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|---|---|---|---|---|
505c35fea16de0d3262e726b81e9fdb04c10c703f05b64e2f18d20076b00c785 | Text | 1,934 | 30 | # ANTEMA
Automated Nanoparticle Transmission Electron Micrograph Analysis
This program is designed to automatically analyze high resolution transmission electron microscopic images (.dm3 files) of nanoparticles for shape and size related parameters by using a neural network for image segmentation.
This program can b... |
ce4f2170c3d05837807699287061c60a783f3f2fd68a0c8910ea3a16bf4139c1 | Text | 1,951 | 26 | # Closed-loop Neuromechanical Arm simulation
Python-MuJoCo framework for simulating voluntary movement with spindle velocity propriocetive feedback using synthetic muscle activation signals.
## Summary
This project implements a closed-loop simulation of a macaque arm model using MuJoCo, where synthetic motor commands ... |
ebf147d5dfc121655be55d9d3c9f76cd11d4676bd026708562c10e83610e7648 | Text | 1,952 | 33 | # schadendorf-pd1
This repository provides sample code to reproduce figures from Liu, Schilling, et al, Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma, Nat Med 2019 (PMID: 31792460 DOI: 10.1038/s41591-019-0654-5) with associated source data (supple... |
3a54fd99358686e6bb43d2adf3a53f013023c2efb935aa841326021d0acb949c | Text | 1,976 | 28 |
[](https://dev.azure.com/OpenGateCollaboration/Gate/_build?defin... |
ba102f19b62ee3226089b97e8985e3268eb5c33de1f5cc294906ac72237ce486 | Text | 1,992 | 43 | # spatiotemporalPRFs
Code repository to reconstruct, fit, and use spatiotemporal pRF models.
This code is used in the following two papers:
1. **Characterizing Spatiotemporal Population Receptive Fields in Human Visual Cortex with fMRI**
by Insub Kim, Eline R. Kupers, Garikoitz Lerma-Usabiaga and Kalanit Grill-Spector... |
43a6bc34bd16c3dc20129407a7a05a66ff37570954d26b5d2db26f0cdd03ab39 | Text | 1,995 | 29 | # ICU_outcome_prediction_Transfer_Learning
Using domain adaptation (DA) and inductive transfer learning (ITL) to improve patient outcome prediction in the intensive care unit
Code used to predict patient outcomes in critically ill patients. Two databases are used. First, a database from Alberta, Canada was used for mo... |
54dd48fc4dcaeda421017238bb166af10f63cac0c08122f1c5db945a1aa1afa2 | Text | 1,995 | 45 | 
[](https://doi.org/10.1038/s41586-024-07680-x)
![PEET](https://img.shields.io/badge/software-PEET-4EAA2... |
14011ecee51c46226d30ef5054121dd0f4873402e0a8f6c6a0629ba4fe9abec9 | Text | 1,998 | 65 | # H-SynEx
A tool for the hypothalamus and its subregions capable of working across different MRI modalities and resolution. H-SynEx was trained on synthetic images derived from high-resolution *ex vivo* MRI.
The model was trained on synthetic images derived from ex vivo MRI label maps:
<img src=https://github.com/li... |
25cffbd5879212332c26f7a8e93008fb8d14cb25ff210bc2c2797ecff8f07def | Text | 2,008 | 53 | # Optim-STED
<a target="_blank" href="https://colab.research.google.com/drive/1ckVkFQnTTZpQIrUTbbz_NsQdrApsEd_1?usp=sharing">
<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
</a>
Welcome to Optim-STED! This project aims to optimize the performance of stimulated emission dep... |
1bc389e85a7f92ec73c578f6367f8f68171b4a09f1332b95e58d18fdf3e5e4d2 | Text | 2,022 | 28 | # Dimensionality reduction of neuronal degeneracy reveals two interfering physiological mechanisms
## What do you find in this repository?
In this repository, you will be able to find all codes and data that were involved in **Dimensionality reduction of neuronal degeneracy reveals two interfering physiological mecha... |
c7cf6671e10ba48413c67c5cbe5898ea42c404270dcc145388b43b1e8f9f27df | Text | 2,046 | 56 | <h1>DUnet</h1>
A 3D convolutional neural network DUnet that derived from DenseNet and UNet for predicting the protein-ligand binding sites.
The datasets can be downloaded from:
https://github.com/devalab/DeepPocket
https://github.com/jivankandel/PUResNet
Please cite the indicated references while using the given datas... |
93f5e43664e42a3c5b68ff1aa83c8a4263de11266379cafac8aa97ffcccf2130 | Text | 2,047 | 32 | # GA4K polygenic score paper code
Scripts are provided to calculate and aggregate polygenic scores (PGS) for a given set of individuals, perform QC, and run regression modeling with permutation testing for rare disease (HPO) case/control cohorts.
# Resource availability
* GA4K data is available via dbGAP using access... |
01d0d8ef6f02af6fa490e0aeabb9c886117a857fa2723214dc81a92c4f60aba1 | Text | 2,058 | 27 | # The Geometric Mental Line
Matlab and Mathematica scripts used to perform the simulations and analyses shown in
Di Antonio, G., Raglio, S., & Mattia, M. (2024). A geometrical solution underlies general neural principle for serial ordering. Nature Communications.
