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a062d8b8a4bb5a38d5c652ef56c78c9b32b5e732f1536eeb6440a2615ee6c525 | Text | 3,854 | 117 | # MetalHawk
This repository provides a Python implementation of the MetalHawk program
to predict metal sites geometries.
M. Vrettas, PhD.
[](https://doi.org/10.5281/zenodo.18297999)
## Installation
There are two op... |
7923b8a979457a79ab54f8e2eca1d1792c6fe2004240fee111124d6ce76b829c | Text | 3,903 | 70 | # Phenexplain — Official PyTorch implementation
## Requirements
* Python libraries: pip install -r requirements.txt
(Main requirements are pytorch, opencv-python, mako. StyleGAN2 currently does not work with the latest PyTorch version.)
* The official[ StyleGAN2 repositor... |
3c15609de51fcd9ad9d403bb8555fc30577fc41332628cc873370f9475e35fbb | Text | 3,922 | 156 | # Title:
Spatial and Amplitude Dynamics of Neurostimulation: Insights from the Acute Intrahippocampal Kainate Seizure Mouse Model
# Funding:
- American Epilepsy Society Research & Training Fellowship for clinicians
- Institutional Postdoctoral T32 Training Grant provided by the National Institute of General Medical S... |
f5a6ee27d490e05dee5157b2e2f196cda26e5879ffa41a44d83ae8437b2fe7f4 | Text | 3,944 | 58 | Dataset Overview
Title: Fetal Head Ultrasound Images
License: Creative Commons Attribution 4.0 International (CC BY 4.0)
Total images: 3,832
Image dimensions: 959 x 661 pixels
Ethics
Utilizes publicly available fetal ultrasound images
Patient confidentiality and privacy protected by using anonymized and de-ide... |
48909e10a7d50b35f2e3a202cd781e595bd304babd27de51e8fed98d1ec86c6b | Text | 3,965 | 60 | # Latent Predictive Learning
This repository contains code for reproducing results reported in our preprint on [LPL](https://www.biorxiv.org/content/10.1101/2022.03.17.484712v1), a framework for biologically plausible self-supervised learning.
## Setup
The deep learning simulat... |
b78cd66216c0a951aaa322fafed5d10163d24c132af5c60d602cd4f0136224e0 | Text | 3,965 | 86 | [](https://bioimagesuiteweb.github.io/bisweb-manual/)
---
[ [JS-npm](https://www.npmjs.com/package/biswebnode)] ]
[ [Python-pypi](https://pypi.org/project/biswebpython/) ]
[ [Docker](https://hub.docker.com/r/bisweb/devel)]
---
](https://www.python.org/)
[](https://opensource.org/license/gpl-3-0/)
[![DOI](https://img.shields... |
3526c9a505fe62f5150a4c988f4d2fca8baca148774b7ccb67231a70b456e86a | Text | 3,978 | 38 | # CVSX
Cardiovascular system models in JAX with Diffrax
## Introduction
This repository contains code for the paper _"A variable heart rate multi-compartmental coupled model of the cardiovascular and respiratory systems"_, submitted to Journal of the Royal Society Interface. The codebase is based on https://gith... |
ddcc7290bb68f38dd3e841a4724cc81a13bc393baf2148050df3100d072571c1 | Text | 3,982 | 98 | # RSNA Bone Age - Artifact and Confounder removal by Hand Segmentation
[](https://github.com/psf/black)
[](https://zenodo.org/records/7611677)
[.
## What is CPA?
`CPA` is a framework to learn effects of perturbations at the single-cell level. CPA encodes and learns ph... |
d2a4b7cb26e85a4d3e16dfe330ef2f2354accedc1caec39da9db2fc50f645a84 | Text | 4,001 | 76 | # Benchmarking SOTA spatial clustering methods
A comprehensive survey of state-of-the-art spatial clustering algorithms in spatially resolved transcriptomics
------
Spatial transcriptomics techniques enable researchers to quantify and localize mRNA transcripts at high resolution while preserving their spatial context. ... |
0ecb3e94a5675a436804354e1d2077b50ab3adacb70acd3a22ca3f3a5d5432ea | Text | 4,009 | 107 |
## Table of Contents
- [Background](#background)
- [Install](#install)
- [Usage](#usage)
- [Example](#example-readmes)
- [Maintainers](#maintainers)
- [Contributing](#contributing)
- [License](#license)
## Background
This is an open-source Python3 package for nanopore adaptive sample ... |
3e0375a7f6b14261ed7b111244e3b14bfe2b90dfb303bfe9374c27e431fa453b | Text | 4,040 | 40 | # Behavioral assays to assess neural development in Xenopus laevis tadpoles
This repository contains a collection of protocols and software tools for behavioral studies in Xenopus tadpoles.
