeg: FastSurfer Database for Age-Specific Brain Volumes in Healthy Children
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.5281/zenodo.12773962)
#... |
266e90af9a72467421a3a6ade6048d05bef6244cb2a980e408428df80675150c | Text | 4,686 | 102 | # Speed Modulations in Grid Cell Information Geometry
## Overview
This repository contains the implementation of the Gaussian Process with Kernel Regression (GKR) method, along with the code to reproduce figures from our paper, "Speed Modulations in Grid Cell Information Geometry." (doi: 10.1101/2024.09.18.613797)
##... |
524fae9471d7f1d06be4f2028d5b34a1f7ba3634b3921c25be855ec7d3708c7f | Text | 4,697 | 70 | # The dynamic interplay between in-context and in-weight learning in humans and neural networks
Preprint: [The dynamic interplay between in-context and in-weight learning in humans and neural networks](https://arxiv.org/pdf/2402.08674)
Abstract: Human learning embodies a striking duality: sometimes, we appear capable... |
943934a809fa029642087c903f2b6c8834107386046bcc0d8133800ae042784c | Text | 4,710 | 136 | # Molecular Property Prediction in the Ultra-Low Data Regime
<img width="1395" alt="Screenshot 2025-02-18 at 11 26 14 AM" src="https://github.com/user-attachments/assets/6b0b8acc-caec-425e-a963-4569d4891658" />
This repository contains the official code accompanying the paper **"Molecular Property Prediction in the... |
a26a99d103b89cd1f6425ea4d626c533d0c919dd2661de80387df5bbbc6b2d60 | Text | 4,721 | 111 | # Code repository for: "Efficient neural encoding as revealed by bilingualism"
<!---
<img src="https://pwdonh.github.io/images/bilingual.png" alt="" height="250">
-->
## Paper reference
Charlotte Moore*, Peter Donhauser*, Denise Klein, Krista Byers-Heinlein, "Efficient neural encoding as revealed by bilingualism." P... |
cdc71ce3a52db937c5d2bd2de1904df7ac2244c75efbe332d199eb114faca22d | Text | 4,724 | 119 | [](https://zntrack.readthedocs.io/en/latest/)
[](https://badge.fury.io/py/mace-models)
# MACE models
Effortlessly integrate pre-trained MACE models into your projects with the user-friendly ... |
d5229fa34fd111574db74806072484d45a5254394401ebbbc2b5cfd3077582ed | Text | 4,739 | 113 | # Consensus Clustering for Chronic Neuronal Hyperactivity Proteomics
This repository contains the Python code used for the consensus clustering analyses described in the following study, accepted in *iScience* (2025):
**Chronic optogenetic activation of hippocampal CA1 neurons triggers Alzheimer's disease-like proteo... |
9997d6637a9dc479fbc43d4908a17aa45d7c32cac427af390f0c3af84c3b5d5c | Text | 4,742 | 127 | # Brain Age Estimation From MRI Using Cascade Networks with Ranking Loss
Pytorch codes for the paper "[Brain Age Estimation From MRI Using Cascade Networks with Ranking Loss](https://doi.org/10.1109/TMI.2021.3085948)", *IEEE transactions on Medical Imaging*, 2021
## Abstract
In this paper, a novel 3D convolut... |
d1794f18d9f0b6cd584b3f367e1155ce9b3a96d19ba3fb9aaac3f725d5d405da | Text | 4,767 | 74 | # Adaptation of reticula for mouse toxicology expression data
## Reference Repository
This repository is based on the work presented in the following repository:
[reticula](https://zenodo.org/badge/latestdoi/212217385)
Accompanying paper:
[Burkhart JG, Wu G, Song X, Raimondi F, McWeeney S, Wong MH, Deng Y. Biology-... |
094b6122d161096ad1e989525fb4e78475f572ea01645f7daac4c775c645a76c | Text | 4,778 | 134 | [](https://opensource.org/licenses/MIT)
[]()
# Woven
Implementation of the Woven model described in:
> **"Computational models reveal that intuitive physics underlies visual processing of soft o... |
50995ed6ee6e938d7aa18c26d9dbc095c76f863573eb2078a749965d20461413 | Text | 4,803 | 129 | # Deep neural networks explain spiking activity in auditory cortex
> 📘 This is the **official implementation** for:
> Bilal Ahmed et al., 2025
> [📄 Read the paper](https://www.biorxiv.org/content/10.1101/2024.11.12.623280v1)
