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f33972581eb63f213b4e79634c2e4d05b93b72427086233442c9d79ef1287e1e | Text | 633 | 16 | # neurodesign
This package allows the optimisation of an experimental design for fMRI studies.
## Documentation
The documentation of neurodesign is available at [ReadTheDocs](http://neurodesign.readthedocs.io/en/latest/).
## File description
```
├── docs Contains the source code to generate the ... |
300ab0fc9120665266082e5dc00678d30d342db9b7de483f142713840358c3b8 | Text | 637 | 20 | # illusion-DNN
This is illusion study on DNNs using Ske's Oblique Grating illusion.
The human subject you can download from（https://osf.io/jznrt/ ）
# Citation
```@article{10.1371/journal.pone.0299083,
doi = {10.1371/journal.pone.0299083},
author = {Zhang, Hongtao AND Yoshida, Shinichi AND Li, Zhen},
jour... |
fa23e5ce89dd0d0cf5b5489b33efd00c8ae91cea8606e5a1dac7654a05f379d8 | Text | 649 | 17 | # Social_Navigation
Code and behavioral data for the research of social navigation task.
SN_LMM.csv - The merged behavioral data of the social navigation task, including five columns:
ID: the ID of each participants;
Response: the participants' choice, 0 for the options decreseing affiliation or power; 1 for... |
6a2be8ef621058dc370d76c20ea015987966bb31767ac8ff3b84d0545fb86cfd | Text | 661 | 22 | # iBRNet
This repository contains the code for performing model training using Elemental Fraction (EF) as the model input.
## Installation Requirements
The basic requirements for using the files are listed in `requirements.txt`.
## Source Files
Use iBRNet.py file to train the iBRNet model.
## Running the code
Yo... |
68ed5c91d7bf3649290a0e3d6673edbfe0cabb85cc268626b887737a68b10757 | Text | 662 | 20 | # PrestoCell
https://github.com/euyuw2/PrestoCell/assets/25143033/eda88b93-f567-4932-a4cb-78add195785d
PrestoCell is an open-source microglia segmentation framework implemented in Python.
PrestoCell uses persistence-based cluster... |
020474c8e6345358b7676ab21a32de060d5823389f010d9dfb43b39bfe2ecf91 | Text | 668 | 24 | # Identification of Rare Cortical Foling Patterns using Unsupervised Deep Learning
Official Pytorch implementation for https://arxiv.org/abs/2211.16213.
The project aims to identify rare cortical folding patterns in the central sulcus region thanks to unsupervised deep learning.
.
The folder Experiment_1_2_3 includes the behavioural analysis of all these experiments as well as the mini meta-analysis for the effect.
The ... |
fafd88d6c5c4da636f3e2e2f147e382de60f0a68b77b57d86ce4060561e57807 | Text | 703 | 33 | UniprotParserJS
---
UniprotParserJS is a JavaScript library for retrieving Uniprot data in tabulated text format from Uniprot Accession IDs.
## Installation
```bash
npm install uniprotparserjs
```
## Usage
```javascript
import {Parser} from 'uniprotparserjs';
const parser = new Parser();
const uniprotAcc = ["Q71U... |
7c7ba597d707f4fded2ffa7bb0845f62ea9ed8ff801b06a1eb9c0627aa2245a0 | Text | 708 | 9 | # EWAS-Lewy_body_dementia
This study investigated DNA methylation modulations in Dementia with Lewy bodies cases and neurologically healthy controls.
The code describes the steps necessary to perform QC and data processing.
The outputs of the EWAS include differentially methylated probes and regions, and a functional ... |
dfd20603861d66b3e3df307868b90d58f5f2df0077a5e1fd54f0eb37c3747b6c | Text | 710 | 11 | # neuroblastoma cell line differentiation response heterogeneity transcriptomic analyses
This repository contains code to generate the figures in Figure 1 of the manuscript: Neuroblastoma cell lines display heterogeneity in differentiation responses (Wellcome Open Research, 2024)
## data availability
The adrenal med... |
26d45276e4e55098a30a4cd4460c4430b78fd3daba76f8d11df3986b5db23914 | Text | 729 | 11 | # article-DA-5HT-UG-SNr
This repository contains data and code supporting:
<a href="https://www.nature.com/articles/s41562-024-01831-w">Batten*, Bang*, Kopell* et al. (2024) “Dopamine and serotonin in human substantia nigra track social context and value signals during economic exchange” Nature Human Behaviour</a>
F... |
cebd67302f04d464088c1078c77b6a428d11da8e6d55c5e1d759ee629422cc2d | Text | 754 | 15 | # KunzNatureNeuroscience2024
Analysis code for Kunz et al., Nature Neuroscience, 2024: "Ripple-locked coactivity of stimulus-specific neurons and human associative memory".
# Overview
The repository contains the folders "Figures" and "OpenField". All code is written in MATLAB (MathWorks, Natick, MA, USA).