See our preprint for detailed instructions, comments, and advice on protocol implementation: https://www.biorxiv.org/content/10.... |
672b4990347bea00374a592f174c5f4237f0325334eceb6e65290fef3910cea8 | Text | 4,059 | 79 | # RectiPy
[](https://github.com/pyrates-neuroscience/RectiPy)
[](https://badge.fury.io/py/rectipy)
[](https:/... |
9c035f4a1e2d6ef751fe7fc7f15d8d3078665d1794109aed48a94e041612d989 | Text | 4,068 | 87 | # Hypothalamus segmentation
This repository provides the source code and models for segmentation of the hypothalamus in T1-weighted MR images in coronal orientation at resolution of 0.125x0.125x0.5 mm3 and intracranial volume (ICV) from coronal MRI images of resolution 0.5x0.5x0.5 mm3. The method is based on a convolu... |
60ca678d91e6d103775bd6adf282ecc7a8a76c565bbd04e0787c40ec3482a5e6 | Text | 4,081 | 91 | # EnzymeNet
Source code for enzyme function prediction and candidate enzyme prioritization.
1. System requirements
2. Installation guide
3. Demo
4. Instructions for use
5. License
6. Related publications
# 1. System requirements
Any Linux operating system with Anaconda is recommended for use.
The software... |
2c1411672c44d35816f89244efee3bf0336d0b21ebad4b848d14bd8f5c960511 | Text | 4,114 | 77 | # Code for "Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy"
[](https://zenodo.org/doi/10.5281/zenodo.10064776)
## Overview
`aav_clean` contains Python sourcecode for training the superv... |
cb3da4bde6ca3f5685a01010807261960d2a1bc8397443d7e215756613fb4dc8 | Text | 4,131 | 108 | # KPGT
## About
This repository contains the code and resources of the following paper:
A Knowledge-Guided Pre-training Framework for Improving Molecular Representation Learning
## Overview of the framework
KPGT is a novel self-supervised learning framework for the representation learning of molecular graphs, consist... |
074db1dc0223d75f38dfe38361f1646b528e37ef6b5c8b2b3a0eba66a811d42a | Text | 4,153 | 44 | # headModel toolbox for MATLAB/EEGLAB
**Note:** I am moving this repo [elsewere](https://github.com/aojeda/dsi) to consolidate the forward and inverse problem solvers into a single toolbox. If you are still interested in the headModel toolbox please download it from [EEGLAB's extention page](https://sccn.ucsd.edu/wiki/... |
524c328432d4fb4dface9327285e5b56e5311d1e218c5905950841b35ca6ba36 | Text | 4,166 | 75 | # Macromolecule data collection
This repository contains a number of pre-processed macromolecule (metabolite-nulled) spectra in Varian format (sometimes converted from Siemens format), acquired at different field strengths from different mammals, including human. These data are represented in Figure 1 of the recently ... |
09dd23a1aa7f74191c89bc343780fe3390a1135672c60b972ce733213bca58c2 | Text | 4,170 | 83 | # HostNet
**HostNet** is a virus-host prediction tool that can predict rabies lyssavirus and flaviviruses and provide prediction services on other data sets.
[English](https://github.com/ChenXJer/HostNet) [中文](https://github.com/ChenXJer/HostNet/tree/main/README_ZH)
## Install
Note that this implementation ... |
1125f55a33d1d495417aa2f5782ae84c4fc570dfc7664529ca705e64416df75f | Text | 4,170 | 101 | # Learning pharmacometric covariate model structures with symbolic regression networks
This repo contains code to replicate the results and figures in the paper "Learning pharmacometric covariate model structures with symbolic regression networks".
We present a novel methodology for automatic and simultaneous covaria... |
176d9dd870542f939747066db42966af24ba3d60458d928b796a7737f691b202 | Text | 4,171 | 58 | # Empirical quantification of predictive uncertainty due to model discrepancy by training with an ensemble of experimental designs: an application to ion channel kinetics
This repository contains the code necessary to reproduce the figures presented in our publication: _"**Empirical quantification of predictive uncerta... |
6b18a6dc87411525e692be78c91bea578521b27d442ed3ed78690a8114c3bb27 | Text | 4,172 | 92 | # SocialGNN: A Graph Neural Network model for Social Interaction Recognition
[](https://zenodo.org/badge/latestdoi/561537272)
<!--
[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](htt... |
c1557eaca6ae4eefead1c7a2a8aaba6847b22739b3aa5a21ca588b7082b6fff2 | Text | 4,174 | 57 | # SILAM
Fit peptides for degradation constant and half-life.