## Guide to reproduce the results
The following code... |
5df9d13cc88b596ef099824c4f013f679b8209fdbe045ff9f585dcb149007369 | Text | 2,061 | 51 | # NeuronalSwitch
Computational scripts for the paper: *Transcriptional dynamics
orchestrating the development and integration of neurons born in the
adult hippocampus*
#### Install
```
devtools::install_github("chernolabs/NeuronalSwitch")
```
Note: the following `R` packages should also be installed in your sy... |
b3f85bf127781d17af2ef33bab4b11339ce62ad993ec40f60c9bbae5de95030e | Text | 2,061 | 51 | This repo contains the codebase for the manuscript:
## Quantitative Modeling of the Emergence of Macroscopic Grid-like Representations
**Authors:** Ikhwan Bin Khalid, Eric T. Reifenstein, Naomi Auer, Lukas Kunz, Richard Kempter
**Publication:** eLife2024;13:e85742
**DOI:** https://doi.org/10.7554/eLife.85742
---... |
eb8199c8eaff6c40b57264648ca9b8d7825192231a43720b137e384640d5ab22 | Text | 2,065 | 55 | # Optim-STED
<a target="_blank" href="https://colab.research.google.com/drive/1ckVkFQnTTZpQIrUTbbz_NsQdrApsEd_1?usp=sharing">
<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
</a>
Welcome to Optim-STED! This project aims to optimize the performance of stimulated emission dep... |
9d2a07fff193d858cd34ae3b4a4d724096bb3c6da4fb9adb35e4f51ee207dbd8 | Text | 2,080 | 54 | # [Merlin Dataloader](https://github.com/NVIDIA-Merlin/dataloader)
[](https://pypi.python.org/pypi/merlin-dataloader/)
](https://github.com/ScreenNeuroPharm/3DNeuronalScaffolds/blob/master/LICENSE)
> The repository contains the data and the functions needed to reproduce the analysis reported in the article "Electrophysiological features of cortical 3D... |
6a57f7f15fc6c35e41954359ca9aa95306fa2608244b095deafd05edc91b0226 | Text | 2,083 | 50 | # Epilepsy2Bids
Library for converting EEG datasets of people with epilepsy to [EEG-BIDS](https://doi.org/10.1038/s41597-019-0104-8) compatible datasets. These datasets comply with the [ILAE and IFCN minimum recording standards](https://doi.org/10.1016/j.clinph.2023.01.002). They provide annotations that are [HED-SCOR... |
070a881dd3dcf7980d20cbd72a3445252df934677bd158309b4fb87e5b729069 | Text | 2,089 | 15 | # mozaik-models
This repository contains models implemented in the Mozaik framework, that were published by the [Computational Systems Neuroscience Group](http://csng.mff.cuni.cz/) at the Faculty of Mathematics and Physics, Charles University.
To run the models present in this repository one must first install the Mo... |
46dcc9acdfe9991cef7da6c3618ad417222b128c12e95c56f53d803c7b7b30bf | Text | 2,100 | 31 | # Zebrafish_SCI_Atlas Codes
This repository contains all the codes that are used in the manuscript titled "Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair" by Saraswathy VM et al. 2024. The instructions to run each code is provide inside the respective folders. A... |
00ec6acbae1a262a32324c5ecb364d0984c6a30900b3f488d788b052c6692f95 | Text | 2,101 | 32 | # FADE_BMS
**Bayesian model selection for the FADE Paradigm**
This code belongs to the paper "Bayesian model selection favors parametric over categorical fMRI subsequent memory models in young and older adults" by Soch, Richter et al. (2021), published open access in *NeuroImage*. For instructions how to process thes... |
a29012e33959afa57f6ec1dc0d3b8c141dd849ddc130f65b2b6c5510669849da | Text | 2,108 | 36 | # DESIGNER-v1
---
## This repository is deprecated. For the current version of designer please see the [designer-v2 repository](https://github.com/NYU-DiffusionMRI/DESIGNER-v2).
Diffusion parameter EStImation with Gibbs and NoisE Removal (“DESIGNER”) is an image-processing pipeline for (diffusion) MRI data th... |
82be35f62e4ec43f0af4023e0ccbf608f98259093c99ede16b42a185554fb0fa | Text | 2,111 | 64 | # J-RESRGAN
This is a fork of https://github.com/xinntao/Real-ESRGAN with some **modifications** to perform super-resolution enhancement specifically for **J-Resolved NMR spectral data**.
## Dependencies, Installation & Usage
- Python >= 3.7 (Recommend to use [Anaconda](https://www.anaconda.com/download/#linux) or ... |
b1ccf754e401228905682b02107ee8bf368b9687528af68bbc699fcc01915dda | Text | 2,114 | 59 | # HNFC Site
This repository provides the frontend code for a fake news detection framework. This application is described in the article ["Building a framework for fake news detection in the health domain"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0305362).
## Installation
This section descr... |
bd321761944322500c35b21629d70a5e59db2cac73734ea7cdb87a0283e44a4b | Text | 2,122 | 41 | # Kine Wheel Arena – DLC
*Kine Wheel Arena – DLC* is an open-source experimental setup for markerless paw tracking of head-fixed mice running on a wheel.