# Figures
T... |
73cbd6c15f5a19c852260290a8f9e479f11d8cd86443c1381fcd0b88957f5a41 | Text | 757 | 12 | ## The psychological, computational, and neural foundations of indebtedness
Codes and behavioral data for
Gao, X., Jolly, E., Yu, H., Liu, H., Zhou, X., & Chang, L. J. (2020). The hidden cost of receiving favors: A theory of indebtedness. BioRxiv, 2020-02. doi: https://doi.org/10.1101/2020.02.03.926295
This paper ha... |
b39804e529c24e9c58316b02686b2b67931c60a721e001572db163160fb8cf29 | Text | 758 | 16 | # Waveform-based Classification of Dentate Spikes (WFbC)
This repository contains the scripts for detecting and classifying dentate spikes according to the following publication:
Santiago, R. M., Lopes-dos-Santos, V., Jones, E. A. A., Huang, Y., Dupret, D., & Tort, A. B. (2023). Waveform-based classification of dentat... |
3172cd69d856163f5cc58e2dbf014860757745582fcc88dfc5e16a03e7378e36 | Text | 766 | 21 | # DMS_V1
Multi-unit spiking activity and behavioural data from two monkeys in a delayed match-to-sample (DMS) task and a passive viewing control (PV) task.
Data inside each file.
MUA: multi-unit activity (channel x trial).
params: parameter codes for each trial.
cond: irrelevant
sample: sample stimulus iden... |
bc2dd347b08fa3701ae6dfd1837cd7cc1e6b79977d6a055d44b13dfb5683d015 | Text | 771 | 14 | # FisherInformationInV1V2MT
This repository contains the code and (most of) the data from the report:
Transformations of sensory information in the brain suggest changing criteria for optimality
Tyler S. Manning, Emma Alexander, Bruce G. Cumming, Gregory C. DeAngelis, Xin Huang, Emily A. Cooper
Code: The "analysisPi... |
1a02bb0192d802ed1de05e796319a7bc999c71ee879f7343978a6af0ba16b522 | Text | 781 | 16 |
# Introduction
**NeuroDecode** provides a real-time brain signal decoding framework.
[Deprecated] The decoding framework was designed for a motor-imagery project.
Modern decoding libraries should be used for the decoding aspects: [braindecode](https://github.com/braindecode/braindecode), [scikit-learn](https://sc... |
c197b9df4a5815f3906088c7b977ff347d187dd080e9dd98a4a496ffa93a764c | Text | 786 | 5 | This repository provides code and analyses as used in [Xu, Ramos, Marshall & Doe (2023) Notch signaling and Bsh homeodomain activity are integrated to diversify Drosophila lamina neuron types, *eLife* (in press)](https://doi.org/10.7554/eLife.90136.1).
The analysis uses CATaDa (i.e. Dam-only binding data) and Bsh TaD... |
b8a844400084e6aa8b9dab94818981fffe3f956d337f8a9394bbcbf44e231484 | Text | 787 | 9 | # lumen_pressure_reading
Enabling live reading, saving and plotting of pressure readings from a Honeywell pressure sensor connected to an Arduino Uno. Used for embryonic brain pressure recordings.
## Usage
Save pressure_read_write_plot.ipynb in a directory and create a virtual environment with the required libraries... |
afa5ff1df9db502e28bb59c4c50a324b7dd72165991087889d0419b9db5c4d7b | Text | 818 | 16 | # barcode
Code for barcode detection and strength tracking
### Requirements
To detect barcodes over regions of interest, the IMF instantaneous amplitude timecourses must first be saved. To do this:
1. Run EMD (or a preferred variant) on the channels of interest.
2. For each channel, to the resulting IMF ar... |
d51e6b03c4e2b7052ee989f4d323ee4216815243eda274ae61e70984634bcdd4 | Text | 818 | 8 | # Scripts for HYlight analysis in worms
Written by Aaron Wolfe.
These FIJI macros were used for analyzing HYlight data in C. elegans as described in Wolfe, A.D. et al, 2023.
Export Z Stack Ratios: used to capture pixel data for neurons in strains expressing pan-neuronal HYlight or HYlight-RA. Neuron regions are thre... |
a502d379af66480b444a4b00ee23ba8a3d325c4fad38d4de2e646dd04871f2ec | Text | 819 | 28 |
# MENDER Package
[](https://zenodo.org/doi/10.5281/zenodo.10216989)
Welcome to the MENDER package repository. This Python package allows you to easily integrate MENDER into your projects.