Project: SILAM
Flow chart:
<img width="827" alt="Screen Shot 2023-10-18 at 5 41 51 PM" src="https://github.com/kchen96/SILAM/assets/53800187/33882515-335a-4ac1-9eaa-972e436e2e13">
Analysis pipeline:
1. **Mass spectrometry data processing**: The DIA-PASE... |
0060297681388f7ee240fe2fce56ac145e3b1bc6e829b7e2fd417738040a3f36 | Text | 4,184 | 85 |
[![Apache License][license-shield]][license-url]
[![Google Scholar][gs-shield]][gs-url]
[![PDF][arxiv-shield]][arxiv-url]
# Conditional Wavelet Flow architecture for 3D reconstruction of XLFM images (CWFA)
* [About the Project](#about)
* [Installation](#installation)
* [Workflow](#workflow)
* [The dataset](#the-da... |
cf6eba8c70ca5ad648966dbb6174b3ed5e6a91f89313d9662f9cb6a3de794e76 | Text | 4,209 | 35 | Nearest neighbor suspect spectral library
=========================================
For more information:
* [Official code website](https://github.com/bittremieux/gnps_suspect_library)
The nearest neighbor suspect spectral library is a spectral library that was created in a data-driven fashion by propagating annotat... |
51cfe7d52cbebf100c793eb909d0933e6f9245aedd0bef3e4fe5dd123c3c42b5 | Text | 4,239 | 85 | ## **CellGO: A novel deep learning-based framework and webserver for cell type-specific gene function interpretation**
## **What is CellGO?**
CellGO is a method designed to discover cell type-specific active pathways of a single gene or a gene set by modeling the propagation of cell type-specific signals through the ... |
6fa9379ab922748205ccf2146806d4e3a443c6747c0b2cff1f39d200328691bd | Text | 4,258 | 91 | ## Detecting mild traumatic brain injury from MEG data using machine learning
This repository contains the code used for the paper "Using normative modelling and machine learning for detecting mild traumatic brain injury from magnetoencephalography data" by Itälinna et al.
**Note:** The directory paths are currently ... |
fac858e51f94c411fe5286ce677c9a90f99b35293c51f5454a8b6740d857a5d5 | Text | 4,284 | 102 | # A rapid and reference-free imputation method for low-cost genotyping platforms
This repository contains a Python implementation of GRUD model, which is a genotype imputation based on deep learning algorithms. In specific, GRUD is composed of two components: *Generator* and *Discriminato... |
9b7f90b76b30ee25918d324a41eeedb1a1377dde52a38591e693b6c86c3bb0a3 | Text | 4,287 | 97 | Probabilistic 20/20
===================
The Probabibilistic 20/20 test identifies genes with signficant oncogene-like and tumor suppressor gene-like mutational patterns for small coding region variants.
Putative signficant oncogenes are found through evaluating
missense mutation clustering and *in silico* pathogenic... |
ca66cfffe257bbae37fc232d2bda3b4c29c54aa8deba6e313df4cb2fbbe1b4e1 | Text | 4,292 | 56 | Generative Linear-Angular Model of Path Integration (GLAMPI)
[](https://zenodo.org/badge/latestdoi/457836867)
======
## Description
This repository contains th... |
58751bbfaef99fb94dc06a8606c063e1b348267e00a9b96d675ca75d7e217f2b | Text | 4,296 | 73 | # Latent Predictive Learning
This repository contains code for reproducing results reported in our preprint on [LPL](https://www.nature.com/articles/s41593-023-01460-y), a framework for biologically plausible self-supervised learning.
## Errata
Despite careful checking, some ... |
eb9dbba179276e558107caceb27cd124163366710d63f53806ceb15d60a9f755 | Text | 4,309 | 107 | 
... |
93569ec52ea6a220cd2b55f86d1df7df90f49988654e2a1c4da84bffecfd423a | Text | 4,321 | 64 |
# This repository is under development. To learn how to use `pynapple`, you can check its [documentation](https://pynapple-org.github.io/pynapple/generated/gallery/)
# pynacollada 🍍 🥥 🍹
Collaborative platform for high-level analysis with pynapple.
- [pynacollada](#pynacollada)
* [Getting Started](#getting-sta... |
a8e38d3c57002a0a31164d078c4f1750cca7a0ca87e30a4676b158156dc19c87 | Text | 4,328 | 156 | # plotly.py
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/plotly/"/>
<img src="https://badge.fury.io/py/plotly.svg"/>
</td>
</tr>
<tr>
<td>User forum</td>
<td>
<a href="https://community.plotly.com/"/>... |
a396e16b0e8ffe1c6367534c8a706e1de90885e4a4139fbf98dcd9f1acaf70ae | Text | 4,337 | 79 | # CEGA v1.3
# 1 Introduction
We developed maximum likelihood method for detecting positive selection or balancing selection using multilocus or genomic polymorphism and divergence data from two species. The method is especially useful for investigating natural selection in noncoding regions.
