sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4a0fcbe7e7e45bb2c4223c3f9405ae7559559b75cbc9e5ce2068eda9fb52c5e4 | Text | 912 | 8 | This repository contains the relevant source code used in the publication
**Progression subtypes in Parkinson’s disease identified by a data-driven multicohort analysis** (Tom Hähnel, Tamara Raschka, Stefano Sapienza, Jochen Klucken, Enrico Glaab, Jean-Christophe Corvol, Björn H. Falkenburger & Holger Fröhlich. npj pa... |
4da567807927170511feeea5ae5191a0722197ad462dabfbd9c689634de5ce92 | Text | 915 | 16 | # two photon collection cannula
The following files describe the conical cannula used to improve collection efficiency in the following work
https://www.biorxiv.org/content/10.1101/2023.08.17.553594v1
## file descriptions ##
reflector_test_with_excitation.zos - This file is for loading in Zemax Optic studio to simul... |
caa977e23eef09f0d17b847c3775ed5fe10a109b536a969051a551e6125aef55 | Text | 922 | 19 | # dCrawler
dCrawler is a fully independent clustering algorithm that only requires a distance threshold (Th(d)) to perform clustering
## Requirements
For now only a MATLAB version of the algortihm is provided.
We have tested this on MATLAB versions 2020 and above and no additional libraries are required
## Installati... |
6aed8b55aaca13d4c916a74f0d266547d3c18ea56843ff3a0c61d5cb9e7b443d | Text | 936 | 18 | # Uncertainty Quantification and Sensitivity Analysis of Neuron Models with Ion Concentration Dynamics
This code was used to produce the results presented in Signorelli L, Manzoni A, Sætra MJ (2024), PLOS ONE 19(5), e0303822: [Uncertainty quantification and sensitivity analysis of neuron models with ion concentration ... |
50a97a77763b9b48a666ce2991ea9973b8c642d861d562107d6b97dc8074f5f6 | Text | 937 | 10 | # Deep-learning-based-MFR
This project contains all the code for the experimental part of the paper "Adaptive recognition of machining features in sheet metal parts based on a graph class-incremental learning strategy."
## Pre-train_Exp
The "Pre-train_Exp" folder contains files for the Sheet-metalNet's network architec... |
d6df515e9e0104fc417bd9098e77dadb387e38217aefb3a5442f81ea82d3459a | Text | 941 | 13 | # WaveICA_2.0
WaveICA 2.0 method is an improved version of WaveICA method to remove inter-batch and intra-batch effects for untargeted metabolomics data without using batch information.The details of this method are in the paper "WaveICA 2.0: a novel batch effect removal method for untargeted metabolomics data without ... |
b8bafe516ebe8394128792e843697420c243a567849a680679d7b2f05c2a151b | Text | 942 | 8 | # optoPAD-software
Bonsai workflow used for control and data acquisition of the optoPAD (Moreira et al., 2019). Requires the visual programming language Bonsai (https://bonsai-rx.org/). This repository contains the following workflow/protocols:
- `optoPAD_Fig4B_Reversal`: script for the dynamic virtual taste reality ex... |
840f1405c70317b83ce3b742c1e206a7765bdd8d1849ff1196b63934ab8f5b67 | Text | 965 | 35 |
# PyDeface-Niftyreg
A tool to remove facial structure from MRI images.
If you find this code useful for your research, please cite the following paper:
```
@article{juvekar2024remind,
title={{ReMIND: The Brain Resection Multimodal Imaging Database},
author={Juvekar, Parikshit and Dorent, Reuben and K{\"o}gl, Fr... |
5e4db8abeaa4e438f598a669c3fe0ee584678de7f2d464fae83e64da6c70a158 | Text | 978 | 12 | # spikefix
Simple scripts for finding and removing spikes from fMRI datasets
Spikefix consists of two scripts, spikecheck and spikepatch. They depend on a working installation of FSL to do most of the heavy lifting.
Spikecheck
==========
spikecheck finds the spikes. Type it without arguments, and it will tell you w... |
67d5e23e78abd95393a175949ecc5540f344891b13aa6aaab93219d38afd686e | Text | 979 | 21 | # LinearUnmixing
MATLAB codes to linearly unmix 4d images (xyz and colour)
## Requirements
mnl_Load4Dimage - available here, https://github.com/mleiwe/QDyeFinder/tree/main/Subcodes
Bioformats toolbox -
## Functions
There are three versions of the same program
sf_unmixing_20xG_3HyD_220823ref.m - Unmixing the data ob... |
662b262a75a71f1d8aeba2dfb5aed1e31a8de6a31a553911cea3c5a8646da570 | Text | 991 | 16 | # Casanovo
**_De Novo_ Mass Spectrometry Peptide Sequencing with a Transformer Model**
If you use Casanovo in your work, please cite the following publications:
- Yilmaz, M., Fondrie, W. E., Bittremieux, ... |
59938e85c464ca9b9363630ebb65cdc72953d90bf718820c4d20ee70ecf2fcdd | Text | 1,000 | 25 | wave_viewer
===========
Wave Viewer is a Matlab-based analysis tool for speech waveforms.
viewer_end_state = wave_viewer(y, [options])
Wave Viewer takes a signal `y` and the following optional arguments:
* `fs` sampling rate (default: 11025)
* `ms_framespec_gram` (default: broadband)
* `ms_framespec_fo... |
c779273f0d670066a56f9bf1467661c618ab9112bc5379f377c88d4c433f3c8a | Text | 1,010 | 38 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
[](https://zenodo.org/doi/10.5281/zenodo.10514841)
# GBA1 and GBAP1 manuscript
This repository contains the code used to generate the plots used in the GBA1 and GBAP1 manuscript.