The apparatus is based on the open-source motion tracking system [(KineMouse Wheel)](https://hackaday.io/project/160744-kinemouse-wheel) designed by [Richard Warr... |
c2824c35efe20bfd57e4a107ac524a72a0ed4874d0537756f8217c47c4f681d2 | Text | 2,122 | 61 | .. image:: https://zenodo.org/badge/doi/10.5281/zenodo.46716.svg
:target: http://dx.doi.org/10.5281/zenodo.46716
.. image:: https://badge.waffle.io/VDBWRAIR/ngs_mapper.png?label=ready&title=Ready
:target: https://waffle.io/VDBWRAIR/ngs_mapper
:alt: 'Stories in Ready'
.. image:: https://readthedocs.org/pro... |
22b6af163c1d1e240e621ca597afdfd738e40fc67ee3699a978b395c1dc862b1 | Text | 2,124 | 12 | Age-related neural changes underlying long-term recognition of musical sequences
Matlab and R leading scripts for the paper entitled: "Age-related neural changes underlying long-term recognition of musical sequences", published in (Nature's) Communications Biology (2024): Bonetti, L., Fernández Rubio, G., Lumaca, M., ... |
692cd6551f9e2f1805380a8aa382d19dbc99f0fe83402b61d838f1c4694cfaec | Text | 2,131 | 21 | Dear reader,
Welcome! You must be an avid profilometry person to be interested in downloading our dataset.
Before you start tinkering with the dataset package please do install the requirements.txt libraries for a more easy step into operating this system.
We hope to have made the hierarchy of the package as clear... |
9d4d309dcd0f087f72a126465f45bb02d867a0533734a291d86376a82001fe8a | Text | 2,145 | 45 | # LazyResampling
A reference implementation of lazy resampling for pytorch, meant to accompany "Lazy Resampling: fast and information preserving preprocessing for deep learning".
This repository is a placeholder for a standalone reference implementation. The current reference implementation used in the paper is availa... |
a004e34bfeb31a6c06cf1a5c259d28d701b6ab12811530095b5b6771b77b4b8a | Text | 2,148 | 38 | # MuLaNa2
Muzzio Lab Neuroscience Analysis -2
This is a set of statistical analysis codes written in R. It is oriented towards the analysis of experimental designs,
both parametric ANOVA and robust ANOVA, including one-way, two-way, three-way and four-way between and within.
On the other hand, Bayesian statistics a... |
cef99053583fa13eb6f9c5d040ad0f9a3a6c6ae0ab376f4c7077756a5773a522 | Text | 2,156 | 10 | # Allele specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
Transcription Factors (TFs) regulate gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Since TF occupancy is driven in part by recog... |
4ef2ea121d332678640e64fb060d7087fb9bcfb576e862d2a6e78cd07bff5ccc | Text | 2,172 | 19 | # Collective dynamics and long-range order in thermal neuristor networks
This repository contains source code for reproducing the results in the paper *Collective dynamics and long-range order in thermal neuristor networks*. ArXiv link: [arXiv:2312.12899](https://arxiv.org/abs/2312.12899v1).
Here is another relevant ... |
b9186f114bc2d8c33e7a834b546d68609015e7c026e5e645aeed2923e7d4086a | Text | 2,179 | 48 | # Low-Quality Image ToolBox
<div align="center">
<img src="resources/lqit-logo.jpg" width="600"/>
</div>
<div align="center">
English | [简体中文](README_zh-CN.md)
</div>
## Introduction
LQIT is an open source Low-Quality Image Toolbox, including low-quality (underwater, foggy, low-light, etc.) image enhancement ta... |
c42300904191fc7a8b9b02d37026ec3893d3052083d1b7aff6600d9e1c063fa0 | Text | 2,186 | 55 | # Brain-inspired multimodal hybrid neural network for robot place recognition
## Table of Contents
1. About
2. Structure
3. Usage
4. Datasets
5. Citation
6. License
7. Acknowledgments
8. Note
## About
This library implements a brain-inspired multimodal hybrid neural network (MHNN) for robot place recognition. The MHN... |
6a07a077155be5b8f72a27aa20ada13b4f00f089a35758b184f55ccdb316aa19 | Text | 2,187 | 27 | # Li_et_al.-Arivis
Codes used in the study by Li et al. 2024
These are custom-built pipelines within the Arivis 4DFusion commercial analysis software. Therefore, they can only be used with an Arivis 4DFusion license. Please find the system requirements, installation guides, and tutorials for how to install and use Ari... |
40ddb2ef0d6b8b1be16f530b2505cddc153d71a82e2f2eb919a6b9366770bf9f | Text | 2,201 | 44 | # Automatic Prediction of Obstructive Sleep Apnea in Patients with Temporomandibular Disorder based on Multidata and Machine Learning
This repository contains the code for the paper "Automatic Prediction of Obstructive Sleep Apnea in Patients with Temporomandibular Disorder based on Multidata and Machine Learning" by ... |
c92b21bd812a54b7390cc34f76266514a655f55d45b2b5d363deebf6289acb2c | Text | 2,207 | 46 | # Cascading Genetic Risk
This repository contains the scripts to conduct the analysis described in /Towards Cascading Genetic Risk in Alzheimer's Disease/ (https://www.medrxiv.org/content/10.1101/2023.12.16.23300062v1). The required data can be obtained from the ADNI (https://adni.loni.usc.edu/data-samples/access-data... |
a12b37a0e51b0aa4559fe3edae9690ba1b818861546873bec74d3c9de8e83ea3 | Text | 2,210 | 55 | # Brain-inspired multimodal hybrid neural network for robot place recognition
## Table of Contents
1. About
2. Structure
3. Usage
4. Datasets
5. Citation
6. License
7. Acknowledgments
8. Note
## About
This library implements a brain-inspired multimodal hybrid neural network (MHNN) for robot place recognition. The MHN... |
e2dd0f2526094e9fbf0aa1d65b295f41a48f8d261337c19620592739a4f3f48d | Text | 2,221 | 67 | # drprobe_interface
drprobe_interface provides a Python interface for using the command line tools of the [Dr Probe
software
package.](http://www.er-c.org/barthel/drprobe/)
## Requirements
[Dr Probe Command Line Tools](http://www.er-c.org/barthel/drprobe/drprobe-download.html) must be installed.