**Main changes of CEGA v... |
64a7ba9b91dc932de6b9eb96941c3bbafee31ba16020895f3e954a71d2700814 | Text | 4,349 | 59 | # Mitochondria Analyzer
<p align="center">
<img src="https://github.com/AhsenChaudhry/Mitochondria-Analyzer/blob/master/misc/MitoAnalyzer.PNG">
</p>
Mitochondria Analyzer is a plugin for ImageJ/Fiji that enables quantitative analysis of mitochondrial morphology, dynamics, and function from confocal microscope acquir... |
6285b0e9b773e0f9a1afcbef2c0e25d9167ec82c552ae377427653794e86c485 | Text | 4,364 | 107 | MURFI (multivariate and univariate real-time functional imaging) is a software package for real-time processing of functional brain images for neuroscience applications. At the moment murfi is fMRI-centric, but we plan to add support for other imaging modalities.
This is an open-source release of the MURFI platform (s... |
bf5f5823afe6d55748f9e6f572dadebe1c94aa38310a1bccfc492549489968db | Text | 4,366 | 89 | ## Summary of Snudda
Snudda creates the connectivity for realistic networks of simulated neurons in silico in a bottom up fashion that can then be simulated using the NEURON software. Neurons are placed within 3D meshes representing the structures of interest, with neural densities as seen in experiments. Based on reco... |
c481a3b810380aa1144f1ef8a7c1d56790c985e12dd3ef8d6bf1bf87765c77f2 | Text | 4,461 | 112 | # BatmanNet : Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation
# Requirements
* RDKit : Tested on 2019.09.3
* Python : Tested on 3.8.13
* PyTorch : Tested on 1.9.1
To install RDKit, please follow the instructions here [http://www.rdkit.org/docs/Install.html](http://www.rdkit.org/docs/Instal... |
81467e8cf96f89b9ea512dcd847428bf4ab9d95b122ddb4f40c5524a5bcb9db7 | Text | 4,487 | 91 | # vampire
[](https://cloud.docker.com/u/matsengrp/repository/docker/matsengrp/vampire/general)
[](https://travis-ci.org/matsengrp/vampire)
T... |
7289307ffe6a8fccd1434e74abb311ab037e04bd9b89fa93e46af08577925e8a | Text | 4,537 | 64 | # CHEX-seq: CHromatin EXposed Sequencing for Single-Stranded Open-Chromatin Analysis
## Overview
Photoactivatable primer based Transcriptome In Vivo Analysis (TIVA) has shown successful application in profiling the transcriptome in live single cells [1]. As one of its successors, CHEX-seq employs 3' blocked, light-act... |
2d69e74003296e53390f2c3076be9a6f4e0cf16a03e1c421f3ec074284982be1 | Text | 4,566 | 114 | # BrillouinAcquisition
**BrillouinAcquisition** is used to acquire Brillouin microscopy data as well as optical diffraction tomography and fluorescence imaging data from custom build Brillouin and FOB microscopy devices.
## 1. System requirements
The software only runs on Microsoft Windows. To build the program from... |
a618b3f4571b981bfcb42908dd867c344f5336fefe521ab02ead2423153a38f2 | Text | 4,652 | 49 | # SpaceWalker
[](https://zenodo.org/doi/10.5281/zenodo.10017489)
Here, we present SpaceWalker, an interactive visual analytics tool for exploration of large patches of Spatial Transcriptomic data. SpaceWalker consists of two key innovations: a real-time spatial exploration... |
b99d1c690396607b7ee0f37af639d30ef6cc76cf9523a3fb7d1918289173277b | Text | 4,667 | 105 | Bleualign
=========
An MT-based sentence alignment tool
Copyright ⓒ 2010
Rico Sennrich <sennrich@cl.uzh.ch>
A project of the Computational Linguistics Group at the University of Zurich (http://www.cl.uzh.ch).