## Overview
This repository provides the code used to model and analyze spiking activity ... |
ebb1e4e17077e05eb475cf15dc54c6e3033ef238efde9038f5fd1ba1c8c7698b | Text | 4,821 | 106 | # A Neonatal EEG Dataset Graded for Severity of Background Abnormalities
The dataset consists of 169 multichannel EEG files of 1-hour in duration, recorded from 53
full-term newborns in the neonatal intensive care unit of the Cork University Maternity
Hospital, Ireland. All 53 infants had received a diagnosis of hypox... |
46237c3976e708b35674748c46626595b4d68684c023368a73eefa7dc338774b | Text | 4,856 | 138 | # Molecular Property Prediction in the Ultra-Low Data Regime
<img width="1395" alt="Screenshot 2025-02-18 at 11 26 14 AM" src="https://github.com/user-attachments/assets/6b0b8acc-caec-425e-a963-4569d4891658" />
This repository contains the official code accompanying the paper **"Molecular Property Prediction in the... |
dddf3b0ac45b0db1df1b70c4a3b2d7c0c7ab900301346fa4d886fba7d0fe9007 | Text | 4,859 | 104 | # Predictive design of crystallographic chiral separation
- [Predictive design of crystallographic chiral separation](#predictive-design-of-crystallographic-chiral-separation)
- [About](#about)
- [Installation](#installation)
- [Usage](#usage)
- [Calculating the representation](#calculating-the-representatio... |
3c7687ab790a93dc5dea73306765c03e46e270973b2df259c2fafa57928dbebf | Text | 4,881 | 136 | # FER-STREs-WOZ
This repository accompanies the paper
_"Facial Emotion Recognition of 16 Distinct Emotions From Smartphone Videos: Comparative Study of Machine Learning and Human Performance"_ by _Marie Keinert et al._
```
@article{Keinert25-FER,
author = {Keinert, M. and Pistrosch, S. and Mallol-Ragolta, A. a... |
c9cb29c3b878b3433ff671de4bca4c3afa248995de896c83b62990e81a9628aa | Text | 4,890 | 132 | # Prostate158
> A collection of prostate MR studies with expert annotations
## What is Prostate158
Prostate158 is a curated dataset of biparametric 3 Tesla prostate MRI images for automatic segmentation of anatomical zones and cancerous lesions. Histopathologic confirmation is available for each cancerous lesion. All ... |
6c01fe589f9bc6c10a32adc1b09a6965e676d6895d6dca5d1a2a69c700493f28 | Text | 4,946 | 115 |
|
.. image:: https://img.shields.io/pypi/v/eigenstrapping
:target: https://pypi.python.org/pypi/eigenstrapping/
:alt: Latest PyPI version
.. image:: https://zenodo.org/badge/710175458.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10218973
:alt: Zenodo DOI
.. image:: https://github.com/SNG-newy/eig... |
ac1a1cbe9f910d3d69340e8b29c20b616e9ef0056920beda75f951b830394e47 | Text | 4,949 | 96 |
#
# 
<div ... |
08c0fc5f8ce3b399861812d49332bf812a0163c824c75c9cd4036820987a79cf | Text | 5,159 | 96 | # reticula [](https://zenodo.org/badge/latestdoi/212217385)
## Graphical Abstract
## Program Flowchart
This repository accompanies our article:
[Burkhart JG, Wu G, So... |
1ae2c5766ff1fd170728b70e4da72130410d31010e37ffbf7ad41f3664c3d231 | Text | 5,191 | 133 | # MIIC
<!-- badges: start -->
[](https://cran.r-project.org/package=miic)
[](https://github.com/miicTeam/miic_R_package/actions)
<!-- badges: end -->
This re... |
6a89c1fb613bbe311f9aa40b91461c284235e4fa1265dda55302687140f90567 | Text | 5,218 | 102 | # HISAT2
## Contact
[Daehwan Kim](https://kim-lab.org) (infphilo@gmail.com) and [Chanhee Park](https://www.linkedin.com/in/chanhee-park-97677297/) (parkchanhee@gmail.com)
## Overview
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome,
transcriptome, and exome ... |
a68c8892336e26d686fe069503344eebab501b22bca5a29b5c090f06e75fd6a4 | Text | 5,226 | 127 | # 3BTRON: A Blood-Brain Barrier Recognition Network
[](https://doi.org/10.5281/zenodo.15682541)
This is the repository associated with the paper "[3BTRON: A Blood-Brain Barrier Recognition Network](https://doi.org/10.1038/s42003-025-08453-6)".