## Installation
... |
9bfcc30e24a75f1fe9ee78c0b9566caf2d0dcebe7e8edde555d47fa64a2a9ffb | Text | 2,235 | 32 | # Pediatric Appendicitis Dataset
This repository holds the data from a cohort of pediatric patients with suspected appendicitis admitted with abdominal pain to Children’s Hospital St. Hedwig in Regensburg, Germany, between 2016 and 2021.
Each patient has (potentially multiple) ultrasound (US) images, aka views, tab... |
dd5ad7b502d76aae761ab0e5ca7a72556b41944d361458e30a58ed046f859ae8 | Text | 2,248 | 46 | ---------------------------
Disclaimer
---------------------------
The software is provided "as is," without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose, and noninfringement. In no event shall the authors or copyright holders... |
7f2c1c4765ced842a9b6c52b9219a63123e8a12ebfb8311bbb68b800d6521db6 | Text | 2,269 | 40 | # simseqPRF
Code accompanying the paper "Rethinking simultaneous suppression in visual cortex via compressive spatiotemporal population receptive fields" by Kupers, Kim, & Grill-Spector
## Goal
The goal of this project is to operationalize and elucidate how simultaneous and sequential visual stimuli are processed with... |
a772558325e2447841aabf2f6a875c6fca84608074caa1207e9080cee0a54671 | Text | 2,281 | 67 | # Changes in this fork
To use this fork of fmralign with conda package manager:
Clone this package into your local directory, then:
```
conda create -n myenvname python=3.9
cd fmralign
pip install -e .
pip install -e .[jax]
```
Changes in this fork compared to parent fmralign package:
1. surf_pairwise_alignment.py ta... |
6322fed271b898f7613ccd25326f01766ef823ba2cac341ffbb68842ff427a2a | Text | 2,285 | 55 | # _fsub-extractor_
This is an application for extracting **F**unctional **Su**bcomponents of **B**undles. This software can take gray matter regions, project them into white matter, and find streamlines that connect to them. It can also produce a visualization of the streamlines and sample scalar values along these str... |
6d77e8521cbc617842f45aa5687fd43c7650b8880a68aa3d44fab323d0d4bc40 | Text | 2,296 | 41 | Welcome to the GitHub repository for the following publication: [The genetic architecture of protein stability (Faure AJ et al., 2023)](https://www.biorxiv.org/content/10.1101/2023.10.27.564339)
Here you'll find an R package with all scripts to reproduce the figures and results from the computational analyses describe... |
83be8733a565689c9c625823207304aea30f2d273c939ac3b832205cdc30c534 | Text | 2,297 | 43 | # Integration
[](https://github.com/ScreenNeuroPharm/Integration/blob/master/LICENSE)
## Details
All uploaded scripts work with either a .mat or a .py format.
To reproduce our analysis is necessary to convert the ```.txt``` format file in ```.mat``` format... |
6c4d6b9593ffe4b027eacb6248f8d60abd3a96fcd1e1590082659a1c19bd4b92 | Text | 2,310 | 18 | # Colorblind image tester
We created this web application as part of a larger project to estimate how often scientific figures in biology-related papers are problematic to people with color vision deficiencies (CVD). After manually evaluating 6,000 images from the [eLife journal](https://elifesciences.org), we found t... |
92fff5d23de5143d0136a414896e0c6b0c268d7ff46f1374116db78255b2c255 | Text | 2,315 | 32 | Processing sciMET datasets (including barnyard / species spike-in)
Barnyard portion
1) unidex to generate demultiplexed reads as fastq files and filter to valid barcodes (scMET mode); this trims the first 10bp of
read 1 which includes the randomer ligation region.