## Code contents
Wi... |
1f2f54225489731329a5eb86d57607df938275c9ce6d96ce18218c408ef21d79 | Text | 1,020 | 15 | For plotting psychometric curves for each participant (and experimental condition):
Download the entire project ("anxiety-main").
Download and install the psignifit4 toolbox (from: https://github.com/wichmann-lab/psignifit) and make sure it is included in the Matlab path (if you are unable to add it to path, copy the ... |
b2b06f7e1a56fc79f0fdab157112f6acde7f900300feaddb967e2eafe3c8650a | Text | 1,033 | 18 | #
[](https://zenodo.org/doi/10.5281/zenodo.11389275)
Cusmtom code for the manuscript "Development of a genetically-encoded sensor for probing endogenous nociceptin
opioid peptide release"
To run analysis:
1. Demo data can be found in the Zenodo repository: https://zenod... |
c6306e9f2039edc0e566382b8564dff419fca4867bbc45bf1c349474b78834b6 | Text | 1,048 | 13 | # one2one-mapping
Model weights, example stimuli, and code for the paper "One-to-one mapping between deep network units and real neurons uncovers a visual population code for social behavior".
## KO Simulations
To test knockout training with a toy problem (two-layer linear network), check out ```/code/extfig2_KO_simul... |
4e1ce863c1afd71343c214289b5c49b59ed01247a965cde37822592bbb143f8f | Text | 1,068 | 11 | # UltrasoundRP
The scripts for neuron signal processing and visualization, and the generation and validation of arbitrary acoustic patterns.
Scripts were tested in MATLAB 2019b.
AS_APM_256.m is the script using the angular spectrum method to compute the amplitude and phase distribution of the 2D array to generate arbi... |
d1b2589e7cc5e43fe03f82be934b9dba31e3626f03f8744d98f8f6e4d4226684 | Text | 1,069 | 45 | The MATLAB functions and script in this repository are developed to process, compute, and visualize data acquired during fiber photometry experiments presented in Taniguchi et al. 2024.
## Dependencies:
Make sure you add to your path the following folders:
1. ~/Photometry-Pipeline
2. ~/Behavioral-Pipeline
Contains... |
3cb1ee42283817c0e6539967978dc7da9a6dd87b096c92406bd32d843d04f6d4 | Text | 1,090 | 13 | # Data Logger: Temperature, Pressure, Humidity, Light Intensity and Color
## Summary:
This is an open-source data logger that can record air temperature, air pressure, relative humidity, visible light instensity, near-infrared light intensity, and visibl... |
f0c8237ade1e9032fadcf7aa8183a05b9f4dc43b0645f4c10ee074fbb5e6ed90 | Text | 1,114 | 16 | # HMSA-DTI
HMSA-DTI: The codes demo for paper "Hierarchical Multimodal Self-Attention based Graph Neural Network for DTI Prediction".
# Required Packages
View requirements.txt and environment.yml
# Datset
Please make sure dataset format is csv, and column name are: 'smiles','sequences','label'. We have provided datas... |
ade0e590429b2df8581161bf8bd16c2edaa303fe1f221f0d48c61e3980adbf1a | Text | 1,116 | 8 | # Code and data for `Machine-learning-boosted ab-initio study of the thermal conductivity of Janus PtSTe van der Waals heterostructures`
Contents:
- `neuralil.tar.xz`: version used in the manuscript of the force-field code described in the articles [A Differentiable Neural-Network Force Field for Ionic Liquids](http... |
731887511ca0b1389dfc67b446f008b8a2a1f9e718cad803df3fd2e2622d4164 | Text | 1,117 | 25 | Title of dataset
Dataset for paper "Micro-CT, Mechanical, and Histological Examination of the Effect of Local Adjuvants on Porcine Cortical Bone Following Intralesional Curettage of Bone Tumors."
Name/institution/contact information
Marcián Petr – Contact person
Institute of Solid Mechanics, Mechatronics and Biom... |
25bd8eb893efe464aa2c552977bc1f119f7def4e94f977cdee2b915f84238966 | Text | 1,123 | 10 | # hEsyt1-spinal-and-systemic-administration
Analysis scripts for locomotion, cognitive performance, weight development, and virus spread from results of intraspinal and systemic hEsyt1 administration.