## Files
Here, we provide... |
2637a0330b2020e787a8fc75ebae512ff33465bee9aa844740f6d3847cee2837 | Text | 5,234 | 222 | Mearns Duncan S, Hunt Sydney A, Schneider Martin W, Parker Ash V, Stemmer Manuel, Baier Herwig (2024) Diverse prey capture strategies in teleost larvae eLife 13:RP98347
https://doi.org/10.7554/eLife.98347.2
Tracking data available at:
https://data.mendeley.com/datasets/m6zs9bm7w3/1
# Metadata
Metadata, tracking files... |
49732b0324ee92b003fffd561016391dc25f9a8ff405f83658d59a19ae81c55e | Text | 5,236 | 106 | # Gut-Brain Nexus: Mapping Multi-Modal Links to Neurodegeneration at Biobank Scale
`CARD ❤️ Open Science 😍`
[](https://opensource.org/licenses/MIT)
[](https://pubmed.ncbi.nlm... |
c6c609fd5a9e83b78dbd95fea7bc58037835921807944bf46763b6c7561eaa21 | Text | 5,254 | 110 | # MagellanMapper
MagellanMapper is a graphical imaging informatics suite for 3D reconstruction and automated analysis of whole specimens and atlases. Its design philosophy is to make the raw 3D images as accessible as possible, simplify annotation from nuclei to atlases, and scale from the laptop or desktop to the clo... |
091f79ab1cd55263fb4116769d8e61ac62336b9161c97b8126890c6387923141 | Text | 5,347 | 136 | # SE-adLIF
[![CC BY-SA 4.0][cc-by-sa-shield]][cc-by-sa]
## Baronig, Ferrand, Sabathiel & Legenstein (2024):
**Advancing Spatio-Temporal Processing in Spiking Neural Networks through Adaptation**
---
## 📌 Getting Started
### Install Dependencies
To set up the required environment, run:
```sh
conda en... |
1553efe3fbe2dc3f9dbe42731da7a0de99122ad970d7d2b42c3cd439b8f0ebef | Text | 5,387 | 45 | # CICADA
Comprehensive Independent Component Analysis Denoising Assistant (for resting and task-based functional magnetic resonance analysis)
Manuscript: https://doi.org/10.1162/IMAG.a.114
CICADA is similar in function to other ICA fMRI denoisers such as ICA-AROMA and ICA-FIX. CICADA is unique, however, in that it bot... |
a707d41d3b73d790d0d910165d161321a54cbc1a6f8716a4197952fcba632762 | Text | 5,430 | 102 | ___ ____ _____ ____ _ _ _____ ___ __
| | /\ | \ | / \ | \ / | | / \ / |
|___| / \ | | | | | | \/ | | | \__
| \ /____\ | | | | | | | | | \
| \ / \ |____/ ... |
f1b2c6b90c90162f8a6f26c51db3935d3b8703884d6a9b31550472b97c0c907d | Text | 5,442 | 101 | ## File Descriptions
### Scripts for Reproducing Original Results
```predict_fitness_with_mlp_embeddings.py```: Trains and evaluates a Multi-Layer Perceptron (MLP) model to predict fitness using pre-computed protein embeddings.
```predict_fitness_with_cnn_onehot.py```: Trains and evaluates a Convolutional Neural... |
e6e11b8770705cbf7511f155d18d15ba1c97ed4cf66d7e88a69b96b48be46cef | Text | 5,557 | 159 | 
[](https://doi.org/10.5281/zenodo.15498139) [](https://doi.org/10.5281/zenodo.13153017)
# About
In... |
fe3fd757e21c260f051b9bbc6d01e889995c2d7dcc4ce3b2d28d07ad5049a2ad | Text | 5,616 | 121 |
|
.. image:: https://zenodo.org/badge/710175458.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10583040
:alt: Zenodo DOI
.. image:: https://img.shields.io/pypi/v/eigenstrapping
:target: https://pypi.python.org/pypi/eigenstrapping/
:alt: Latest PyPI version
.. image:: https://github.com/SNG-newy/eigens... |
203cbd13bac6887a74884da2fc197204c6fa34defb6e12b27a84dcc113c68392 | Text | 5,793 | 171 | # Rica
[](https://zenodo.org/badge/latestdoi/391155862)
[](https://me-ica.github.io/rica/)
[](https://rica-fmri.goatcounter.com)
... |
bf362a3f75a9fdeaf89b76def9e215d30de43b3053e03fa0d40228bbcb8219ee | Text | 5,818 | 127 | # Predictive design of crystallographic chiral separation
- [Predictive design of crystallographic chiral separation](#predictive-design-of-crystallographic-chiral-separation)
- [About](#about)
- [Installation](#installation)
- [Usage](#usage)
- [Calculating the representation](#calculating-the-representatio... |
3aa5c9714b4b459309ceafe9c30a600faa261babdb9b851dd48d8b9f2a9f9f65 | Text | 5,966 | 169 | # EsophagealPeristalsisModel
Mathematical model of human esophageal motility
## Reference
This repository accompanies the following paper:
> **A mathematical model of human oesophageal motility function**
> Takashi Miura, Hiroshi Ishii, Yoshitaka Hata, Hisako Takigawa-Imamura,
> Kei Sugihara, Shin-Ichiro Ei, Xiaope... |
b2f84fea41312999401cde730af79c5b11d4ef2c75d09aaeb592c6a564dbbda3 | Text | 6,016 | 125 | # Pipeline for system-dependent geometric distortion correction in UHF-MR images
## Repository Description
Ultra-high field (UHF) magnetic resonance (MR) systems are advancing in clinical and especially preclinical imaging research offering the potential to enhance radiation research. However, system-dependent factor... |
0bc3d824c7b04045f6b58fd96ac0683cef86756133e3f4bc7b1eec9d8b106644 | Text | 6,038 | 93 | # myphdlib
This is a joke of scientific software and analysis documentation that was written during my graduate research.