3) sciMET_trim.pl - runs trimmomatic using sciMET... |
1d9c0436360d42afd9b6c539d2a25a89c03aaa35320ab3ac6c30b727346925d9 | Text | 2,340 | 51 | # scPriorGraph：Constructing Biosemantic Cell-Cell Graphs with Prior Gene Set Selection for Cell Type Identification from scRNA-seq Data
<img src="./figure.jpg" width="900">
We created a method scPriorGraph based on Python and R that uses `torch` to identify cell types in scRNA-seq data. This project is a simple imp... |
6cc376d874d0c5f322391a8f51cb59e83e1e19e1011262986a5a0d41a48c200b | Text | 2,355 | 18 | # Colorblind image tester
We created this web application as part of a [paper](https://elifesciences.org/reviewed-preprints/95524) to estimate how often scientific figures in biology-related papers are problematic to people with color vision deficiencies (CVD). After manually evaluating 6,000 images from the [eLife jo... |
428d98631879750c94ea19624ebd54106c5328271268aa9711f21aef38e321a0 | Text | 2,364 | 66 | # selective_recruitment
Contains code to make the dataframe for selective recruitment testing.
For more information, see (selective recruitment paper)
## Installation and dependencies
This module uses the Functional Fusion and corticco_cereb_connectivity packages and assumes that your data is organized according to t... |
cd8657e7cc7dd8ab13b6ab545c4e0062cc38997751d6a9e1ce0575af1e34c533 | Text | 2,372 | 58 | # Eventer
EVENTER v1.0.1
Software for the detection of spontaneous synaptic events by Fast Fourier Transform(FFT)-based deconvolution followed by event selection using Random Forest Machine Learning
For standalone executables (Windows, Mac and Linux), please visit https://sourceforge.net/projects/eventer/
... |
d9918c29285e462ebfd7ce3c8a4d655aeae99eb6981a14af1270bb78bf1aec3e | Text | 2,378 | 68 | # LCNet
This is the repo for the following paper:
Lu, Q., Nguyen, T. T., Zhang, Q., Hasson, U., Griffiths, T. L., Zacks, J. M., Gershman, S. J., & Norman, K. A. (2023).
**Reconciling Shared versus Context-Specific Information in a Neural Network Model of Latent Causes.**
In arXiv [q-bio.NC]. arXiv. http://arxiv.or... |
355b2605ff4c851d97541fda92b4e29195f1bdfc1dd493b511f0a4e23503219d | Text | 2,382 | 70 | # OPIPP: Optimization-based Pairwise Interaction Point Process
A Python implementation of **OPIPP**, a method for precisely generating artificial **retinal mosaics**, the spatial organization of retinal neurons. [Here](tutorial/0.background.md) is a short introduction to the background.
## Pipeline
![overview](tutor... |
ad22635aa178bfa538b622a3649c364b8ff33ff0c8552570ce5e8467b34e4d56 | Text | 2,389 | 46 | # Welcome to the ARViS!
The goal of this repository is to help advance and disseminate automated injection technology to the neuroscience community. While the automated injection platform described here is not an off-the-shelf commercial solution, we have made efforts to make it as easy as possible for any neuroscienc... |
633695f6a48af9cb4c69a93635cf257e504fb45fed1264833c01cfeefa25407c | Text | 2,390 | 79 | PURPOSE
-------
The archive "supplementary_data.tar.gz" contains structures, training data, models and an evolution script obtained and reported in the study:
"Exploring Inhomogeneous Surfaces: Ti-rich SrTiO3(110) Reconstructions via Active Learning".
FILES DESCRIPTION
-----------------
./training_data : The complete... |
aa3d21adcb3e51e7fa88aa57b99758ff35df355e36fd7ad478d2ac20b2dd8d5a | Text | 2,391 | 68 | # HNFC Agent
This repository provides the backend code for a fake news detection framework. This application is described in the article ["Building a framework for fake news detection in the health domain"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0305362).
## Installation
This section descr... |
07218b1e0e743d214aeab7ec8c7710f6817df31c61791a67b54e0346dd79421e | Text | 2,398 | 54 | # DBScope as a versatile computational toolbox for the visualization and analysis of sensing data from deep brain stimulation
DBScope is described in the following paper published in npj Parkinson's Disease:
Oliveira AM*, Carvalho E*, Barros B, Soares C, Ferreira-Pinto MJ, Vaz R, Aguiar P., <i>DBScope as a versatile ... |
63f0597e22f7074e6db3144140c32a60dab16c00b8cc4489cd63b9f7e1b47357 | Text | 2,400 | 62 | # emilys
Electron Microscopy Image anaLYSis tools
Version: 0.1.9
## Authors and Copyright
Juri Barthel,
Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
Copyright (c) 2019 - 2026 - Forschungszentrum Jülich GmbH
Published under the GNU General Public License, version 3,
see <http://www.gnu.org/licenses/> a... |
a5444a71237e354d13247e29d336a10f18bd6e1e8292d47e851ae764b78c5cdb | Text | 2,400 | 24 | # Acoustic and linguistic ecoding analysis pipelines for mTRF models based on natural continuous speech
This repository hosts the data processing pielines and statistical models described in our paper entitled *Neural encoding of linguistic speech cues is unaffected by cognitive decline, but decreases with increasing ... |
0e0ea8e4d4595062d0508192b5e1ed6a2620d8eb0224c80a513f5bf2a5ec89f6 | Text | 2,403 | 82 | <h1 align="center">SPIRED-Fitness</h1>
<p align="center">An end-to-end framework for the prediction of protein structure and fitness from single sequence</p>
## Install software on Linux (Conda)
1. Download `SPIRED-Fitness`
```bash
git clone https://github.com/Gonglab-T... |
b93361ca31ca28bff052963d615d36c1896566e53ca00b2447e6e5d325238295 | Text | 2,407 | 76 | # Cardinal
## Mass spectrometry imaging tools
*Cardinal* provides an interface for manipulating mass spectrometry (MS) imaging datasets, simplifying most of the basic programmatic tasks encountered during the statistical analysis of MS imaging data. These include image manipulation and processing of both images and m... |
59a65b9d8f539c2d7a70679690663d354ec1bbe8dff862983a768c6d60024ad2 | Text | 2,472 | 45 | [](https://zenodo.org/doi/10.5281/zenodo.11671164)
Welcome to the GitHub repository for the following publication: [The genetic architecture of protein stability (Faure AJ et al., 2023)](https://www.biorxiv.org/content/10.1101/2023.10.27.564339)
Here you'll find an R pack... |
899fadc8dc9e474932557d4d488c913754ad5ebcf4ec61e7cef6c895e2717128 | Text | 2,474 | 36 | # simseqPRF
Code accompanying the paper "Rethinking simultaneous suppression in visual cortex via compressive spatiotemporal population receptive fields" by Kupers, Kim, & Grill-Spector (2024) published in Nature Communications.
