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763fac4c9e9aedb5c671ad6398cf0b31766be21b89b0ec06fb9eece0c4ad3309 | Text | 4,077 | 46 | Official code for paper "Towards Ignoring Backgrounds and Improving Generalization: a Costless DNN Visual Attention Mechanism" (https://arxiv.org/abs/2202.00232), based on PyTorch (originally implemented with PyTorch version 1.11.0).
Abstract:
This work introduces an attention mechanism for image classifiers and the c... |
ac54832bafd32436b00aad4990ab052cd2128f7ac5a7a963df064d01ed93b9ba | Text | 4,111 | 39 | # The-Hybrid-Virtual-Brain
# Update: Please use updated version TVBii_update.c to address numerical instability leading to accumulation of machine precision errors on some machines. In the updated version simple checks were added that re-set the state of synaptic gating back to its plausible range between 0 and 1 if i... |
874509e16d2627decc13f8a1e4bc0d7524f7fde48dee436a52e62876601e70f8 | Text | 4,157 | 63 | <!--
Copyright © 2023 German Cancer Research Center (DKFZ), Division of Medical Image Computing
SPDX-License-Identifier: Apache-2.0
-->
# Radiomic Tractometry (RadTract)
Copyright © German Cancer Research Center (DKFZ), [Division of Medical Image Computing (MIC)](https://www.dkfz.de/en/mic/index.php). Please make su... |
fbdce66e5be0c539ada51e554ca1d3cf46f29323144a255bf89b32e07c860db0 | Text | 4,163 | 160 |
# Deepdefense: Automatic annotation and classification of immune systems in prokaryotes using Deep Learning
Deepdefense is a tool to serach for immune system cassettes based on the Doron system. To achieve this
Deepdefense uses two distinct prediction modules. The first module consists of an ensemble of Deep Learni... |
d5cbac5c85ffa7cd77e059b491d6fdf0b8eda467fffcd6bf4a62ecf7fd30e88c | Text | 4,189 | 109 | <img src="./logo.svg" alt="NeurIPS Logo" style="width:30%; height:auto;" align="center"/>
# 🤖🔗🧠 Model Based Inference of Synaptic Plasticity Rules
[](https://docs.python.org/3/whatsnew/3.11.html)
[![JAX](https://img.sh... |
e0d21b27659ba71f8b5e707a30b90c5505b121be2947c3db9e536416fe01def9 | Text | 4,196 | 49 | # MEISTER
Multiscale and integrative analysis of tissue and single cells using mass spectrometry with deep learning reconstruction.
This is the code repository for the paper "Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry", **Nature Methods, 2024** [link](h... |
0ab4909a2585f57991d54c5af167445e2867d0bcded8982435c488899632a959 | Text | 4,199 | 50 | # SynerGNet
[SynerGNet](https://www.mdpi.com/2218-273X/14/3/253) is a machine learning tool to predict synergy effects of anti-cancer drug combinations. Given the gene expression, copy number variation (CNV), mutaion types, and gene ontology (GO) terms of the cell lines and drug-protein association scores of the paired... |
67280eb90a7706b724b8dba359af8b8f8a5b939fdd6b426a7e1cf3f7e7420048 | Text | 4,264 | 153 | # snakedwi
[](https://snakedwi.readthedocs.io/en/latest/?badge=latest)
BIDS app and Snakemake workflow for diffusion-weighted imaging (DWI) pre-processing.
## Overview
snakedwi is a comprehensive workflow for preprocessing diffu... |
5a224d281f2007663c10e7277ed779d1061497dc3fa61f24249189441ef84ab5 | Text | 4,316 | 58 | # scSPORT
*Copyright (c) 2023 Yue Wan Lab*. This project is licensed under the terms of the MIT license.
__scSPORT__: a Single-cell RNA Structure Probing Method
## Introduction
RNA structure is critical for multiple steps in gene regulation. However, how structures of transcripts differ both within and between indiv... |
c856282aa2f99db67a6ea8ad2a8da37f6ef4bec7b843b38af641831fbd760a22 | Text | 4,318 | 79 |
# Cell-type-specific expression and regulation in atypical Schinzel Giedion Syndrome (SGS)
__Jordan Whitlock, Tabea Soelter, Timothy Howton, Elizabeth Wilk, Vishal Oza, Brittany Lasseigne 2023__
__The University of Alabama at Birmingham (UAB), Heersink School of Medicine__
## Data Availability
All data for this pr... |
55c412fd0ebd04e6b5673468b3b3d532797f6256f7a342432d8d2e9fac410e62 | Text | 4,328 | 100 | # PySurvival
<center><img src="docs/pages/images/pysurvival_logo_black_blue.png" alt="pysurvival_logo" title="pysurvival_logo" width="50%", height="50%" /></center>