## Datasets ##
The processed data for each session is stored in an H5 file named `output.hdf`. Within this file, there are datasets grouped by the associated data processing step.
### Stimulus ##... |
e81c4279ff7acc67d6ed2931a353daeb31d3ba905b86f112c9badb1d61a47569 | Text | 6,064 | 197 | PROV Database Connector
=======================
Introduction
------------
.. image:: https://zenodo.org/badge/68604048.svg
:target: https://zenodo.org/badge/latestdoi/68604048
:alt: Latest release
.. image:: https://badge.fury.io/py/prov-db-connector.svg
:target: https://pypi.python.org/pypi/prov-db-conne... |
d15dfd37eb31311c500fda2d0b7cf393408fe4365fda910030e7af592aa230be | Text | 6,110 | 89 | # AstroResp
AstroResp code is a custom made code to analyse Ca2+ recordings from astrocytes.
#AstroRespCode: INSTRUCTIONS FOR A TYPICAL ASTROCYTIC Ca2+ PEAK ANALYSIS SESSION.
# 1. SYSTEM REQUIREMENTS
This code was written in MATLAB, and it runs on the Windows and MAC operating systems. The following MATLAB Versi... |
949d777d88dcd13d7811eca8fcad6b6aa997cd3ff3511974f156de265d8e4e28 | Text | 6,115 | 121 | <body><div class="wrapper">
<header>
<h1><a href="https://jerkwin.github.io/gmxtools/">gmxtools</a></h1>
<p>scripts/programs/utilities/tools for GROMACS</p>
<p class="view"><a href="#Introduction">Introduction</a></p>
<p class="view"><a href="#Tools">Tools</a></p>
</header>
<h2 id="Introduction">Intr... |
34b8aefa73e6b630c5ddad1eed4a8a20da76e5cb6b7ec3a8877824c9fb23ab60 | Text | 6,118 | 109 | # FLAMES has since been upadted to FLAMESv2
You can find the upadted source code, pre-print and tutorials here: https://mritchielab.github.io/FLAMES/index.html
# FLAMES
<img src="img/flames_logo.png" width="400">
Full-length transcriptome splicing and mutation analysis
# Installation
The easiest way to instal... |
049373343c4a0dce31cd4206a4179fcdd7364c9f7777b3fa853e3fffde04fcaa | Text | 6,142 | 91 | # FastPETDenoising
Adaptation of the U-Net architecture for denoising fast-acquisition PET images.
C. Silva, L. et al, An AI-Based Solution for Denoising Fast-Acquisition [<sup>18</sup>F]FDG PET: Clinical Feasibility and Quantitative Assessment, <i>J Digit Imaging. Inform. med.</i> (2025). https://doi.org/10.1007/s1... |
e58a69c50e4536c31e9d951e3809cb741cedad915cddbdd1d370b2dc09951ff2 | Text | 6,392 | 106 |
# Glioma Radiotherapy Design by Optimization of a Data and Physics-Informed Discrete Loss (GliODIL)
## Introduction
This repository contains the implementation of the GliODIL framework, as introduced in our paper "Glioma Radiotherapy Design by Optimization of a Data and Physics Informed Discrete Loss." \[1\] GliODIL... |
dad4f756541ccb2e3b16906d339189af3a40ca19083d8416cfde10272caf2d07 | Text | 6,415 | 153 | <img src="pic/new_logo_m.png" width=45% align="right" />
[](https://ag-peter.github.io/encodermap/_static/html_test_runner_report.html)
[.