Project Homepage: http://github.com/rsennrich/bleualign
This program is free software; you can redistribute... |
7468eeff4e296a69d0656c0823d92ab45ca1fc45c633412699d9443dc10bf1b5 | Text | 4,692 | 125 | # Deep Learning on Graphs
This repository contains code for deep learning on graphs using various graph neural network models. You can use this code to train and evaluate models such as GCN (Graph Convolutional Network), GIN (Graph Isomorphism Network), GAT (Graph Attention Network), and DNN (Deep Neural Network) on g... |
461a544c13f3041ab0a9ac542850d3a3ee84a71bb8ea35bc7d6db6b93325b891 | Text | 4,746 | 72 | # Lieconv-Tg
This is the code repo for the paper Large-scale Glass Transition Temperature Prediction with Equivariant Graph Neural Network for Screening Polymers .We collected most of the homopolymer data from Polyinfo and further processed it to obtain a larger dataset containing 7166 homopolymer data.We used this dat... |
bb58a4524ed827da14813f120f69135f35e27085eb8aa5caae3d10526ddf7dcd | Text | 4,806 | 112 | ## The RIESLING ATAC-seq Pipeline [](https://travis-ci.org/GordonLab/riesling-pipeline)
The RIESLING (Rapid Identification of EnhancerS LInked to Nearby Genes) ATAC-seq pipeline is designed to be an efficient set of standalone scripts ... |
df74cfe2ed41316a81c5e393f213d6cb562a1f560e96e7421b74afcc886d6594 | Text | 4,813 | 97 | # Single-cell based prognosis modeling identifies new breast cancer survival subtypes by cell-cell interactions
## Description
This is the github repository for the project **Single-cell based prognosis modeling identifies new breast cancer survival subtypes by cell-cell interactions** by Shashank Yadav, Shu Zhou, Bi... |
889d637101b5e34bc0b9f54ce94970a64a108d36f4a56c4602a0ba26b57b1bce | Text | 4,826 | 79 | # Head CT preprocess
This is a pipeline for preprocessing computed tomography (CT) head scans. It converts them from DICOM format to NIfTI, **corrects their orientation and position, removes non brain tissue and performs HU windowing**.
](https://pre-commit.com/) [](https://github.com/psf/black)
## Important Notice
### The team that has been maintaining Gym since 2... |
60bf84ad9cdb98f97e9ea19364001da9be2dda424e5d231931e1c8a5f16a6ccb | Text | 4,873 | 120 | # **Skeleton-Guided Bodypart Segmentation for Thermal Imaging**
## **Overview**
This project integrates **DeepLabCut (DLC)** skeleton tracking with **Mask R-CNN** to improve object segmentation in thermal imaging. The goal is to use skeleton keypoints as guidance to enhance mask predictions, making it useful for track... |
d2318eed0c25d8e12c1bd86d7f1fd0f4c26ba238f4d112ec41d6c4964375f2e8 | Text | 4,901 | 86 | # scDeepFeatures: Deep learning-based feature selection for single-cell RNA sequencing data analysis
In this work, we explore the utility of various deep learning-based feature selection methods for scRNA-seq data analysis. We sample from Tabula Muris and Tabula Sapiens atlases to create scRNA-seq datasets with a rang... |
6419b17dfc077bae1d09d00dad1f8b5c527eea1886019d6156ee522777073daa | Text | 4,906 | 155 | # Scalable Multi-Task Learning for Particle Collision Event Reconstruction with HGNNs Dataset
This dataset was used in the paper _“Scalable Multi-Task Learning for Particle Collision Event Reconstruction with Heterogeneous Graph Neural Networks”_. This paper presents a scalable heterogeneous graph network with integra... |
83de820fcd3dcb2688242a22cb0ff40ca5e2d34d7f1714b28a2a265e835b2ac2 | Text | 4,909 | 113 | # CLDF dataset derived from Wichmann et al.'s "ASJP Database" v17 from 2016
Cite the source dataset as
> Wichmann, Søren, Eric W. Holman, and Cecil H. Brown (eds.). 2016. The ASJP Database (version 17).
This dataset is licensed under a https://creativecommons.org/licenses/by/4.0/ license
Available online at https:/... |
e2d0b01cf018fb7ef1f5d7628b63015d12c338cb886fc5f4b8b955c602eb2bc5 | Text | 4,918 | 84 | # Project Deep Learning NNLS Tissue Deconvolution
## 1. Introduction
This project allows you to deconvolute tissue types from RNA-seq expression data by leveraging a pretrained deep neural network.
The nueral network is extensively trained using GTEx datasets v8.
We also include other functions such deep-learning singl... |
08a1797ef979aff98c5a0962c599690658183cda5757f8b09127172776856575 | Text | 4,931 | 142 | # TopoProGenerator
Generating protein sequences with specified topological structures.
## Download project
```
git clone https://github.com/AI-ProteinGroup/TopoProGenerator.git
cd TopoProGenerator
```
## Install Requirements
### 1. In... |
2ed38de132ca9e9c5a14f289f14674ebcc5ef091568bacb5670cf9a67ec075a7 | Text | 4,950 | 105 | [](https://badge.fury.io/py/seqdata)
<img src="docs/_static/seqdata_xr.png" alt="seqdata xr" width=350>
# SeqData (Annotated sequence data)
[[documentation](https://seqdata.readthedocs.io/en/latest/)... |
75942b18d3858c291c552c8c8c6212382351e908d61c329a40be16381813b159 | Text | 4,967 | 122 | # CLDF dataset derived from Wichmann et al.'s "ASJP Database" v21 from 2025
## How to cite
If you use these data please cite
- the original source
> Wichmann, Søren, Eric W. Holman, Cecil H. Brown, Matthew S. Dryer, and Qibin Ran (eds.). 2025. The ASJP Database (version 21).