## What is Pysurvival ?
PySurvival is an open source python package for Survival Analysis modeling - *the modeling concept used to analyze or predict whe... |
ae69d71acfe466b19e2b8a11e7fbad530fcd582eab230de75d0d8aaa0a8a05ae | Text | 4,344 | 32 | # A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1
Ling Hai (1,2,3,4)+, Dirk C Hoffmann (2,3,4)+, Robin J Wagener (2,3), Daniel D Azorin (2), David Hausmann (2,3), Ruifan Xie (2), Magnus-Carsten Huppertz (5), Julien Hiblot (5), Philipp Sievers (6,7), Sophie Heue... |
50f5ad9ed8638e1cda6147bd30250bdda559dc438863d54036e8022ed62d15c3 | Text | 4,365 | 134 | # CurtainUtils
A utility package for converting different MS output files into a format usable by Curtain (https://curtain.proteo.info) and CurtainPTM (https://curtainptm.proteo.info)
## Installation
The package can be installed using the following command.
`pip install curtainutils`
## Convert MSFragger PTM single s... |
724790b4d72cc86b1a9d3d76e17f21cc338dc1f8b93984d454e435258b6d0d5f | Text | 4,444 | 67 | Analysis glioma
===============
This code reposotory explains the statistical analysis performed in the paper [*Spatiotemporal analysis of glioma heterogeneity reveals Col1A1 as an actionable 1 target to disrupt tumor mesenchymal differentiation, invasion and malignancy*](https://www.biorxiv.org/content/10.1101/2020.1... |
1e1cfee75b4437c57ba0a8eff4b74f89396afb531bcfc7c1642093c009758c6b | Text | 4,451 | 71 | <a href="/img/openMINDS-SANDS_logo_light.png">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="/img/openMINDS-SANDS_logo_dark.png">
<source media="(prefers-color-scheme: light)" srcset="/img/openMINDS-SANDS_logo_light.png">
<img alt="openMINDS SANDS metadata model" src="/img/openMINDS-SANDS... |
6bede58ce43d88de502837e1bf725680c3e6f436d8d160976874f6c276f003eb | Text | 4,457 | 80 | # pyhddmjags
#### (Repository version 0.7.1)
Repository for example Hierarchical Drift Diffusion Model (HDDM) code using JAGS in Python
**Authors: Michael D. Nunez from the Psychological Methods group at the University of Amsterdam**
### Possible citation
Nunez, M. D., Fernandez, K., Srinivasan, R., & Vandekerckhove,... |
2b41725bf47eaa7eb46447517e5cd819837bcd2d70637034c0463faa0d385404 | Text | 4,476 | 119 | # Neonatal brain dynamic functional connectivity in term and preterm infants and its association with early childhood neurodevelopment
[](https://doi.org/10.5281/zenodo.10050537)
#... |
2525b67ace97f67ff72efb246ff663c073a1628cd4a9adfe9e767c4a62278a85 | Text | 4,483 | 44 | # ASAP - Automated Slide Analysis Platform
[](https://ci.appveyor.com/project/GeertLitjens/asap)
ASAP is an open source platform for visualizing, annotating and automatically analyzing whole-slide histopathology images. It consi... |
9150a2cfcbb8f08ae366efcf5b3716cf5341dee22e78752f34b5ddee57993f0c | Text | 4,523 | 75 | # Deep Learning Segmentation of Organs-At-Risk with Integration into Clinical Workflow for Pediatric Brain Radiotherapy
Journal of Applied Clinical Medical Physics, 2024
## Getting Started
The pretrained model can be downloaded from: `https://github.com/JHU-MICA/JACMP2024_PedsBrainSeg/releases/download/Model/model.p... |
9cfd87b2e3f50e334d876a7edba88057a5d889e6e29a0c066db621a97eb20a9e | Text | 4,633 | 96 | README
================
2023-08-02
# The landscape of *SETBP1* gene expression and transcription factor activity across human tissues
## Authors
**Jordan H. Whitlock Elizabeth J. Wilk, Timothy C. Howton, Amanda D.
Clark, Brittany N. Lasseigne**
The University of Alabama at Birmingham (UAB), Heersink School of
Medic... |
c2d67b1d0a4e8d04d590aa7bfb76db83369d968861d31750b79ddc5fcfc7006e | Text | 4,656 | 84 | <img align="right" width="200" height="200" src="dynFC_logo.png">
# dynFC: CoDe-Neuro's Dynamic Functional Connectivity Tools
[](https://github.com/CoDe-Neuro/dynfc/actions/workflows/python-package.yml)
[![docs](https... |
9e9ea35d657092d46233ad03291e6ede28f2221931b30a038943bfdde96cf750 | Text | 4,681 | 114 | # Lightweight CNN and Transformer Detectors for Date-Fruit Variety Recognition — Reproducibility Package
This repository contains the code, configurations, and processed results for the study
*"Lightweight CNN and transformer architectures for real-time date fruit sorting on edge
GPU hardware."* It is provided so that... |
d7be0d4f7f09cb937f95b47f330bc6e0ec8befc985ecef7e0af3d253fab6a007 | Text | 4,701 | 40 | # Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data
In recent years, convolutional neural network (CNN)-based methods have shown remarkable performance in the denoising and reconstruction of super-resolved structured illumination microscopy ... |
7507b8ecbcea8a6b92da1d6827a76c9c4a65786d4b7d10511b64f289782d9b2a | Text | 4,704 | 135 | # 2023_InfraRed_Image_Restoration
This repository contains the code used for the manuscript "Image restoration of degraded time-lapse microscopy data mediated by infrared-imaging."