DTINet is a computational pipeline to predict novel drug-target interactions ... |
212320c2d93d3ef5bfe4892799bab2272e4c0696f4d588eb937eda37a60bb461 | Text | 6,591 | 130 | # SoccerTrack
[](https://soccertrack.readthedocs.io/en/latest/?badge=latest) [](https://hub.docker.com/r/ssaha078/sam_plus_vnc)
[](https://hub.docker.com/r/ssaha078/vnc_quant_gui)
[![Cite Pape... |
9672311329369756345d0c38a4436b536354f15f913aa72b125e9754177c4546 | Text | 6,632 | 174 | # README: C. elegans Chemotaxis Simulation
## 📚 Associated Publication
Hironaka Masakatsu, Sumi Tomonari “A neural network model that generates salt concentration memory-dependent chemotaxis in *Caenorhabditis elegans*” *eLife* **14**:RP104456 (2025).
[https://elifesciences.org/articles/104456](https://elifesciences... |
fe58b9425f457b25ac64514b0f98e178de52a8e14350c00e3b2b08a4d4163e3b | Text | 6,666 | 189 | ## Aortic Aneurysm Analysis
This repository contains the implementation code for our published research on automated aortic aneurysm detection and volume estimation using deep learning approaches.
**📄 Published Paper**: [*Automated Aortic Aneurysm Detection and Volume Estimation Using Deep Learning*](https://www.mdp... |
94130c4b9b7890e9fade84611a4df9351eefab07a7a73c9acb51be792ebdda8f | Text | 6,668 | 175 | # trusTEr - A trusting TE cluster analysis
**Version 0.1.1, written in Python 3.6.6**
Takes fastq files from 10x single cell RNA sequencing, clusters cells using Seurat, and can be used to produce
read count matrices in a cluster level. You can also quantify reads per cluster having predefined clusters.
## Requirem... |
b5baed1740345387cbba86e798a260b9baaf1c3c22871f7771cbca5379cade0a | Text | 6,671 | 107 | Code for the publication "PanThera: Predicting the effect of Combination Therapy using Deep Neural Networks", accepted for publication in Briefings in Bioinformatics.
# Overview
PanThera aims at predicting arbitrary combination therapies. A pre-trained ensemble containing 10 replicas of PanThera trained on different s... |
e6e974e27f28969de4dc5ac6d63ba3a8b56b49bb39e1c59af309bae93c8e66d7 | Text | 6,709 | 107 | # **README on BinocularDisplayChecker**
<div align="right">
Created : "2016-01-17 14:57:53 ban"<br>
Last Update: "2021-12-13 07:28:12 ban"
</div>
<br>
<div align="center">
<img src="https://img.shields.io/badge/LANGUAGE-MATLAB-brightgreen" />
<img src="https://img.shields.io/badge/DEPENDENCY-Psychtoolbox3-green" /... |
ed6c923bbba0a33f61f5d3e6d24e52ed2ef8301cfce7f870b8d8eca93f0054e1 | Text | 6,731 | 134 | # BrainBuilder
[](https://github.com/tfunck/brainbuilder/blob/main/LICENSE)
[](https://github.com/astral-sh/ruff)
[](https://github.com/bothlab/pomidaq/tree/master/contrib/screenshots)
[](https://github.com/bothlab/pomidaq/actions/workflows/buil... |
ec6fbebdf8ae4c4d2ed2b545616c4fca37ddb7e5cc1a1ada2403e36b5ab97a11 | Text | 6,830 | 139 | =============
**HeuDiConv**
=============
`a heuristic-centric DICOM converter`
.. image:: https://joss.theoj.org/papers/10.21105/joss.05839/status.svg
:target: https://doi.org/10.21105/joss.05839
:alt: JOSS Paper
.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:latest-brightgreen.svg?logo=docker&... |
484a800eff5041ec184759263320ee6c771e8acb9ac671df4bb7a4c20b636eb4 | Text | 6,872 | 190 | # A fork of 3DMolCSP to run comparative experiments against the [Diastereomeric Resolutions](https://github.com/RokasEl/DiastereomericResolutions) paper