## Installation
You can install the MENDER package using pip. Run the following c... |
61a6a516b89aa72f9381fd5878d4163ff24cc9aecbfd9dcccfd8715f9941f4c9 | Text | 835 | 15 | # Machine Learning with Chaotic Strange Attractors
This repository contains code used for the manuscript titled as Machine Learing with Chaotic Strange Attractors by Kesgin and Teğin. https://arxiv.org/abs/2309.13361
# Content
Content contains raw data and Python and Matlab codes for tasks given in aforementioned manu... |
6a5ebebb575c561f0f602b02f8dd63e92b086eabc3082603b08c0637e17c0bf1 | Text | 875 | 12 | # 5xFAD-PCx-proteomic-data-analysis
The decreased astrocyte-microglia interaction reflects the early characteristics of Alzheimer’s Disease
https://www.sciencedirect.com/science/article/pii/S2589004224005029?via%3Dihub
If you use the code/resource or conclusion, please cited the paper:
Liu K, Aierken A, Liu M, et al. ... |
9a104c0a14afc16c178c7b52c8b9cf3f56e7d11a5e10ebb3566e849ef3d557ef | Text | 885 | 5 | This repository provide access to supplementary data related to Nature Communication "Large amyloid beta aggregates activate peripheral monocytes and protect against neuropathology" by Kristian Juul-Madsen, Peter Parbo, Rola Ismail, Peter L. Ovesen, Vanessa Schmidt, Lasse S. Madsen, Jacob Thyrsted, Sarah Gierl, Mihaela... |
00085a2f35dbeb9083e1f0522c43bac27d4725bcb7e768dc600b7d0e887b33dc | Text | 893 | 14 | # The influence of carbon dioxide on cerebral metabolism and oxygen consumption: combining multimodal monitoring with dynamic systems modelling
This repository contains model definitions and input data used in Cooper et al (2021), *The influence of carbon dioxide on cerebral metabolism and oxygen consumption: combin... |
d922732ea37c14c6ca57d951f536a5b730689b2b4efd3707d831f965b4741a53 | Text | 900 | 15 | file name：olfactory_bulb_correction_gmm.h5ad
file description：
The Stereo-seq sequencing data of mouse olfactory bulb, the data is StereoCell processed to single cell resolution, this data is neither normalized nor smoothed.
file name：olfactory_bulb_correction_gmm_after_smooth.h5ad
file description：
The Stere... |
e4c8568006db7e98cc077417ed3d3cf90a4768ca7cb14691be8aa41c2fcce3ae | Text | 901 | 21 | ### Code for Trained recurrent neural networks develop phase-locked limit cycles in a working memory task.
[click here to go to the paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011852)
First install the conda environment:
```conda env create -f phase_env_ubu.yml```, if you are on ... |
4e804ccdf8b1bac7163725c2cdbc79f8faadc00f1887459ac7540bc299376b17 | Text | 917 | 11 | # The landscape of transcription factor activity across human GTEx tissues
[](https://doi.org/10.5281/zenodo.8225317)
This repository contains all the GTEx TF Activity Shiny Application code. The interactive web page can be accessed at: https://lasseignela... |
7bc4b1caea5d8ad6a5bae3b176791fe985238515827bb2dc875197e4072ba5fa | Text | 924 | 17 | # CFAS-and-ADNI-Neuropathology
Feature-feature Correlation Biases Ranking of Dementia Features in Machine Learning Studies (Python Code Scripts)
### Three folders are included along with 4 Python notebook scripts:
1. CFAS and ADNI: the scripts will use this folder to save and create other folders.
2. Dataset: 3 file o... |
fc942890eb185cc13cc1f882f75a8ad7a8a894f8250597f988c6a9207df29124 | Text | 926 | 17 | # drosSleepStages_SciAdvances2023
Repository for reproducing figures in the paper drosSleepStages_SciAdvances2023
## Data extraction
To utlize the code/analysis scripts in reproducing the figures from the paper follow the below steps:
1. Extract the results zip file [data](https://zenodo.org/doi/10.5281/zenodo.1027... |
a7d0ae5840b01e98f0337865c51ff6dbaa788a4318543c8253611f67114770f9 | Text | 940 | 16 | # ASRT_tACS
Created by the Non-invasive Brain Stimulation Lab (University Medical Center Göttingen) (PI: Andrea Antal)
For the project titled:
"Can we enhance Non-Declarative Memory Functions in Older Adu... |
3a01c8baeaacb37b359f62452e52dbc508152c989a0ef292907bb70eddf9d85d | Text | 958 | 14 | # GOI
Retrieving the Gradients of O-information (GOI) from data.
Current version is only for a zero-lag analysis, which works both for time series and for data collected across multiple subjects/trials; dynamical analysis will be implemented in the future (feel free to contribute).
It uses the gaussian normalizati... |
e9a661727c15dbf92236a3580402d6f8334d7b3cfd5bf1f18486d1c7dfdcae59 | Text | 1,001 | 21 | # Cell type-specific <em>cis</em>-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells
This is the code repositry for the [preprint](https://www.biorxiv.org/content/10.1101/2023.05.22.541747v2).
Data availability: [GSE232949](https://www.ncbi.nlm.nih.gov/geo/qu... |
a1bc4d479524c2eba1a8bcaf7bff5833456ed76e8f9a02b287abc19e4948e20d | Text | 1,008 | 16 | |  |  |
| ---- | ---- |
# JAMS_BW
<p align="center">
Just a Microbiology System (JAMS) - a suite for analyzing microbiological sequencing data for use on NIH HPC systems... |
52b696c8d42084337f69b3c9ed9b96c77c2dcad89586b48bb863ac0cb2983fa7 | Text | 1,032 | 34 | # ML-SPM
Machine learning for scanning probe microscopy
[](https://ml-spm.readthedocs.io/en/latest/?badge=latest)
. Extend... |
72b601e7fab898db1680de6600fb30b6561d81339e1637c7cf77d533225c4812 | Text | 1,057 | 21 | Fig1_data.mat - Fig6_data.mat, FigS1_data.mat - FigS3_data.mat, and FigS5_data.mat: Individual quantitative observations underlying the data summarized in Figs 1-6, S1-S3, and S5.