Repository structure:
- Figures: contains the code used to generate the figure of the paper.
- IR2_training_prediction: contains the code ... |
bed234eb24bbb2f717879d61b79c50a0aaf6fd84cd60599d10095b1a25f8a1e0 | Text | 4,741 | 81 | # Pathofusion
A deep learning based framework for recognition and fusion of multimodal histopathological images
### Labelling website
#### The source for Labelling website is now released, please see the folder "LabelingWebsite" or visit standalone code base: https://github.com/guoqingbao/Patholabelling
#### Importa... |
3174c5efcad4c92203f46dc18afc4c35a8adf91ab8155b67cf8158d32b42999f | Text | 4,833 | 53 | # adnexal-mass-classifier
[The Use of Machine Learning Models and Radiomics for Segmentation and Classification of Adnexal Masses on Ultrasound: A Multi-Cohort Retrospective Study](https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4427456)
This repository contains the code and resources for the machine learning stu... |
b0bb5503db1e3d41875fa617983edcf41ff81fec72894d559b07ff7b903f941f | Text | 4,833 | 80 | # Snakebids
[](https://github.com/khanlab/snakebids/actions/workflows/test.yml?query=branch%3Amain)
[](https://codecov.io/gh/khanlab/snakebi... |
d52db887c5d412059c85e56e0f5feb96edd948ab30778a0746cf78703c7f7375 | Text | 4,902 | 69 | # Live2p
**Live2p** - online implentation of [CaImAn](https://github.com/flatironinstitute/CaImAn) for realtime analysis 2-photon calcium imaging with [ScanImage](http://scanimage.vidriotechnologies.com/).
## Installation
1. Download and install [miniconda](https://docs.conda.io/en/latest/miniconda.html) or [Anacon... |
ebea7cb3697d42b44791debe2f1a6c1d0f0d80b29dcc08e5c9b8b4e2f683005c | Text | 4,907 | 65 | # Sleep EEG Event Detector (SEED)
Repository for the code and pretrained weights of our deep-learning based detector (SEED) described in:
Tapia-Rivas, N.I., Estévez, P.A. & Cortes-Briones, J.A. A robust deep learning detector for sleep spindles and K-complexes: towards population norms. _Sci Rep_ **14**, 263 (2024).
... |
26d8b2c5a7323bb07c8e989d8fa2be0aaf14eb0ad9c09cae6eef5dcca9df7723 | Text | 4,946 | 140 | # dscNanoSeq
Data preprocessing and analysis pipeline for dscNanoATAC & dscNanoCUT
- [dscNanoSeq](#dscnanoseq)
- [Introduction](#introduction)
- [Install](#install)
- [Prepare references](#prepare-references)
- [Usage](#usage)
- [1. demultiplex of sequencing library](#1-demultiplex-of-sequencing-libra... |
c38467855f8b47752ca195ce02597b2debc311c08260c77d5a2289bd40839d24 | Text | 5,017 | 89 | ---
title: 'LungTumorMask: Automatic lung tumor segmentation in CT'
colorFrom: indigo
colorTo: indigo
sdk: docker
app_port: 7860
emoji: 🔎
pinned: false
license: mit
app_file: demo/app.py
---
# Automatic lung tumor segmentation in CT
[](https://github.com/pyrates-neuroscience/PyRates)
[](https://circleci.com/gh/pyrates-neuroscience/PyRates/tree/master)
[](https://doi.org/10.5281/zenodo.10210141)
This is the code and data archive accompanying the publication
> Gutzen, R., De Bonis, G., De Luca, C., Pastorelli, E., Capone, C., Allegra Mascaro, A. L., Resta, F., Manasanc... |
9d85d5afb125cdf07415cea04ad8a59171c4cdd4d68017f32bf9f09677084e49 | Text | 5,163 | 145 |   
## IPEV: Identification of Prokaryotic and Eukaryotic Virus in virome data using deep learning
# M2OR : Database of Olfactory Receptors-Molecule Measurments [1]
The sense of smell, is initiated by the activation specific receptors expressed at the
surface of olfa... |
80d95680671a8e950ad0bd4550ef3055fc301f95f884549e9e734888a9070e17 | Text | 5,183 | 106 | # TFCE: Threshold-Free Cluster Enhancement
Non-parametric permutation inference with threshold-free cluster enhancement, for 3D volume and
surface data - as an **SPM toolbox** and as a **Python package**.