## Changes made to the original code
In the `./notebooks` directory, there are notebooks showing the needed data preprocessing. After generating the SDF files, w... |
68a72d158e1449fe0b303af9b7b6d940b97ad32a5538250a895812cdf14ae1cd | Text | 6,946 | 112 | Atomic-scale 3D structural dynamics and functional degradation of Pt alloy nanocatalysts
Chaehwa Jeong1†, Juhyeok Lee1,2,3†, Hyesung Jo1†, KwangHo Lee4†, SangJae Lee4, Colin Ophus5,6, Peter Ercius3, EunAe Cho4* and Yongsoo Yang1,7*
1 Department of Physics, Korea Advanced Institute of Science and Technology (KAI... |
fa783623be7a010c0669c62a1b9c3aad42c552bc8f3dd153353c0ee1676c86d7 | Text | 7,024 | 122 | # Thymus
***Unraveling the spatial organization and development of human thymocytes through integration of spatial transcriptomics and single-cell multi-omics profiling.***
<p align="center">
<img src="vignette_files/Thymus.jpg" alt="Resized Image" width="800">
</p>
### ***Data Availability and Citation***
(1). All... |
6940417f04e35252551ed33e22ae0cfc6a02d366e8e583004463157a14724941 | Text | 7,029 | 166 | # 🧊 ARCTiC ❄️
**A**utomated **R**emoval of **C**orrupted **T**ilts **i**n **C**ryo-ET
📄 Published in [*Journal of Structural Biology: X*](https://www.sciencedirect.com/science/article/pii/S259015242500011X)
## ⚙️ Installation
* Get ARCTiC source codes
```
git clone https://github.com/turonova/ARCTiC
cd ARCTiC
`... |
dee18bad9caa1138c040c917764b0a281cc3ac4df935ee1cefdbb40d202c9405 | Text | 7,037 | 140 | # Pipeline for benchmarking atlas-level single-cell integration
> [!IMPORTANT]
> This pipeline was tailored for the scib integration benchmark, but is not being developed for general-purpose dataset integration and benchmarking.
> There are two follow-up project from this benchmkark that you can check out instead:
>
... |
0f87845207afdc17e7900cf4fe5ff23f8bdd8b4bc344e5173275922be71abf95 | Text | 7,047 | 188 | # KinderSeg: FastSurfer Database for Age-Specific Brain Volumes in Healthy Children
[](https://opensource.org/licenses/MIT)
### Code for the paper:
```
Zughayyar, I., Bauer, M., Güttler, C., de Almeida Marcelino, A.L., Kühne, F., Buss, C., Heim, C., Aigne... |
36b8836273677ccedc4da93672e20a2626ac2f5b445fb90ce88d1d737c32e70d | Text | 7,187 | 147 | [](https://huggingface.co/spaces/sfaezella/AllerTrans)
[](https://doi.org/10.1093/biomethods/bpaf040)
[![Code Ocean](ht... |
3b16b47d5cd1b41e5b0e1b5c67a5990dd6d56ff390e05a82234879eaff7a8317 | Text | 7,204 | 220 | # <img src="./logo.png" align="left" height="150" /></a>
<strong>DECLUST</strong> is a Python package developed to identify spatially coherent clusters of spots by integrating gene expression profiles with spatial coordinates in spatial transcriptomics data. It also enables accurate estimation of cell-type compositio... |
4b8869f8561fb5d22a711e489b690b0fbe98bbdc5112da1a81cb3bc50d00276a | Text | 7,221 | 179 | # graphTRIP: Graph-based Treatment Response Interpretability and Prediction
This repository contains the full codebase for reproducing results from our study *Accurate and Interpretable Prediction of Antidepressant Treatment Response from Receptor-informed Neuroimaging*. It also includes some hopefully useful guidance... |
e1190cda26f1c8a94711d71a19606d50de589d197f45f3c3a514b41bd95e15d5 | Text | 7,237 | 128 | # OCP magmom model for modeling magnetic materials.
## Overview
This repository houses all the code and data that should allow for the reproduction of the results in the paper: 'Spin-informed universal graph neural networks for simulating magnetic ordering'.