- the derived dataset using the DOI of t... |
e5294337ae7916f5a0ad54362d6ecef8570e726c86677b9d1c26b031360a7fd7 | Text | 4,996 | 125 | # Image-funcut
In 2017–2018 supported by RSF grant 17-74-20089
## Overview
The `image-funcut` project is kind of a sandbox or testbed for utilities to
view, analyse and transform two-photon microscopy data or any other series of
images.
At the moment, the project includes the following `Python` modules:
- `imfun.... |
9333ba1cc267894cca9d498f93e4c8fb58977f0ee58ac8363e81c7b0c3e947ea | Text | 5,000 | 114 | #########################################################
**XCP-D** : A Robust Postprocessing Pipeline of fMRI data
#########################################################
.. image:: https://img.shields.io/badge/Source%20Code-pennlinc%2Fxcp__d-purple
:target: https://github.com/PennLINC/xcp_d
:alt: GitHub Repo... |
efc79982e208778aeed2db70e6ec0bf999525a2abb2c79ebd9a020b671ac5368 | Text | 5,016 | 80 | [](https://github.com/PalamaraLab/ASMC/actions/workflows/ubuntu-unit.yml)
[](https://github.com/PalamaraLab/ASMC/actio... |
5d21474f82fc7488434a5a170517f37035c5089f51d03823ede13df7a29d8e8d | Text | 5,021 | 68 | Journal Name: PLOS ONE
Title: Cortical effects of wrist tendon vibration during an arm tracking task in chronic stroke survivors: An EEG study.
Authors:
Dylan B. Snyder (1), dylan.snyder@marquette.edu
Scott A. Beardsley (1), scott.beardsley@marquett.edu
Allison S. Hyngstrom (2), allison.hyngstrom@marquette.... |
4e023acee77d6811ca6336d0eaa4517f846b5005f9976b3d9a2e6a6d25930bae | Text | 5,050 | 75 | # InSpect toolbox for qMRI analysis #
Author: Paddy Slator (p.slator@ucl.ac.uk), Centre for Medical Image Computing, University College London
## Required Matlab toolboxes ##
* Optimisation Toolbox
* Deep Learning Toolbox
* Image Processing Toolbox
## Main Functions ##
There are three main commands:
* inspect_seg... |
93c7cdc0f525bb9cb1001a4479661112151b5701705c361eaebc217caea49d26 | Text | 5,071 | 81 | # Video_Prediction_ZOO
This is a zoo that contains all kinds of video frame prediction papers and code (reimplementation or offofficial implementation). The purpose of this repository is to make it easy for newbies in the video prediction field to get started.
## Latest papers
### [Disentangling Physical Dynamics fr... |
61c5b8c2a822d3c2f68f879e731cac24e7ef738394626fffd6b2ceb0c706727b | Text | 5,098 | 87 | # scDeepFeatures: Deep learning-based feature selection for single-cell RNA sequencing data analysis
In this work, we explore the utility of various deep learning-based feature selection methods for scRNA-seq data analysis. We sample from Tabula Muris and Tabula Sapiens atlases to create scRNA-seq datasets with a rang... |
5e162c5136d328077ad445f48a3aab117b9dc3a6e003942684dc1eec81c8426e | Text | 5,103 | 110 | # Alice dataset for Eelbrain
This repository contains scripts and instructions to reproduce the results from [*Eelbrain, a toolkit for time-continuous analysis with temporal response functions*](https://doi.org/10.7554/eLife.85012).
# Setup
## Download this repository
If you're familiar with git, clone this reposi... |
ce69fa50ccd95ff1170378c710e46b30d8de7a4e236a67c9f1e80c77952e3f68 | Text | 5,103 | 96 | # Reproducible And Clinically Translatable Deep Neural Networks For Cervical Screening
This repository will allow you to reproduce the experiments in our paper titled "Reproducible And Clinically Translatable Deep Neural Networks For Cervical Screening".
## Get started
1. Clone github repository
```bash
git clone... |
71b78033f70b80ce50544ea4913770ce842334a533b068d72b7a5072738c81f3 | Text | 5,116 | 79 | # PySlowFast
PySlowFast is an open source video understanding codebase from FAIR that provides state-of-the-art video classification models with efficient training. This repository includes implementations of the following methods:
- [SlowFast Networks for Video Recognition](https://arxiv.org/abs/1812.03982)
- [Non-l... |
fe2500c876db1fe462e39ea91e861f6dbfdf1b748b873edf87d8489ac0522450 | Text | 5,137 | 102 | # Fixel_NMF_development
This repository is divided into three sets of scripts:
* **Preprocessing** takes the raw diffusion data to Fixel Density Cross-Section (FDC) metric using the QSIPrep preprocessing pipeline and the Fixel-Based Analysis pipeline from MRtrix3.