Fig1_data.txt - Fig6_data.txt, FigS1_data.txt - FigS3_data.txt, and FigS5_data.txt: The readme texts for Fig1_data.mat - Fig6_data.mat, F... |
64cc9aeb82d51d7656eaca7c81058374c697df3659506ae27ae09259cc5e1831 | Text | 1,064 | 27 | # CurtainTwo
This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 13.3.3.
## Development server
Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The application will automatically reload if you change any of the source files.
## Code scaffolding
Run `n... |
689ffbc4820fdafef9b21fc3885c49471b562c329a6479b18b3b07258b327cc7 | Text | 1,065 | 27 | # CurtainPTM2
This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 13.3.3.
## Development server
Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The application will automatically reload if you change any of the source files.
## Code scaffolding
Run `... |
5b69794b434a73db0c3b4769a4312bc76aef30aee13b639b4e26faecb92cd3ff | Text | 1,078 | 32 | # Deep-learning image analysis for high-throughput screening of opsono-phagocytosis-promoting monoclonal antibodies against Neisseria gonorrhoeae
Scripts for running the analysis described in
<!-- the paper <link_to_paper>. -->
## Environment setup
```
conda create -p ./.env --file ./requirements.txt
```
## Model tr... |
ded4ca4c30fdede07cc2073aab6ca14499a588a3b9d0d0e3b841da3b4e8c82fd | Text | 1,091 | 27 | # CurtainTwo
This project was generated with [Angular CLI](https://github.com/angular/angular-cli) version 13.3.3.
## Development server
Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The application will automatically reload if you change any of the source files.
## Code scaffolding... |
1b6bca4cc6ddea491cb5c4cfe385de053cd9416293035600f7b4a1aec1cd23cb | Text | 1,100 | 18 | [](https://doi.org/10.5281/zenodo.10277466)
Repository for reproducing figures in the paper: [](https://doi.org/10.1126/sciadv.adj4399)
## Data extraction
To utlize th... |
63e3712dc6f3edcc65f743e2e27bcbf4e356628e59c87d1cfc692d3e825e9919 | Text | 1,111 | 25 | # VilleneuveLab - Publication-related code
:sunny: Welcome to the VilleneuveLab Github repository on publication-related materials! :sunny:
:question: For any questions, feel free to reach out to us at [villeneuvelab@gmail.com](mailto:villeneuvelab@gmail.com)
---
**List of publications**
Below are a list of the pub... |
035a67b26d2666d2af8dbdf629c4b9ff7ee5d602fb72107077ff42dc3801bbf9 | Text | 1,115 | 39 | To use FluoroTensor, create a fresh python 3.8.10 virtual environment in an IDE of your choice. We recommend PyCharm.
Download the zipped folder containing FluoroTensor assets, unzip the folder, and copy the files from 'FluoroTensor Project Version 6.6.8 Release' into the folder of the python project created in the IDE... |
1d629ec4f81f7caf9728a7cd3f63bfc6ef7a88297f479a2ceaeaf43a4a793591 | Text | 1,120 | 30 | ## Denoising task-correlated head motion from motor-task fMRI data with multi-echo ICA
This analysis code is shared alongside the manuscript found here: https://doi.org/10.1162/imag_a_00057
Relevant data files can be found on OpenNeuro: https://doi.org/10.18112/openneuro.ds004662.v1.1.0
## Code
### MRI pre-processing... |
51189a5023d39be821d5ca631b585bd75da4f71b2740ccfee381faeaf2d1843a | Text | 1,147 | 26 | # mouse_dist_wm
Code for the distributed working memory model of mouse brain in Ding et al., “ Cell type-specific connectome predicts distributed working memory activity in the mouse brain", eLife.
Please run jupyter notebooks in the following order. It will generate figures or data and might take long time.
loadDa... |
61aad9c73be82b85270be7c79b082949d6ee377fc2c77ca103d5c7766c59aa04 | Text | 1,150 | 25 | # Cornean_Molina-Obando_etal_2024
This repository includes scripts for analyzing and generating figures from the publication titled "Heterogeneity of synaptic connectivity in the fly visual system."
The organization follows the data and experiment types used in the publication.
The data is accessible on Zenodo: http... |
b45833fa2c9f8ec1dfe7915c31b0bfb9ca129c228165ab2f7ee9ad91fbe46693 | Text | 1,160 | 30 | # Novel Symmetry-preserving Neural Network Model for Phylogenetic Inference
Xudong Tang, Leonardo Zepeda-Nuñez, Shengwen Yang, Zelin Zhao, and Claudia Solis-Lemus.