- Toy datasets are provided in the directories "test_set" ... |
def7beae6a6e9e2649ba23443f914063db6489628c6958786788eac9fe65b202 | Text | 7,307 | 167 | - [PepLand](#pepland)
- [Introduction](#introduction)
- [Pepland Architecture](#pepland-architecture)
- [Fragmentation Operator](#fragmentation-operator)
- [Multi-view Heterogeneous Graph](#multi-view-heterogeneous-graph)
- [Installation](#installation)
- [Inference using pretrained PepLand](#inferenc... |
37cc85ca69ced837c2e155581710d778cd29a80d3504a1a2e598d54e61e5b4de | Text | 7,345 | 202 |
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<a name="readme-top"></a>
<!-- PROJECT SHIELDS -->
[![Contributors][contributors-shield]][contributors-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issu... |
6b1280b5f7ee7966c78347381753633858a93713e2cd2e135a7bc9dbcf1b8cdf | Text | 7,394 | 155 | # PHIMO+: Motion-Robust T2* Quantification from Low-Resolution Gradient Echo MRI with Physics-Informed Deep Learning
**Hannah Eichhorn**, Veronika Spieker, Kerstin Hammernik, Elisa Saks, Lina Felsner, Kilian Weiss, Christine Preibisch, Julia A. Schnabel
**Published at Magnetic Resonance in Medicine:** [https://doi.o... |
265ef5af560a2f737efbaca794db5f5f3b9b591d6c95636a6a5375eab8e09623 | Text | 7,433 | 197 | # Knowledge Graph Exchange
[]()
[](https://kgx.readthedocs.io/en/latest/?badge=latest)
[![Quality ... |
aa8d33cab5d5a3966023193a10156869e36686f8dffb0db293ec4fa0c06bf3e1 | Text | 7,434 | 202 |
<!-- Improved compatibility of back to top link: See: https://github.com/othneildrew/Best-README-Template/pull/73 -->
<a name="readme-top"></a>
<!-- PROJECT SHIELDS -->
[![Contributors][contributors-shield]][contributors-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issu... |
10251c837318f6bac1c779a3abd5ed54975aa7906d19289f48521501a30520d1 | Text | 7,445 | 235 | <img src="./egnn.png" width="600px"></img>
** A bug has been discovered with the neighbor selection in the presence of masking. If you ran any experiments prior to 0.1.12 that had masking, please rerun them. 🙏 **
## EGNN - Pytorch
Implementation of <a href="https://arxiv.org/abs/2102.09844v1">E(n)-Equivariant Graph... |
765b9f7c46a60fef70fb88b1d8fbbf2c320674e5ee3f509dc68be19180868ab8 | Text | 7,464 | 188 | # Lower Limb Motor Imagery EEG Dataset
## Overview
This dataset contains EEG recordings collected from 30 subjects performing a motor imagery (MI) task involving the left and right leg. Each subject performed five sessions, where they were instructed to imagine flexion and extension of either their left or right leg.... |
b5f9e1482f4333ba908749bbdc66f22eebde251a9047b1eae1abe56a4c2bb780 | Text | 7,504 | 225 | # <img src="./logo.png" align="left" height="150" /></a>
<strong>DECLUST</strong> [1] is a Python package developed to identify spatially coherent clusters of spots by integrating gene expression profiles with spatial coordinates in spatial transcriptomics data. It also enables accurate estimation of cell-type compos... |
c6b8ff6a1300a1ae1def7b63f8c5ad3e9b970ea96983ce5a2c688b897b77377f | Text | 7,603 | 145 | Spinal Cord Toolbox
###################
|badge-releases| |badge-forum| |badge-mailing-list| |badge-stats| |badge-twitter| |badge-downloads| |badge-ci| |badge-doc| |badge-license|
.. |badge-releases| image:: https://img.shields.io/github/v/release/spinalcordtoolbox/spinalcordtoolbox
:alt: Releases
:target: htt... |
5ecc14bc117b2da493ee5708b02e8559abeef13a4511d123a961e7c343204921 | Text | 7,635 | 51 | # Project overview
The Developmental Mouse Brain Atlas (DeMBA) is a four-dimensional atlas encompassing each postnatal day from 4 to 56, with delineations that are fully compatible with the Allen Mouse brain Common Coordinate Framework (Allen CCF) delineations. The atlas was created by 3D-to-3D registration of the Alle... |
1ed0a60e39372db7033a68230ae25a032217a0b8ce8e03bd8b1f43d76f528b5a | Text | 7,653 | 164 | # Self-Contrastive-Forward-Forward
This repo implements the official code of the article: ["Self-Contrastive Forward-Forward Algorithm"](http://arxiv.org/abs/2409.11593)
## Description
The Forward-Forward (FF) algorithm is a recent, purely forward-mode learning method, that updates weights locally and layer-wise and s... |
098eedfc737f71337c448086f78a52cc06b1ebee8b0262503ac75f3835eb3f37 | Text | 7,662 | 72 | # Bright-et-al-2025
This repository contains the code associated with the study "Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice".