## Goal
The goal of this project is to operationalize and elucidate how simultaneous and s... |
f6b1c1b5130d455fd6699c714c52ce3d3faf16472199a5870323ebd6018a926e | Text | 2,475 | 50 | # TUnA: Transformer-based Uncertainty Aware model for PPI Prediction
# Notice (Dec. 2025)
Check out the streamlined version of this codebase, [TUnA-R](https://github.com/young-su-ko/TUnA-R). The new repo is heavily refactored and the core logic of our model should be easier to u... |
0948d7ac83e2f8289aa722a529628831e97f885dc543bf1c63f042192552cdb8 | Text | 2,494 | 21 | # Phase coherence Kmeans
## Github repository for [this](https://doi.org/10.1101/2023.12.19.572402) publication
#### (In case the link doesn't work: P.CASTRO et al, 2023, Biorxiv, https://doi.org/10.1101/2023.12.19.572402)
## Overview
To analyze brain dynamics from functional magnetic resonance imagery, we computed, ... |
8f66935d29bc6daa0ba36878c2dd9b990e0063227e3192d6b1c9dcf6a3a14688 | Text | 2,515 | 55 | # NeuralHiddenMarkovModel-OneEmissionVariable
## Overview
This repository contains a MATLAB implementation of the Hidden Markov Model (HMM) used in Diomedi et al. (2021), Diomedi et al. (2022) and Vaccari et al. (2024) for analyzing spiking neural data.
## Table of Contents
- [Citation](#citation)
- [Introduction](#i... |
4db0753c7c9ede476a58fa4545a3595e26a12afd906a6fc38609bee204c5f2d3 | Text | 2,518 | 63 | # pyMBEANN
An implementation of Mutation-Based Evolving Artificial Neural Network (MBEANN) written in Python.
## Background
MBEANN is an alternative algorithm for *Topology and Weight Evolving Artificial Neural Networks (TWEANNs)*, which evolves both the values of the synaptic weights and the topological structure of ... |
b3b9638fb00a30c7a20597cef3ae7b377bc1fea16fb4e93ff7e8c350ae673425 | Text | 2,524 | 41 | # Generating realistic neurophysiological time series with denoising diffusion probabilistic models
Code for [Generating realistic neurophysiological time series with denoising diffusion probabilistic models](https://www.biorxiv.org/content/10.1101/2023.08.23.554148v1).
The repository contains all the scripts to run ... |
5e44a7e40a2cfd314358174f604c9019b2d51758e9afe1a4db99c192cd1cf390 | Text | 2,538 | 88 | # Synsor
Synsor is a tool for identifying engineered DNA sequences. To accomplish this, Synsor leverages k-mer signature differences between natural and engineered DNA sequences and uses an artificial neural network to predict which sequences are likely to have been engineered. The model was trained on the 7-mer frequ... |
571966c99be2b971204d9b85cd0bc4dda92ca01204625e4f9f46927910a4c93c | Text | 2,548 | 51 | # Motor Cortex Simultaneous Coding
MATLAB code that generates the figures from the paper
> Motor Cortex Latent Dynamics Encode Spatial and Temporal Arm Movement Parameters Independently
>
> Andrea Colins Rodriguez, Matt G. Perich, Lee E. Miller, Mark D. Humphries
>
> Journal of Neuroscience 28 August 2024, 44 (35)... |
45bffa840309b99b59af812084ac10232fdd85fbde91b6a9e9e10e988e7efc5f | Text | 2,552 | 33 | # About this repo
This repo contains the analysis code underpinning our paper "Neuro-evolutionary evidence for a universal fractal primate brain shape" [eLife 2024](https://elifesciences.org/reviewed-preprints/92080).
It relies on a data folder to run, which be found on zenodo: [DOI:10.5281/zenodo.12820611](https://ze... |
ed4532ceb2e6a59180b48101e3bd78739aa1399310eac8db3257b87074e900bb | Text | 2,564 | 22 | # cerebellum-podcast-fmri
Statistical fMRI data and processing scripts for the publication titled, "The cerebellum is sensitive to the lexical properties of words during spoken language comprehension" accepted on Oct. 30th 2023. See link to preprint copy: 10.31234/osf.io/t9fyc.