## Citation
```
@article{tang2023novel,
title={Novel Symmetry-preserving Neural Network Model for Phylogenetic Inference},
author={Xudong Ta... |
ce0485e00c1897dca631d0c9647446db3fc5b761a5594696efdcd86733383662 | Text | 1,169 | 28 | # ReptiLearn
__ReptiLearn__ is an open-source software system for building automated behavioral arenas, running closed-loop experiments based on realtime video analysis, and collecting behavioral data.
__ReptiLearn__ was created to help us run continuous, long-term, learning experiments tailored to the specific nee... |
5d98da16fd3a75e3c628c16501d9a332659d13ab04ab690a93b2c56913c4feac | Text | 1,175 | 39 | .. image:: https://img.shields.io/pypi/v/fimpy.svg
:target: https://pypi.python.org/pypi/fimpy
.. image:: https://img.shields.io/travis/portugueslab/fimpy.svg
:target: https://travis-ci.com/portugueslab/fimpy
.. image:: https://codecov.io/gh/portugueslab/fimpy/branch/master/graph/badge.svg
:ta... |
369435c83abc4911936ea926f8452caccc8b4e45fba4c8cdf2c4059c6ec21651 | Text | 1,190 | 43 | # Undrift
Corrects local, non-linear drift in tissue by estimating dense optical flow and
using it for warping images back to first frame.
It comes as command line tool for Python >= 3.6
Please refer to Hansen et al 2022 for citation: https://doi.org/10.1093/oons/kvac009
### What does it do?
#### Original movie with... |
d5167ac6fa810c48223a3702ce31d85090c09b8d5a32bcc6be3103a4c1035e9f | Text | 1,190 | 12 | # Evaluation of sample-specific network inference methods
Code accompanying the paper "Evaluation of single-sample network inference methods for precision oncology"
## Folder resources
- Driver genes per cancer subtype, downloaded from [IntOGen](https://www.intogen.org/search) and [COSMIC](https://cancer.sanger.ac.... |
6d534c2d3da982d6e4098d228d955b3d0ba3a38266fea95f3922a3ed87effd19 | Text | 1,201 | 54 | # Spike sorting : how good are we to correct for motion ?
Here all the material to generate and reproduce all figures for the paper
**A modular approach to handle in-vivo drift correction for high-density extracellular recordings**
preprint here: https://www.biorxiv.org/content/10.1101/2023.06.29.546882v1
## ste... |
5dd6dec8ccb682909d71bdc60fcc0b455aba6adeda2f48614d5850bf261f5ee0 | Text | 1,213 | 11 | # Dynaphos experimental scripts
Code repository for the experiments and figures in the eLife publication. (*Note, this repository only contains the experimental scripts. The published software module for differentiable phosphene simulation can be found [here](https://github.com/neuralcodinglab/dynaphos)*)
van der Grin... |
75456499dedb98b15cb6617674103922e9cc13aa47c69c373246a59c8ee4d757 | Text | 1,270 | 35 | # Directory Structure
## fairseq：Running the foundational toolkit for machine translation.
## model-code：Core code related to the model.
```markup
SGSE: The method proposed in this paper.
baseFunc.py: Fundamental methods for constructing DGL graphs, message passing, and building edges.
buildGraph.py: Building DGL ... |
4abfe13a0b530e55bd7e6e1773a84d729ef1d87a3de3d4eecde4b5cb7d1a5ef2 | Text | 1,276 | 36 | # Dresden in vivo OCT Dataset of the Middle Ear
This git contains the most relevant scripts used to create the Dresden in vivo OCT dataset of the middle ear (DIOME).
The DIOME can be downloaded from this [link](http://dx.doi.org/10.25532/OPARA-279)
## Merge segmentation masks
The segmentation masks were stored un... |
f12e67810915e88e243f11e9463d4efd0c097855069b8d91b060de0956a4afd4 | Text | 1,276 | 45 | # Undrift
Corrects local, non-linear drift in tissue by estimating dense optical flow and
using it for warping images back to first frame.
It comes as command line tool for Python >= 3.6
Please refer to Hansen et al 2022 for citation:
Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migratio... |
a3aaa8592934785b5b21b6d36a77d4c6ab5e02c9027795b1be3e758b5f1f5362 | Text | 1,291 | 40 | This repository includes Generative models for medical imaging, primarily focused on Brain MRI
Training several of the generative models was performed using the supercomputing resource Berzelius (752 Nvidia A100 GPUs) provided by the National Supercomputer Centre at Linköping University, Sweden. It was donated by the ... |
2e2f0de6791bcec83cb6e29f394f5402c4049920138c563b4226c7f7f95298bb | Text | 1,305 | 9 | # Analysis code for Independent morphological variables correlate with aging, Mild Cognitive Impairment, and Alzheimer's Disease
Description of the procedures and analysis present in de Moraes et al., in submission - **Independent morphological variables correlate to aging, Mild Cognitive Impairment, and Alzheimer's Di... |
1ab561add70d480aecd7e9b1e115e78789becb70ebb72cb0761d8320f1450beb | Text | 1,354 | 19 | # About the project
A fully differentiable and biologically plausible simulation of cortical prosthetic vision, which can be used for end-to-end optimization.