## Authors
Ann Rose Bright, Yana Kotlyarenko, Florian Neuhaus, Diana Rodrigues, Chao Feng, Christian Peters, Ilaria Vitali, Elif Dönm... |
cd5a308877e0202974647e58043e93d39757cd948d4fe448cca5b9be27d4cd94 | Text | 7,679 | 76 | # DynaMight
[](https://github.com/schwabjohannes/dynamight/raw/main/LICENSE)
[](https://pypi.org/project/dynamight)
[![Python Version](https://img.shields.io/pypi/pyversions/dynamight.svg?... |
2244687a122a826ffaf7f6555a2a61bd37c233560f45b6b650647f683bab008f | Text | 7,730 | 179 | Journal Paper
==============
Sára Sáray, Christian A. Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen A. Lupascu, Luca L. Bologna, Werner Van Geit, Armando Romani, Andrew P. Davison, Eilif Muller, Tamás F. Freund, Szabolcs Káli: HippoUnit: A software tool for the automated testing and systematic c... |
3d2a5740270c673dbe1bc6afbc927df9f114b090199e8365dd90796c2198da72 | Text | 7,751 | 87 | ## Introduction
This repository contains the code and analyses associated with the manuscript titled "Epigenetic priming of neural progenitors by Notch enhances Sonic hedgehog signaling and establishes gliogenic competence" ([https://doi.org/10.1101/2025.01.20.633996](https://doi.org/10.1101/gad.352555.124)). It includ... |
c2a3069f09e32cdf05ad8062137565c13e1c337fed21b309b4c6c85a3a57a4dc | Text | 7,761 | 170 | # MolDiff-SiMGen integration
This repository is a fork of the [MolDiff](https://github.com/pengxingang/MolDiff). We have added an integration with [SiMGen](https://github.com/RokasEl/simgen) to do guided generation. The main changes are all inside `./models/guided_model.py`. Generation can be run with `./guided_moldif... |
458c39bde4d7e20a5c31bcbdc9a7827f9899ea7e0fdf4ec70eadf56382fdc7cd | Text | 7,765 | 178 | # NF Meta-Analysis: Analysis Code
R code for the meta-analysis published as:
> Galang EV, Velásquez MA, Elcin D, O'Connell S, Wieck J, McNair S and Colombo PJ (2025)
> *Systematic review and meta-analysis of the relationships between real-time neurofeedback
> training parameters and acquisition of neural modulation.*... |
f72d6f20ce41dad2a6e4611be905a2cd09b26e5d3507594879632133d8c800d9 | Text | 7,809 | 155 | # Investigating the Volume and Diversity of Data Needed for Generalizable Antibody-Antigen ∆∆G Prediction
## Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity
<p align="center">
<img src="Graphinity_architecture_ddg_horizontal.png" alt="Graphinity archi... |
6d5d0663a48a41fa008d88df8e405110fca4da1ef12e107710fe48638c1c35c6 | Text | 7,951 | 172 | [](https://arxiv.org/abs/2402.08708) [](https://zenodo.org/badge/latestdoi/899077041)
# MolDiff-SiMGen integration
This repository is a fork of the [MolDiff](https://github.com/pengxingang/MolDiff). We have added an... |
9add68634f883fb211cf4138a8753cd9b36e6f4d32fcefe214e92c13affe62ff | Text | 8,005 | 221 | # A foundation model to predict and capture human cognition
<img src="https://marcelbinz.github.io/imgs/centaur.png" width="200"/>
- **Paper:** [A foundation model to predict and capture human cognition](https://www.nature.com/articles/s41586-025-09215-4)
- **Point of Contact:** [Marcel Binz](mailto:marcel.binz@helm... |
e06f6a9617c4b0bc3b460fd7ff4613d76aec809cb2823f340c20f283c9d8a446 | Text | 8,027 | 170 | When Age Tips the Balance: a Dual Mechanism Affecting Hemispheric
Specialization for Language
================
[](https://zenodo.org/doi/10.5281/zenodo.10253278)
------------------------------------------------------------------------
## Contents
- [Background](#backgro... |
aa3b9a08c87dbf570f0698fad1e730d9b91415968ee9a1b990fedc54a3e70d5c | Text | 8,110 | 141 | --------------
Breaking News!
--------------
This codebase is in the process of being split up to better support long-term maintenance and modular aspects of different tools
available. The new repositories will be:
- [JuiceboxGUI](https://github.com/aidenlab/juiceboxgui) for visualization of Hi-C maps with Juicebox De... |
8dfde5e02d1aa029021e0bdea6b60af96a190ae7a8d75b7d20f7f5b20737d0f5 | Text | 8,144 | 171 | When Age Tips the Balance: a Dual Mechanism Affecting Hemispheric
Specialization for Language
================
[](https://zenodo.org/doi/10.5281/zenodo.10253278)
------------------------------------------------------------------------
## Contents
- [Background](#backgro... |
d2ae61bb12291b4bb672308ffde8b4b8756f4afbcbc6d062661f775a5c038af5 | Text | 8,170 | 144 | <p align="center">
<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
<!-- ALL-CONTRIBUTORS-BADGE:END -->
<img src="https://user-images.githubusercontent.com/54367954/195647242-1258eaf4-f838-43ea-b65c-f94dfe005e6b.png" width="500">
</p>
<h1 align="center">
spacetop preprocessing
<... |
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