TFCE combines focal effects of large height with broad effects of large extent, and needs **no
cluster-forming th... |
19ad49140dd2397db91eb79d9633063c7c3f0b07e2f3a13b4e6c11731d49afba | Text | 5,195 | 103 | PyRates
=======
[](https://github.com/pyrates-neuroscience/PyRates)
[](https://circleci.com/gh/pyrates-neuroscience/PyRates/tree/master)
[
The following code and data are for non-commercial and academic purposes only.
# Software requirements
This ... |
e078fa9053b4b82b821ba42bb0b3ae482dec0e38212faf9c588950876b13f5f2 | Text | 5,232 | 163 | # sscNOVA
Welcome to the ``` sscNOVA ``` framework repository!
``` sscNOVA ``` is a semi-supervised convolutional neural network algorithm to identify functional regulatory variants from GWAS and eQTLs dataset and exploring the functional characteristics of regulatory variants in autoimmune diseases.
# Requirements
... |
653c63ff6e8dbc049a899d83c257764fb496256d809b8c85c3cbba48a474cd7f | Text | 5,282 | 119 | Copyright (C) 2024 ETH Zurich, Switzerland. SPDX-License-Identifier: Apache-2.0. See LICENSE file for details.
Authors: Thorir Mar Ingolfsson, Simone Benatti, Xiaying Wang, Adriano Bernini, Pauline Ducouret, Philippe Ryvlin, Sandor Beniczky, Luca Benini & Andrea Cossettini
# EEG Analysis: Artifact and Seizure Detecti... |
053b3d5649caf62f687ce1141fea56114417bff479f3656da78befa87e39adbb | Text | 5,291 | 50 | 
## DIDA: The largest historical handwritten digit dataset with 250k digits
DIDA is a new image-based historical handwritten digit dataset and collected from the Swedish historical handwritten document i... |
b1dfd9378f2c0dcb78bf2017c642c584c819b92b14d7c121eae174c3e7038c33 | Text | 5,291 | 84 | # Structure Index
Welcome! This repository hosts the implementation for the Structure Index (SI), a graph-based topological metric able to quantify the amount of structure present at the distribution of a given feature over a point cloud in an arbitrary D-dimensional space. See the [publication](https://journals.plos.... |
4e7164b5b44ab028e5de95aeaab5fd8dcbb688bf8a7794e9b3ecb494e7f4bd32 | Text | 5,353 | 107 | # moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud
moSCminer is a web-based platform with cloud computing for cell subtype identification using the single-cell multi-omics datasets. For multi-omics integration, each omi... |
b0c4ee9d7b005db189016f325a0d5eb78a0fe1ddc2a17fa489d7061a98081c4a | Text | 5,370 | 61 | # NetF: A Novel Set of Time Series Features
This is the original implementation of ***NetF*** for the paper ["*Novel Features for Time Series Analysis: A Complex Networks Approach*"](https://doi.org/10.1007/s10618-022-00826-3) published in Data Mining and Knowledge Discovery.
Please cite our paper if you use the code... |
25cf7d15ca05a25d0d8c5706b3561fe518664701356b909f9ec2c211c567bf03 | Text | 5,402 | 88 | # Parkinson's Disease classification using the Travelling Model paradigm
<div align="center">
</div>
<p align="center">
<img src="fig1_version4.png?raw=true">
</p>
Implementation for distributed learning using the Travelling Model for a Parkinson's disease classifier that is published by the Frontiers in Artificial... |
bce47ef7cf161bb97b93fb3fd83c084a37a36c631605d6881c6138e85a7905d3 | Text | 5,453 | 102 | # ODIL
ODIL (Optimizing a Discrete Loss) is a Python framework for solving inverse and data assimilation problems for partial differential equations.
ODIL formulates the problem through optimization of a loss function including the residuals of a finite-difference and finite-volume discretization along with data and r... |
7f459276777c6cfadee6be14d51cb37b4c2b5de36784aa9d980c5cc7500d98df | Text | 5,483 | 100 | # ReaMVP
Data and codes for the paper "[Prediction of Chemical Reaction Yields with Large-Scale Multi-View Pre-training](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00815-2)".
## Corrections (September 25, 2026)
We thank a researcher for reporting the Suzuki–Miyaura split issue below. We have corr... |
57f04aeca832bf372ce18d8b5b1e31b65e33bdf18c9266d8cbdf296e2bf293ed | Text | 5,511 | 56 | # Nature Communications - Walitt et al. source code and data
Source data and code for analysis and figure creation associated with the Walitt et al. Nature Comms paper on MECFS
All of the DNA sequencing data has been deposited to the [Sequence Read Archive (SRA)](https://www.ncbi.nlm.nih.gov/sra) of the National Libra... |
5e805bb722a05c2c7fcdfbd1a69be8e9bdae17340bde3adde02d91e464a60ef0 | Text | 5,690 | 134 | [](https://pepy.tech/project/EAGS)
.