## Installation
`pip install dynaphos`
## Getting Started
- Download the default configuration file (config/params.yaml) from [our repository](https://github.c... |
ed52181160064f29a7e31c77866c09611cf35ec5de52b80f4e38bab780c8e1b6 | Text | 1,399 | 30 | [](https://dev.azure.com/igraph-team/igraph/_build/latest?definitionId=1&branchName=main)
... |
ccb478f6dd8ea5a1aca2f9ddc015a947c1a0671c2ca4c8fbf1adbd75ea529c2f | Text | 1,400 | 10 | # Cleaning-ABCD-hormone-data
These scripts clean the salivary hormone data of the ABCD study.
The script hormone_cleaning_baseline_2year_g.Rcontains several steps to clean the hormone data and confounds and correct the hormone levels for confounds.
It first follows the decision tree in Herting et al. 2021 (doi: 10.33... |
72cab770bab30d6d5c3a06457bc8ceafb6af4ab717a503f1c5341797fe8a0847 | Text | 1,410 | 20 | ## X-ray diffraction denoising using deep convolutional neural networks
This repository contains Python source code for training a deep convolutional neural network to denoise experimental low-counting statistics X-ray diffraction data. It provides the neural-network definitions as well as a training pipeline. The exp... |
e859e092305933f360cdcd00ceddb52d281d6f3ee65892e172a1ca8e994a6e4e | Text | 1,427 | 20 | ## X-ray diffraction denoising using deep convolutional neural networks
This repository contains Python source code for training a deep convolutional neural network to denoise experimental low-counting statistics X-ray diffraction data. It provides the neural-network definitions as well as a training pipeline. The exp... |
2ed2adc6db8ae9634baeb0cda9bcc9a5c7b62866750c9cdef96013a45b1ddf6f | Text | 1,466 | 27 | **Package for MRI reconstruction. Supports:**
- non-Cartesian regridding
- iterative SENSE (Cartesian or non-Cartesian)
- iterative SENSE for higher order models that may include:
- a B0 map
- time varying spherical harmonics of phase accrual
**Before Usage**
- run setPath.m to add all the directo... |
43cdcda11707c9408501ea18314f0b80edeeabc64ce31bed1161b310d370ba51 | Text | 1,484 | 28 | .. image:: https://travis-ci.org/AllenInstitute/bigfeta.svg?branch=master
:target: https://travis-ci.org/AllenInstitute/bigfeta
:alt: Build Status
.. image:: https://codecov.io/gh/AllenInstitute/bigfeta/branch/master/graph/badge.svg
:target: https://codecov.io/gh/AllenInstitute/bigfeta
.. image:: https://readth... |
527982ff32eb726412fec8fd2202846604704ee5960416a644ae9fa8f2d9a3d4 | Text | 1,489 | 41 | Stopwords Bengali (BN)
=======
[](https://travis-ci.org/stopwords-iso/stopwords-bn)
The most comprehensive collection of stopwords for the bengali language.
A [multiple language](https://github.com/stopwords-iso/stopwords-iso) collect... |
1688f94ce1ccde48833ae5660edd1c619c5ebf0a1d975d8f84511af695cc8a9e | Text | 1,493 | 3 | # BacLAB-Deep-Learning-Neural-Network
The rise of antibiotic-resistant bacteria presents a pressing need for exploring new natural compounds with innovative mechanisms to replace existing antibiotics. Bacteriocins offer promising alternatives for developing therapeutic and preventive strategies in livestock, aquacultu... |
698cb719c5bdf963216e7df162ac0e849baf4fcff37c9a970b623063f2dae2a4 | Text | 1,512 | 33 | # Multimodal Bioage Prediction
This repository contains the implementation of a multimodal image classification model that uses Swin Transformers for feature extraction from different types of images (e.g., face, tongue, and fundus) and a cross-attention mechanism to integrate features for final classification.
## St... |
f808574069f194d60fd0717e646a7d2edba95890c2274f191610306e8784a518 | Text | 1,525 | 29 | # Python_DAQmx_examples
NI's officially supported DAQmx package, [nidaqmx ](https://github.com/ni/nidaqmx-python), was released in 2017 for Windows only.
`nidaqmx` wraps the DAQmx C API using `ctypes` and is documented [here](https://nidaqmx-python.readthedocs.io/en/latest/index.html).
This repository provides more ... |
69f6016eea2388211db679b167c07b94c5a5fe77271cbf38e231e727318fb18c | Text | 1,572 | 41 | # EEG-brain age prediction model trainning
“ Dense_train.py” is a data loading and training code for EEG_BAI.
Preprocessed EEG data were converted into scalograms based on the continuous wavelet transform method using complex Morlet wavelet function.