* **NMF** includes the steps required for the non-n... |
cf0f7981bdb54ca5af00f533756dec604f2d0c98bc9189252aabbbd348476d33 | Text | 5,151 | 107 | Papaya
======
Papaya is a pure JavaScript medical research image viewer, supporting [DICOM and NIFTI formats](https://github.com/rii-mango/Papaya/wiki/Supported-Formats), compatible across a [range of web browsers](https://github.com/rii-mango/Papaya/wiki/Requirements). This orthogonal viewer supports [overlays](http... |
0fdf9c10d992d89d12dcef7b5f424b4ff047c3ed8411ffe7a365529eb565b953 | Text | 5,171 | 87 | # PsychRNN
[](https://github.com/murraylab/PsychRNN/actions?query=workflow%3Atests)
[](https://codecov.io/gh/murraylab/PsychRNN)
[
[](https://github.com/andrrizzi/tfep/actions?query=workflow%3ACI)
[](https://codecov.io/gh/andrrizzi/... |
a242f3b81f247e59f64a63c4dfcef09dc71c023aab2448f2eedd779b88189495 | Text | 5,224 | 92 | # TAFKAP
Matlab & Python code for the probabilistic brain decoding algorithms "PRINCE" and "The Algorithm Formerly Known As PRINCE"
This code runs the PRINCE or TAFKAP decoding algorithm. The original
PRINCE algorithm was first described here:
https://www.nature.com/articles/nn.4150
The new TAFKAP a... |
10f70611911ccc7e5c5aad0afbe3bcb102602e9e274abfc5666033642ed9ac9e | Text | 5,276 | 104 | # DeNoise
[](https://github.com/ludgerradke/DeNoise/actions/workflows/BM3D.yml/badge.svg)
[](https://github.com/ludgerradke/DeNoise... |
c16fb52f2342a5658c942762e32c121a3260d9c3e7f805eda5bd416029a75dfd | Text | 5,338 | 48 | # sn_cocaine_rats
This repository contains relevant code/pipelines for work done in our paper ["Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition"](https://www.nature.com/articles/s41593-023-01452-y).
## [`rna_analysis`](https://gi... |
3cbebb4a430149a2d7d8b0b3734ed49da6fcdf363ea84f1db19434c66c05c9b4 | Text | 5,343 | 139 | # XASNet - Graph Neural Network models to predict X-ray absorption spectra
XASNet is a graph neural network (GNN) model to predict X-ray absorption spectra (XAS) of small molecules while maintaing the explainibility of the predicted spectra. It can be chosen based on differ... |
a87c114223e8cd7042476b2892640f70c99a81f7d18493e6841681ecd9f988a7 | Text | 5,344 | 147 | spiketools
==========
|ProjectStatus|_ |Version|_ |BuildStatus|_ |Coverage|_ |License|_ |PythonVersions|_
.. |ProjectStatus| image:: http://www.repostatus.org/badges/latest/active.svg
.. _ProjectStatus: https://www.repostatus.org/#active
.. |Version| image:: https://img.shields.io/pypi/v/spiketools.svg
.. _Version: ... |
74351a3cad2856fba74eaecd95c4399337512f1e37ae994827dcf679f1398116 | Text | 5,345 | 112 | # cgp-convert-counts
[![Quay Badge][quay-status]][quay-repo]
| Master | Develop |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][travis-master]][travis-base] | [![Deve... |
4270f84385f697406fab084b217c9c9f6b3c8b2c2eaf9551e68dd3b31173da3d | Text | 5,389 | 175 |
<!-- 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][i... |
775a57c60d103ff1f82e881d24c7b3a62c497fd02f323edcce51f606157f1097 | Text | 5,502 | 42 | # CVPCR
Cross-Validated Principal Component Regression for voxelwise magnetic resonance imaging (MRI) images
## Table of Contents
1. [Project Overview](#Project_Overview)
2. [Setup](#Setup)
3. [Usage](#Usage)
## 1. Project Overview <a name="Project_Overview"></a>
This repository contains the code used for the diffe... |
6b91780eb3d4ae0a0e0e1407b2498816a002ddeec7082f6f750dad92b47822c8 | Text | 5,547 | 141 | # Keras 3: Deep Learning for Humans
Keras 3 is a multi-backend deep learning framework, with support for JAX, TensorFlow, PyTorch, and OpenVINO (for inference-only).