Getting Started
---------------
#... |
cf5996a63d5e36f43ea559ecb7564291593b4109fa96e0a3aa8d86b149fa62ea | Text | 5,835 | 167 | .. image:: docs/PydFC_logo_dark_round.png
:alt: pydfc Logo
:align: left
:width: 250px
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10161176.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10161176
.. image:: https://img.shields.io/pypi/v/pydfc.svg
:target: https://pypi.org/project/pyd... |
6c49a074468f1ac6144ab0bb0e0fbb90e09cc28f0d4bb14bbc94252791a051f4 | Text | 5,894 | 119 | # GAiN
GAiN generates large synthetic cohorts using small training sets of gene expression data from samples of two different phenotypes. It then performs differential expression (DE) analysis on the synthetic cohorts, returning a list of candidate DE genes.
## Prerequisites
Please make sure you have installed the ... |
846b1d435aa4755254dab04b3832c244d987ace020161bf659faeecc61278d7b | Text | 6,036 | 62 | # Supporting data for “On the variability of dynamic functional connectivity assessment methods, Torabi et al., GigaScience 2024”
## Authors
Kassinopoulos M; Xifra-Porxas A; Torabi M; Poline JB; Mitsis GD (2024)
## DOI: http://dx.doi.org/10.5524/102489
## Purpose of this repository
This repository is a gateway for t... |
bfb606b49264465c818eb01e17f6128993f1ed46d42a6b464e58e743fe1843c1 | Text | 6,150 | 156 |
# FiPhA
FiPhA (**Fi**ber **Ph**otometry **A**nalysis) is a platform for
interactive dataset exploration, event visualization, and summary
analysis of fiber photometry datasets in neurobehavior experiments.
Alongside a variety of data transformations, event series can be defined
as sets of named intervals of interest... |
36ca6df46281f12d422b2c6cc003f40dd3094f9c912e7bc0784fc25f8fa95b51 | Text | 6,161 | 170 | # Analysis and modeling of CA1 pyramidal neurons for the article: Deficits in neuronal architecture and their role in reduced neuronal network activity in a mouse model of overexpression of Dyrk1A
<!--[](https://www.biorxiv.org/content... |
744286e71a2320512d4ad6471110412c1b87860e555e839ce8e6ab56f35b00cc | Text | 6,173 | 181 | # CLIMATv2: Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data
This is the implementation of the paper CLIMATv2: https://arxiv.org/abs/2210.13889. Its previous version (CLIMATv1) can be found at https://arxiv.org/abs/2104.03642.
The concept of the framework is as foll... |
f70fe47704156e63f9ebe90d5faaa4f39479dd1692315d6eeac5cafce456b82a | Text | 6,173 | 135 | WORK IN PROGRESS
# SSSort
A dedicated spike sorting algorithm for single sensillum recordings
## Authors
+ Georg Raiser, PhD, Champalimaud Research, grg2rsr@gmail.com
+ Alicia Garrido-Peña, Universidad Autonoma de Madrid, alicia.garrido@uam.es
+ Lydia Ellison, University of Sussex, Ellison@sussex.ac.uk.
## Summary
... |
6ff3cd5d6ff1e033d904eaeefe0a05c8dccf8aa77524b4df5e0c5b288ec0f37f | Text | 6,199 | 98 | [](https://www.python.org/)
[](https://spatialign.readthedocs.io/en/latest/?badge=latest)
[](https://pe... |
77f1ce73c0a2d1528f7b35a1eb3f185b73cbc904abb7be9b78cef51fe5f40e34 | Text | 6,219 | 185 | # Humatch
**Fast, gene-specific joint humanisation of antibody heavy and light chains.**
```
@
) __QQ --> /||\
(__(_)_"> /\
```
<!--- INSTALL --->
## Install
Follow the steps below to download the code and the necessary packages. Requires **Python 3.9**.
`... |
5428fef4dc0798fbff79a8ad4a0f7e31b7644853055341046ab8e975d59639f1 | Text | 6,242 | 81 | # Encoder Dimensionality
---
Code for a project investigating the effective dimensionality of deep neural networks, and its relationship to their ability to predict neural activity in visual cortex. Described in the paper: [High-performing neural network models of visual cortex benefit from high latent dimensionality... |
76795774da1002b4fbbc600e6f83aea24af87104ef2142d10012b8b65da5bedd | Text | 6,332 | 172 | 
[](https://readthedocs.org/projects/gutils/?badge=latest)
[](h... |
8f0045d42b885770ca44c4ee01f08e72573a9eb5a73db1cf86385d402a2c4e70 | Text | 6,426 | 81 | # MetaLDA
MetaLDA is a topic model that leverages either document or word meta information, or both of them jointly [1].