A note -- these analyses were conducted ... |
be66e81baa3debecefc9943fc11b0ac5fff41252e0dd85d4af01c5ac76ff420f | Text | 2,566 | 19 | # Single Neuromorphic Memristor closely Emulates Multiple Synaptic Mechanisms for Energy Efficient Neural Networks
This repository reproduces the experiments of the paper titled: *Single Neuromorphic Memristor closely Emulates Multiple Synaptic Mechanisms for Energy Efficient Neural Networks*. The main part of the cod... |
467ae2efb87b480e6c353841e30600636a26e1aa57750ce3148dabe77f3fe6b3 | Text | 2,567 | 36 | ## Immuno-oncology_nanostring
Example scripts for NanoString immuno-oncology assay data processing and Tumor Inflammation Signature (TIS) calculation.
This includes a self-contained workflow with example test data and random TIS weights (see Notes below, actual weights must be obtained from patent filing). These scri... |
af1fca9daac2fecace622d3cb1b30d194b0a57e8943576ac9e2ab6d3b7f75131 | Text | 2,570 | 32 | # singlecell-miracidia
This contains all the scripts associated with the paper: A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni: cell types, developmental pathways and tissue architecture
1. ###import_QC_sample1_v10.Rmd: import and QC miracidia sample 1
2. ###import_QC_sample2_... |
c969be9b1aa2efd72412fc1821e60c55d473407383760a4ebc5f592b198b3131 | Text | 2,576 | 57 | # GenNet-multi-omic
This repository contains the code to reproduce the experiments in: [Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data](https://www.biorxiv.org/content/10.1101/2023.04.16.537073v1.full.pdf)
> [!NOTE]
> This reposisitory contains the code to recre... |
9d6e69dfc8defb7894cb22f4fd9c5459e50430f2db692ce6eb08f860e0bf13cc | Text | 2,578 | 43 | # Generating realistic neurophysiological time series with denoising diffusion probabilistic models
Code for the paper ["Generating realistic neurophysiological time series with denoising diffusion probabilistic models"](https://www.cell.com/patterns/fulltext/S2666-3899(24)0018... |
3e882d258bde691af5c4f62eed23b0f040d2609e8c03cc1b60d53d0f42ba886c | Text | 2,598 | 57 | # Practical Bayesian Inference in Neuroscience: Or How I Learned To Stop Worrying and Embrace the Distribution
This repository is a supplement to Coventry and Bartlett's tutorial on using Bayesian methods in neuroscience studies using PyMC.
- [Preprint](https://arxiv.org/abs/2302.01941) (not up-to-date)
- [GitHub](https://github.com/ChenAo-Phys/MinSR)
- [Zenodo](https://zenodo.org/doi/10.5281/zenodo.7657551... |
633dd19ba642d1bef45d559766b1586b649868fdc04d4bb97e8d38bbc01de47d | Text | 2,613 | 44 | # DepoScope - Predict and annotate phage depolymerases
[](https://colab.research.google.com/drive/1A2XJ_oUtlmIfU3XXmev5dzJUNxqR6VV9?usp=sharing)
## General information
This is the repository related to our manuscript *DepoScope: accurate phage... |
fccf530a8221444e7bfc6df2d5e4d6a5a41a2596e4db5c4591ab38a6253abee5 | Text | 2,618 | 7 | Title: Elucidating molecular mechanism and chemical space of chalcones through biological networks and machine learning approaches
Abstract: We developed a bio-cheminformatics method, exploring disease inhibition mechanisms using machine learning-enhanced quantitative... |
eb3cb762b0d9570c83ef908522296d022be767281dbfc790fe39ecece7e9e8ef | Text | 2,630 | 30 | #########################################################################
# Repository of data for Jonas Yeung's Ccl2 CRT 4CG publication #
# Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON, Canada #
#########################################################################
The data here was used ... |
c869648c67da25f5c0247a25461372618efe6c7ed9441b808d45e141690a617a | Text | 2,631 | 97 | # MinSR
Repository for the paper
_Empowering deep neural quantum states through efficient optimization_
Related links:
- [Paper](https://www.nature.com/articles/s41567-024-02566-1)
- [Preprint](https://arxiv.org/abs/2302.01941) (not up-to-date)
- [GitHub](https://github.com/ChenAo-Phys/MinSR)
- [Zenodo](https://zenod... |
23a0031a921727f3935a0a2a73c6777cde9432dc7fe150839e51b4919479ef59 | Text | 2,649 | 33 | # Task-specific invariant representation in auditory cortex
#### Heller, C.R., Hamersky, G.R., David, S.V.
This repository contains the code to run all analyses presented in [Heller et al, 2023](https://elifesciences.org/reviewed-preprints/89936). The data is publicly available at: [Dryad](https://datadryad.org/stash/... |
6f1fa94f2406afe6493ee6d6c9260ddad434f375e071861ff605613502e6c58e | Text | 2,650 | 52 | ## Hippocampal connectivity patterns echo macroscale cortical evolution in the primate brain
Nature Communications (2024). DOI: TBC
Nicole Eichert<sup>1,*</sup>, Jordan DeKraker<sup>2</sup>, Amy F.D. Howard<sup>1</sup>, Istvan N. Huszar<sup>1</sup>, Silei Zhu<sup>1</sup>, Jérôme Sallet<sup>1,3</sup>, Karla L. Mille... |
d84f0193f2a563a4a012525a2d3743a25489dd161da465ab9c902fbe481ac044 | Text | 2,667 | 62 | # ultramnist
Official Repository related to UltraMNIST classification benchmark
## Getting Started
You will need [Python 3.9.12](https://www.python.org/downloads) and the packages specified in _requirements.txt_.