We chose to use 16 frequency bands of the center frequency C, which w... |
2d10a5eb6031fad95c7af2ae787ad394a05706d2beb45fa47d796adb14fa64b1 | Text | 1,575 | 37 | # regNet
regNet is an R package that utilizes gene expression and copy number data to learn regulatory networks for the quantification of potential impacts of individual gene expression alterations on user-defined target genes via network propagation.
# regNet installation
1. Download the folder 'regNet'.
2. Start R a... |
59248e3fd3f4160b21e28750b7380d944894242b276a1cd3451bb351474cd119 | Text | 1,577 | 20 | # SCZ-Synaptic-Circuit-Failure-Model
This repository provides the codes for the spiking network model simulation and the mean field and linear stability analysis presented in the paper: [A prefrontal network model operating near steady and oscillatory states links spike desynchronization and synaptic deficits in schiz... |
717b38ffb8d49fede59432bb94b9e401f3a37ada276a699fac3138764841863c | Text | 1,589 | 63 | # Curtain Web API
---
This is a node.js package used to interact with the Curtain Web REST API.
## Installation
```bash
npm install curtain-web-api pouchdb -s
npm install @types/pouchdb -D
```
## Usage
```typescript
import { CurtainWebApi } from 'curtain-web-api';
const curtainAPI = new CurtainWebApi("https://cu... |
bb3ad02de56f0139f9cc86f539e1f7449be6f3390c7240b8a25fec7a4b9d090d | Text | 1,640 | 50 |
---
# Emergence of music detectors in a deep neural network trained for natural sound recognition
[](https://doi.org/10.1101/2021.10.27.466049)
Authors: Gwangsu Kim<sup>1</sup>, Dong-Kyum Kim<sup>1</sup>, and Hawoong Jeong<sup>1,2</sup>... |
a5420bb232aaff1e9f58d973fb7720ace5d462417a57065504aa6b773addccb5 | Text | 1,645 | 37 | <img src="icon/familiar.svg" align="right" width="120"/>
](https://www.python.org/downloads/)
[](https://github.com/cudmore/SanPy/actions/workflows/tests.yml)
[ code repository provided by [Yigit Demirag](https://yigit.ai).
### Getting Started
To install the dependencies, run:
```
conda env create -f mosaic-env.yml
conda activate mosaic-env
```
To train neuromorphic Mosaic archite... |
897fd4ffc025bb25db633e997f20c54488290695e63a9b9746e331c052ce3480 | Text | 1,714 | 58 | **SMITHERS**: Smithers' a Mathematical Interdisciplinary Toolbox for Helping Engineers Researchers and Scientist
## Description
**Smithers** is a generic library for scientific computing developed in Python
that aims to facilitate the development of many typical routines. It is
substantially a multi-purpose toolbox th... |
6238512631d1bc0c69959fc0c5b1fa6791e442874a2e958f0719a9d38615e308 | Text | 1,724 | 20 | # iDeepViewLearn
We present iDeepViewLearn (Interpretable Deep Learning Method for Multi-view Learning)--a method for learning nonlinear relationships of data from multiple views that is capable of feature ranking. iDeepViewLearn combines the flexibility of deep learning with the statistical advantages of data- and ... |
2681474d2c46a592fb129ead4a98bc249fc24ed8d56abf908fc59ba0ae7a59f1 | Text | 1,730 | 47 | # EVAC+
This is a repository to run [EVAC+: Multi-scale V-net with Deep Feature CRF Layers for Brain Extraction](https://arxiv.org/abs/2206.02837)
## Pre-requisites
This model depends on the implementation of the CRFasRNNLayer, which is from this repository : https://github.com/MiguelMonteiro/CRFasRNNLayer.
Files we... |
d575f132095ad5f8f7508efd54bad44dd40888e619c9c34d8d3891ac786fd52c | Text | 1,732 | 45 | # ReptiLearn
__ReptiLearn__ is an open-source software system for building automated behavioral arenas, running closed-loop experiments based on realtime video analysis, and collecting behavioral data.
__ReptiLearn__ was created to help us run continuous, long-term, learning experiments tailored to the specific need... |
93b4efafc6adefca0108528d12bbc052d5ff93379e9c4e105e8a70500ce24101 | Text | 1,740 | 15 |
## Overview
Code for analyses presented in Single-cell multimodal glioma analyses reveal epigenetic regulators of cellular plasticity and environmental stress response. [Paper link](https://www.nature.com/articles/s41588-021-00926-8).
## Data availability
Processed data is available at: https://www.synapse.org/single... |
026977c2788883b7ad91a8bd16328f1582a286b6ed7cfe81033b179b9d813ecf | Text | 1,753 | 33 | # jPCA for Neural Data Analysis in Python
This is an implementation of the "jPCA" technique from "Neural Population Dynamics During Reaching" by Churchland, Cunningham et al (Nature 2012). It closely mirrors the original MATLAB codepack published by Prof. Churchland. More information about the JPCA technique, and the M... |
a81b67eaf61bd0d11784de5c066017952b877c998939e3f3a9b49f9e6aadc89c | Text | 1,758 | 13 | # FID-A
Toolbox for simulation and processing of in-vivo magnetic resonance spectroscopy data
Getting Started (requires a working internet connection):
1. EITHER a) Go to https://github.com/CIC-methods/FID-A and click on the "Clone or Download" -> "Download ZIP" button to download the package. Unzip the downloaded "F... |
4e032040568072562706556bf3b0aefd81a4b47b583acab5a35956fc81b59724 | Text | 1,768 | 18 | # Photometry data processing
This processing pipeline of fiber photometry recordings was developed by Ekaterina Martianova in Christophe Proulx lab at CERVO Brain research center, Laval university, Quebec, QC, Canada, 2019.