Key features:
1. Incorporates both document and word meta information in binary format
2. Implemented on top of [Mallet](http://mallet.cs.umass.edu) in JAVA
- Works with Mallet input format
- Runs ... |
8a9cb0048ec98e55cb3a0d7c81aafda481b13fad82e644e2b4349e948060d69b | Text | 6,527 | 125 | ## ViRal and Circular content from metAgenomes (VRCA)
**Note: previously this software was called *VICA*, but the name has been changed to reduce confusion with another new software tool with this name. If you want to use the code in this repository, please cite:**
*Crits‐Christoph, Alexander, et al. "Functional inte... |
192b88b8070995563897552d1a3c23459d1341baef00aa83d60bfee6d6d2d357 | Text | 6,625 | 224 | Merge Allen
================
This is a simple script to download the Allen Institute Brain atlas
(ccfv3) and merge smaller ROI togethers as a function of their parent
branches.
These are the packages you need to install and import before running the
script.
``` r
library(xml2)
library(nat)
```
Loading required ... |
91c2a2a29f1d2527766e97627cfe4a8aa9a334a10af692bf51e3711ac799633c | Text | 6,687 | 70 | PsPM-DoxAv2 dataset
=================
Repository Version: 2023.02.03
This dataset contains skin conductance responses (SCR), electrocardiogram (ECG), respiration, electromyogram (EMG), pupil size (PSR), and gaze coordinates measurements for 100 healthy individuals (50 females) participating in a double-blind, pl... |
29d53ce86ed21810d96198e3c238252ebb82d1c1f2fdc23a0d8077c5d1cbcbeb | Text | 6,771 | 120 | [](https://deepd3.forschung.fau.de/)
[](https://deepd3.readthedocs.io/en/latest/?badge=latest)
# DeepD3
We provide DeepD3, a fram... |
c38b7474486e5bf86e9aec6cfc6a9f1f6d07a145bae54292c70256e9c3a167cb | Text | 6,774 | 187 | # GeNNius
GeNNius: An ultrafast drug-target interaction inference method based on graph neural networks
This model has been publised in Bioinformatics (January 2024), you can find the full publication here: https://doi.org/10.1093/bioinformatics/btad774
## Abstract
**Motivation**:
Drug-target interaction (DTI) predi... |
435c2d1dfc657c7e167d9d63344b203c9420e0085247d39f94657d93de118891 | Text | 6,931 | 125 |
<h1 align="center">
<img src="https://raw.githubusercontent.com/jonescompneurolab/jones-website/master/images/frontpage/logos/logo-hnn-medium.png" alt="Logo of HNN, the Human Neocortical Neurosolver" width="300">
</h1><br>
# hnn-core
[
### Con... |
5d8ae18be02be88fe5dfb7d92e3810eb79c169d684baec8ba1afb2011920c830 | Text | 6,965 | 88 | # Point Cloud Datasets
This repository provides ShapeNetCore.v2, ShapeNetPart, ModelNet40 and ModelNet10 datasets in HDF5 format. For each shape in these datasets, we use farthest point sampling algorithm to uniformly sample 2,048 points from shape surface. All points are then centered and scaled. We follow the train/... |
65727479967a9129e0ba9011bbefec8cab22a6a3bd36f4ec04c86206df7071a3 | Text | 7,003 | 117 | # Bayesian Lesion Estimaton with a Structured Spike-and-Slab Prior
## Data
### Abstract
- Simulation study: 2D lesion masks generated via data generating process described in Supplementary Materials Sec. 5
- UK Biobank: 3D lesion... |
0d29996067bb4ac8b1b1fc9fd1c91f6c75d5a71b1fb869f485cbe811de69b606 | Text | 7,073 | 93 | # BNPower - a power calculation tool for data-driven network analysis for whole-brain connectome data
## Overview
BNPower is a specialized tool designed for power calculations in data-driven network analysis of whole-brain connectome data. This tool accompanies our paper, "BNPower - A Power Calculation Tool for Data-D... |
3c9a64e11c04b61cb57a57ca1a07baad9e94416280cfcac2583962ba76579630 | Text | 7,097 | 131 | # Pediatric Brain Tumor Processing Pipeline
This pipeline can be used to generate AI-predicted brain tumor segmentations for pediatric patients with multi-parametric MRIs. It was trained using the nnU-Net framework on a multi-institutional, heterogeneous dataset (see reference).
The overall pipeline includes:
1. Pre-... |
7cfd327e7ce08ede98bf82faeeaabee88aff70aa20b3e29f0a9f42a4195abcc0 | Text | 7,147 | 124 | # MTSim: Microtubule Simulator
This code was used in the research for the paper titled "Switching from weak to strong cortical attachment of microtubules accounts for the transition from nuclear centration to spindle elongation in metazoans".