Effortlessly build and train models for computer vision, natural language processing, audio processing,
timeseries forecasting, recommender systems, etc.... |
4f5916b88aed59b3a39c2ad3f765d72811e9f352ad4172b6a82d40a3525f2c80 | Text | 5,607 | 91 | # GM network modeling
Gut microbiota (GM) is a micro-ecosystem formed by a large number of microorganisms through competition and cooperation. The project constructs a complex network-based GM modeling approach to evaluate the topological features of the GM micro-ecosystem and provides computational simulations for use... |
77d111a11250449101131ffc570062ad0cf69e211f6ac2dddd840f8f9618ab65 | Text | 5,635 | 73 | # Automated MRI liver segmentation for anatomical segmentation, liver volumetry, and the extraction of radiomics
Moritz Gross<sup>1, 2</sup>, M.S.; Steffen Huber<sup>1</sup>, M.D.; Sandeep Arora<sup>1</sup>, M.D.; Tal Ze'evi<sup>3</sup>, M.Sc.; Stefan P. Haider<sup>1, 4</sup>, M.D.; Ahmet S. Kucukkaya<sup>1, 2</sup>, ... |
2e900f517c9ccd8ba6eec93c1720ade199f32f1b26b056378242414ab266ef74 | Text | 5,644 | 126 | ## SMG: self-supervised masked graph learning for cancer gene identification.
## Installation
1. Clone the repository:
```shell
git clone https://github.com/C0nc/SMG.git
```
2. Navigate to the project directory:
```shell
cd SMG
```
3. Install the required dependen... |
0ce11e80fc9ba47265b9d085e7764e049d697ed104ea3f1612a91a9bf0bbf435 | Text | 5,651 | 119 | # Automated three-dimensional image registration for longitudinal photoacoustic imaging
[](https://github.com/meetshah1995/pytorch-semseg/blob/master/LICENSE)
## Contents
- [About](#about)
- [Context](#context)
- [Installation](#installation)
- [Da... |
02a088144261df2f0a6d0044584191ac8f602fe77a4678cba5a883202e44269e | Text | 5,683 | 141 | # An AI-based segmentation and analysis pipeline for high-field MR monitoring of cerebral organoids
[](https://github.com/deiluca/cerebral_organoid_quant_mri/actions/workflows/pylint.yml)
This repository reproduces ... |
cb1d5301b004fb5a192518b8d1ef307d743f7b68dc79b233ca23a174d976c3b1 | Text | 5,748 | 134 |
# <div align="center">Characterizing Weighted Structural Brain Networks</div> #
**<div align="center">by Mark Cameron Nelson</div>**
This library of code can be used to
* preprocess multi-modal MRI data,
* compute a range of weighted connectomes and
* run simple analyses summarized with pretty pictures. ... |
72d39d296c5ee8499f8e95a823a82b7a397e6c5d80342e886ad5e9c3e9d04791 | Text | 5,803 | 131 | # Green Algorithms
**www.green-algorithms.org**
[](https://shields.io/)
[](https://GitHub.com/Naereen/StrapDown.js/graphs/commit-activity)
[ trained using transfer learning to predict changes in stability for protein point mutants.
For details on ThermoMPNN training and methodology, please see the accompanying [paper](https://doi.org/10.1073/pn... |
1a5a6e135ee840b84292a62b79a5708f2b36fffd49c86d0ea730c76978354cf5 | Text | 5,859 | 142 | <p align="center"><img src="https://i.imgur.com/AA7IdbQ.png"></p>
<p align="center">
<a href="#features">Features</a> •
<a href="https://github.com/jsbroks/coco-annotator/wiki">Wiki</a> •
<a href="https://github.com/jsbroks/coco-annotator/wiki/Getting-Started">Getting Started</a> •
<a href="https://github.com/... |
ae78b9f51f46af62158dd93d79a597c88771df83abb429a8bfcdd6d32bfc4007 | Text | 5,946 | 104 | # Histological methylation subtype classification
## System requirements
### Software dependencies
Most sofware dependencies are specified in the Docker File. Additionally a installed version of [CUDA](https://developer.nvidia.com/cuda-toolkit) is needed to enable GPU Support. If you want to use [Docker](https://w... |
be672630283191e9f14c8e28bb47030f76c60cb36aaa4c6b49f28b70662b6c45 | Text | 5,948 | 107 | <p align="center">
<img src="./Data/ColorfulTelencephalon_smoothed.jpg" width="280" height="280">
</p>
# Analysis code for zebrafish telencephalon sequencing data
In this repository, we provide the analysis code for scRNA-seq and bulk sequencing data from zebrafish telencephalon.
[*.
**QMSum** is a new human-annotated benchmark for query-based multi-domain meeting summarization task, which consists of 1,8... |
330a80d887059ab92e30c39aaa59815627b1eba974bd909ef69699b7985a6d6a | Text | 5,960 | 130 | # Relay Learning: a Topologically Secure Framework for Clinical Multi-site Deep Learning
This is the official code repository for the Relay Learning project: [https://doi.org/10.1038/s41746-023-00934-4](https://doi.org/10.1038/s41746-023-00934-4).
Relay Learning is an offline deep learning paradigm providing topologi... |
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