In order to use, please copy the notebook ___Photometry_data_processing.ipynb___ to your googl... |
89f2ee40ca1b562816be97fd6fc3fc0ce6ed894f9190913d5c2d31ba019e936b | Text | 1,773 | 52 |
---
# Emergence of music detectors in a deep neural network trained for natural sound recognition
[](https://doi.org/10.1101/2021.10.27.466049)
Authors: Gwangsu Kim<sup>1</sup>, Dong-Kyum Kim<sup>1</sup>, and Hawoong Jeong<sup>1,2</sup>... |
deeac609bddaad38f0fefea9c4a4b8cc2ae6df93b91ba2a094ce667e7e66aeb7 | Text | 1,798 | 24 | # EEG-Epilepsy-Seizure-Prediction-The-Post-processing-Stage-as-a-Chronology
Scripts used to develop the methodology proposed in "EEG Epilepsy Seizure Prediction: The Post-processing Stage as a Chronology".
You can not execute these codes as it is necessary the preprocessed data from EEG recordings. As the used datas... |
0a8c0d6bc863aba59fb1bdca3c76940169f42d10a93ce62be84f97df22f93c36 | Text | 1,801 | 16 | In order to view these datasets, you'll need MATLAB, Octave, or a similar program that can open .mat files.
Supplemental Videos 1 and 2 raw data is located in the file "supp_video1and2.mat". The variables are as follows:
- gcamp_C is the raw neural data for the control condition. This data is 3 dimensional, and is ... |
ee16ab8683a1c6066515dc48c21f93cbaad07bcdcb0b824aa788bc8562eade54 | Text | 1,841 | 54 | # The Healthy Brain Network Preprocessed Open Diffusion Derivatives (HBN-POD2)
This repository contains code, results, and the manuscript for the Healthy Brain Network Preprocessed Open Diffusion Derivatives (HBN-POD2) project.
## Project Organization
.
├── LICENSE <- BSD-3 license
├── Makefil... |
e68bc5832f829b5ca492089df64f12aa1fa009d072bae31fefb7667a819f0975 | Text | 1,893 | 71 | # QSM.jl
[](https://kamesy.github.io/QSM.jl)
[](https://kamesy.github.io/QSM.jl/dev)
[](https://github.com/ka... |
1a0e67347a0e99065c94f5c0772899670d45f7cb076c8403b606ba2166717f1b | Text | 1,902 | 41 | # ORGANIC
**ORGANIC** ([Objective-Reinforced Generative Adversarial Network for Inverse-design Chemistry](https://chemrxiv.org/articles/ORGANIC_1_pdf/5309668)) is an efficient molecular generation tool, able to create molecules with desired properties. It has a user-oriented interface, and doesn't require a HPC cluste... |
fe81b90fe4a0aae7e24b7c7c5f44361d3dab59ceb92477f0efaae0a44a494a13 | Text | 1,923 | 44 | # Deep Inversion Validation Library
Library for testing and comparing deep learning based methods for inverse
problems, written in python.
See the [documentation](https://jleuschn.github.io/docs.dival/).
The project is also available on [PyPI](https://pypi.org/project/dival/).
## Standard datasets
One main goal of... |
8139d9d2ab2c343c1eba5d72c197d2592d427fc0130ab2c8aacb8ebb5974b9ac | Text | 1,956 | 53 | # A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction
<!-- [PAPER link]() -->
PNAS paper link forthcoming
## Results
### Main
### Supplementary
## Getting ... |
c9cfee926f088006aabecb2b05a71fe4ea3372bd459e988ac9e5ef748fa324cb | Text | 1,963 | 34 | # Gaussian_LDA
Implementation of the paper - <a href="http://rajarshd.github.io/papers/acl2015.pdf">"Gaussian LDA for Topic Models with Word Embeddings"</a>
### Data Format
* Embedding file: Each line of the file should contain the embedding (dense vector representation) for a word. Each vector should have the same d... |
6dc7b110d0368fb5f467d51c2e228618a2fa300aba5423c6f6eb735dc6c72bd5 | Text | 1,978 | 67 | # Welsh Mouse Embryo Stager
Stage a mouse embryo in the age range `E14` -> `E15` by drawing a spline on a photographic image.
## Install and run
- Install miniconda (if needed) from [here](https://docs.conda.io/en/latest/miniconda.html).
- Install [`vedo`](https://vedo.embl.es/) and `scipy` by typing:
```bash
pip i... |
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