## Screenshot
- 1.1. [Set up environment variables](#Setupenvironmentvariables)
- 2. [Structure of the code](#Structureofthecode)
- 3. [Run the code to reproduce experiments and figures](#Runthecodetoreproduceexperimentsandfigures)
- 4... |
421abd8706a40952e5862abe57cff9757c6297214b68c8a28c4083ea3a0dacfd | Text | 7,504 | 201 |
# :bell: Archiving Note
Since DeepRank-GNN is no longer in active development, we migrated our DeepRank-GNN-esm version to our new repo at [haddocking/DeepRank-GNN-esm](https://github.com/haddocking/DeepRank-GNN-esm).
For details refer to our publication "DeepRank-GNN-esm: a graph neural network for scoring protein... |
d2ada46e8df2d30abffbb68db3d8825919efc848f9b890ecf7ed66abb497dabd | Text | 7,508 | 146 | # Celsus-Django
Back-end architecture for Celsus and Curtain web applications.
## Installation instructions
The first step for installation is downloading the content of the following github repoes
1. https://github.com/noatgnu/netphos-web (wrapper for web usage of NetPhos 3.1)
2. https://github.com/noatgnu/celsusdjan... |
bff21f0506de10d28dc9340014b1c67dfb3c623458739f0068dc2d888b86331a | Text | 7,557 | 111 | This code repository contains analysis code for the GOLD Depression Study, carried out at the Family Centre for Research with Ubuntu (FAMCRU), Tygerberg Hospital, Cape Town, South Africa.
The associated dataset for this study is available publicly at https://doi.org/10.7488/ds/7507
For any questions about the code or... |
a509867bef95ca5f5ef55fab33992cec4762321cddcb8efd477d46b556f30680 | Text | 7,632 | 166 | 
[](https://opensource.org/licenses/MIT)
<h1 align="center">
<img src="imgs/BioDeepFuse.png" alt="BioDeepFuse" width="300">
</h1>
... |
c1d23e93d1fc39885f80bbd947fe5d90e798194e9f84742c75dd29b212167912 | Text | 7,878 | 212 | <!-- README.md is generated from README.Rmd. Please edit that file -->
# muxViz v3.1: The R package <img src="man/figures/logo.jpg" align="right" />
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#exp... |
ec504799b0bc290b0500c37ba3f0bab60469557d03512bc7939f549f0d6309e6 | Text | 7,880 | 159 | # NALSM: Neuron-Astrocyte Liquid State Machine
This package is a Tensorflow implementation of the **N**euron-**A**strocyte **L**iquid **S**tate **M**achine (**NALSM**) that introduces astrocyte-modulated STDP to the Liquid State Machine learning framework for improved accuracy performance and minimal tuning.
The pap... |
5816d8a8d55921f3c34cb01b9949c2b7e0755a8e33cdfaf09fa2313fceee99d8 | Text | 7,991 | 87 | # Brain Hierarchical Atlas 2 (BHA2)
Elucidating the intricate relationship between the structure and function of the brain, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Magnetic Resonance Imaging (MRI) has helped in the understanding of this matter, with diffusion images pro... |
5b1cc4bdc8131f6b2018f0222bc894a414b57abc6edd635e783e09d7268345db | Text | 8,065 | 157 | [](https://www.python.org/)
# SGAE: Deciphering spatial domains from spatially resolved transcriptomics with Siamese Graph Autoencoder
## Overview
Spatial transcriptomics (ST) is a newly emerging field that facilitates a comprehensive chara... |
34131e6729c9f5d8c6f7f1271a314d1f399bd9f24091a5f2388e7af96134151c | Text | 8,206 | 110 | <div align="center">
<img src="https://github.com/securefederatedai/artwork/blob/main/PNG/OpenFL%20Logo%20-%20color.png?raw=true" width="70%">
</div>
<div align="center">
[](https://pypi.org/project/openfl/)
[](https://pypi.python.org/pypi/crepe)
[](https://opensource.org/licenses/MIT)
[](https://travis-ci.o... |
c5b7b00c0f40954688aa7422648cc935bec880dbc533866b3516f7f8dd3ced79 | Text | 8,369 | 153 | # Gene-SGAN
Gene-SGAN is a multi-view semi-supervised clustering method for disentangling disease heterogeneity. By jointly considering brain phenotypic and genetic data, Gene-SGAN identifies disease subtypes with associated phenotypic and genetic signatures. Using healthy control (HC) populations as a reference distri... |
c9c57e5c67c8c2ba723fd1c8629ac9ce1f6a224369452e435eed5c25ab387788 | Text | 8,400 | 113 | =====================================================
Collaborative Brain Wave Analysis Pipeline (Cobrawap)
=====================================================
.. image:: https://readthedocs.org/projects/cobrawap/badge/?version=latest
:target: https://cobrawap.readthedocs.io/en/latest/?badge=latest
:alt: Docum... |
0f18a8cf74ff9ebe809da7de995e5f081a5f3543bd5c1c36e8bb91f24da9a2ad | Text | 8,445 | 113 | # DAQmx Examples
<img src="https://github.com/tenss/MatlabDAQmx/blob/master/code/%2Bvidrio/%2Bsync/phase_example.jpg" />
These examples show you how to interact with [National Instruments](http://www.ni.com) devices using [MATLAB](http://www.mathworks.com/).