We recommend setting up a [virtual environment with pip](https://packaging.python.org/guides/installing-... |
d59ea289aebca6aedf4bb19b90f662ce2d4cadce77a58bf90977006e170efd0f | Text | 2,689 | 79 | # visual_behavior_ssn_modeling
Code repository for the SSN modeling work on Visual Behavior Neuropixels data. This
repository is made for a reference purpose, and not inteded to be run on a local machine.
To completely reproduce what has been done, it requires intense computation on a cluster
machine.
The data necess... |
42886c8351f760e3245bcbe9a4095d40554ddffb9ce6559baa55d5c179a4ed5a | Text | 2,692 | 58 | # Real-Time Intermediate Flow Estimation for 3D tomography
## Introduction
This project is a modified implementation of [Real-Time Intermediate Flow Estimation for Video Frame Interpolation](https://arxiv.org/abs/2011.06294), developed within a paper that is currently under review.
More details will be added once the p... |
f7f47743a2b1aca0177de4de223e66eb5238f0a5e8489e79c672d582f31d7acd | Text | 2,702 | 101 | This folder contains 22 functions. Install the following libraries before running the function.
Install MATLAB library:
https://sccn.ucsd.edu/eeglab/index.php
Install Covariance Toolbox：
https://github.com/alexandrebarachant/covariancetoolbox
Usage:
Running the "PlotFigure.m" function to plot ERP、TimeFr... |
51a15514cf1419fde0208fb0cb185969560d784d9a73b6ae831e06d7a2ea920b | Text | 2,711 | 34 | ## Corpus of Spanish song lyrics labeled for gender-based violence detection
#### Code folder
Includes a Google Colab notebook ([https://github.com/somos-ubb/Lyrics_Gender_Violence/blob/main/code/BETO/model.ipynb]) used to generate a model adjusted to our purpose, gender-based violence against women. We use as a base ... |
c5f19b4eb9fe2fb51315b6c1c8f47628a9631dca12c96c1450a5e41d67c655a5 | Text | 2,717 | 49 | # Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network
This repository contains the data and codes of the paper:
*Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network (NIPS 2017)* [PDF](https://arxiv.org/abs/1709.04555)
## Updated Version
We have updated our reaction predictor model and... |
ac380fd1763d8054a1cb0e265f5194a765a1f164180eec79fbdd3210cc786714 | Text | 2,721 | 106 |
# Eisch Lab - Touchscreen Data Analysis App
The EL Touchscreen Data Analysis App takes in complex raw ABET data and returns a csv file with usable data ready to be used for graphing mice performance over the span of the experiment.
This application can be used for the following test:
* Habituation 1 and 2
* Initial ... |
f65cf563ed03a6b0f909eff66b90e6d04c375c998118805ab4ae99ab789c6f42 | Text | 2,721 | 70 | [](https://pypi.org/project/sinabs/)
[](https://sinabs.readthedocs.io)
[](https:... |
dd4160bc157f6b9861e6596651724c9099e9bf5140523dbb773f4eea6f097159 | Text | 2,724 | 73 | # Allocator: a graph neural network-based framework for mRNA subcellular localization prediction
## Introduction
The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins with-in human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivota... |
95c5cf9cebfa3148c80632ba1b6b2e0e458fd7dc9a68de44c0a27b6976887d1d | Text | 2,730 | 69 | # Gillespie_eLife_2024
Analysis code for Gillespie et al, eLife 2024, "Neurofeedback training can modulate task-relevant memory replay rate in rats"
Please contact Anna Gillespie (annagill (at) uw.edu) with any questions about this codebase.
Franklab repos needed:
- for data processing: trodes2ff_shared
- for analysi... |
66e225598ecc021868974cc9de66e5f439fac00b4ba84ad01b500d6f08b49881 | Text | 2,742 | 85 | # This is NOT the newest version
The newest version with trained model is placed in the following repository:
https://huggingface.co/pfnet/GenerRNA
# GenerRNA
GenerRNA is a generative RNA language model based on a Transformer decoder-only architecture. It was pre-trained on 30M sequences, encompassing 17B nucleotides... |
f7884003bbdf7a3505897454faebbf3a5b523861507a3095d9134da1c632b3f1 | Text | 2,745 | 95 | # Local Environment of Fluorine (LEF) Shift Prediction Tools
## Getting Started
A PyPi package is available:
```
pip install lefshift
```
You can also clone the repo manually and then install the lefshift package:
```
git clone https://github.com/PatrickPenner/lefshift.git
cd lefshift
pip install .
```
Be aware that... |
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