The focus is [Vidrio's](http://scanimage.vidriotechnologies... |
2e703d253c623e9cd311a2f1af119c0a658a8c3a47dc8a6d7601506c4c8dbe67 | Text | 8,452 | 108 | <p align="center">
<img src="./logo.png" width="50%" title="NequIP" alt="NequIP"/>
</p>
<br/>
[](https://nequip.readthedocs.io/en/latest/?badge=latest) [](https://pypi.pyth... |
9536fb2e9547e015badc2c1da7dfa0e254ffd2bfef24b06585c9ddd3c420d1e3 | Text | 8,596 | 139 | # VDJDB: A curated database of T-cell receptor sequences of known antigen specificity
[](https://docs.isalgo.dev/vdjdb-db/)
[](https://zenodo.org/records/22104776)
[ | [Open access full text](... |
7eec9c6279d34880c328600e8f2f3d569adaef24d33b61b46bba3b007e877f10 | Text | 8,607 | 131 | # <b> BANKSY </b> (version 1.1.0)
## <b> Neighbourhood Informed Clustering for Cell Type and Tissue Domain Annotation </b>
### *Vipul Singhal\*, Nigel Chou\*, Joseph Lee, Jinyue Liu, Wan Kee Chock, Li Lin, YunChing Chang, Erica Teo, Hwee Kuan Lee, Kok Hao Chen<sup>#</sup> and Shyam Prabhakar<sup>#</sup>*
## <b> Over... |
4e335006edd546eb85b52a9952b310a2afd81a183043249547c5a86c5e1d3aa3 | Text | 8,741 | 258 | # Jags
![][CI-build]
[CI-build]: https://github.com/jagsjulia/Jags.jl/workflows/CI/badge.svg?branch=master
## Purpose
A package to use Jags (as an external program) from Julia. Jags.jl has been moved to JagsJulia.
For more info on Jags, please go to <http://mcmc-jags.sourceforge.net>.
## What's new
### Version 3... |
5114ef18c64def762b2ccc42062d0ac88e89e2ef4c39998a1ae7e261933c4ac4 | Text | 8,768 | 163 | # CLEAN
**Clusterwise inference leveraging spatial autocorrelation in neuroimaging**
R package to apply **CLEAN**, **CLEAN-R** and **CLEAN-V** to neuroimaging data.
CLEAN/CLEAN-R/CLEAN-V supports fast and powerful group-level clusterwise inference for neuroimaging data registered in the cortical surface. The curren... |
b2a2ffa1da36ea25ecec6c77def29116e525d5d43f3575f1ac58911e1ea4ad0b | Text | 8,801 | 72 | # Human-in-the-Loop Decision Support in Process Control Rooms Dataset
## Overview
This repository contains a comprehensive dataset to assess cognitive states, workload, situational awareness, stress, and performance in human-in-the-loop process control rooms. The dataset includes objective and subjective measures from... |
7e03a85e06659127ae778c2ea8d4be16733ba31e87cb2b11259f6c244ede93d1 | Text | 8,810 | 186 | # drosSleepStages_Datasettools_SciAdvances2023
Repository for extracting and using dataset described in the paper drosSleepStages_SciAdvances2023
## Dataset location
The original dataset location is present as a multi-part series in `dryad`
To get the location of individual flies they are present in the [dataset_detai... |
8c144eacaef05be7836a92d9d9fb07c01ea21fa77e84138ce4fa662cc9480633 | Text | 9,069 | 72 | # Human-in-the-Loop Decision Support in Process Control Rooms Dataset
## Overview
This repository contains a comprehensive dataset to assess cognitive states, workload, situational awareness, stress, and performance in human-in-the-loop process control rooms. The dataset includes objective and subjective measures from... |
97861802f9575d7e32a215b02e456443a7836af04adcaac71f0bd32226fdbbda | Text | 9,167 | 317 | # DeepONet for Acoustic Wave Propagation
Train and deploy Deep Operator Networks (DeepONets) for simulating sound propagation in 3D scenes. Based on the PNAS paper: ["Sound Propagation in Realistic Interactive 3D Scenes with Parameterized Sources Using Deep Neural Operators"](https://doi.org/10.1073/pnas.2312159120) b... |
2de7371f2f49c89971c8c104439d46e960126b8169f50d0a62f269219cb4cc23 | Text | 9,183 | 187 | [](https://doi.org/10.5281/zenodo.10277443)
Repository for extracting and using dataset described in the paper: [](https://doi.org/10.1126/sciadv.adj4399)
## Dataset ... |
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