This repository contains the code for the analysis of behavioral data from gait analysis of wt, En1cre, SOD1, and SOD1... |
c203c747b22044659fb990861a6c3cc7d00f886555240beba056d111f15712f3 | Text | 1,126 | 28 | wave_viewer
===========
Wave Viewer is a Matlab-based analysis tool for speech waveforms.
viewer_end_state = wave_viewer(y, [options])
Wave Viewer takes a signal `y` and the following optional arguments:
* `fs` sampling rate (default: 11025)
* `ms_framespec_gram` (default: broadband)
* `ms_framespec_fo... |
2182a14db37598e6c69868e1e237b1f13982897c0d4e344eed696b063441db9a | Text | 1,129 | 21 | # Population variation in the immune response to influenza
code necessary to reproduce the main analyses published in:
Genetic ancestry effects on the response to viral infection are pervasive but cell type specific (Science, 2021)
HE Randolph, JK Fiege, BK Thielen, CK Mickelson, M Shiratori, J Barroso-Batista, RA La... |
bc44f13a43d5323035a2f9e2998d9546f0be40be7ec0c00084dfec05bddfc761 | Text | 1,137 | 20 | # FCEst-benchmarking
[](https://github.com/astral-sh/ruff)
Functional connectivity (FC) estimates are sensitive to choice of estimation method (e.g., sliding windows, MGARCH, Wishart processes, hidde... |
ad3c3e01c18a6b1d227aaa2b74c86b507b371d5fdfc82b5989e78acb169ce04e | Text | 1,152 | 26 | # SpeckledNeuronsControl
---
**asome code still need to be cleaned and properly commented**
---
main files:
* **calibrate_beads_sample.m** - calibrate the bottom camera with the DMD, and create a T.mat file which must be called afterwards since gives the parameters of the affine transformation between the two space... |
c1763e01caa37629efb34b41ad58c08b6bc22104817a6ccc3bc31a2e59631b02 | Text | 1,155 | 20 | # Single-MITOchondrion (SMITO) Data Analysis Scripts
## Overview
This repository contains code for SMITO data analysis.
For SMITO computational pipeline, see [smito-pipeline](https://github.com/kimpenn/smito-pipeline).
## Author
Youtao Lu (<luyoutao@sas.upenn.edu>)
## Copyright
```
Copyright (c) 2021-2023, Youtao Lu,... |
44b2cd285e70a3bbdba85e3cc1b125efbd7177d2c1eb54012435ccbfeae0c550 | Text | 1,161 | 49 | # HyPhy standalone analyses
This repository contains various analysis scripts for [HyPhy](https://github.com/veg/hyphy) -- a molecular evolutionary analysis platform.
```
git clone https://github.com/veg/hyphy-analyses.git hyphy-analyses
```
Unless otherwise stated in directory - specific README file, all analyses ... |
e266726a2105ca2823ab96d010d029a2093b90e05226526fb8a28490839e9205 | Text | 1,162 | 10 | # Cholinergic_Analysis
The following code corresponds to the analysis of two macaque fMRI time-series data (data originally published in 10.1016/j.neuron.2018.01.032). It includes all code relating to the analysis of the data using the attractor landscape analysis, information theory analysis and the simple neural mass... |
366c9c4e433e36d44d67215a47a24c1ddee54a2be9f09d5128d7a05bed172dec | Text | 1,181 | 52 | # Frechou-et-al.-datasets
This page page contains links to the datasets included in the Frechou et al. publication "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"
<p>
<b>RC Dataset: </b> <p>
doi: 10.5281/zenodo.10934021 ( https://doi.org/10.5281/zenodo.10934021 )
<p></p>
<b>EE ... |
32993a71784c85268dede1c5a2c0607238c5f8bcaf80d35d7bd998975ed3b771 | Text | 1,195 | 18 | File "Images and Labels":
"Normal_Image.mat" is the original image data simulated by using single-channel array (SCA) sensor.
"Normal_Image_NoFinger.mat" is the original image simulated by SCA sensor for curled fingers imaging.
"Sensor_Image_new.mat" is the simulated image generated by "Normal_Image.mat" using mult... |
9ef9794d305c24dade2fce732b851fd7cd7a0714f2019a980ca0eb28ebde9ff1 | Text | 1,197 | 15 |
# chrombpnet-workflow
This repo contains a Krews workflow for running ChromBPNet on ATAC-seq and DNase-seq datasets. It currently supports human data aligned to the hg38 genome. It consists of the following steps:
1. *Training*: trains a bias and ChromBPNet model given filtered BAMs
2. *Prediction*: predicts bias-cor... |
35799178502ac8c436bd9d9f3bf9e66fdb9cb440d3bd842171b92de6ede408a2 | Text | 1,199 | 14 | # PINNs-for-high-resolution-weather-reconstruction-from-sparse-weather-stations
[](https://creativecommons.org/licenses/by/4.0/)
Scripts of the article 'Physics-informed neural networks for high-resolution weather reconstruction from sp... |
171bc9d9c5b38861390d4d5e060df9b9a16b06918f482f8f9ba2475fbd2c4640 | Text | 1,222 | 19 | # Casanovo
**_De Novo_ Mass Spectrometry Peptide Sequencing with a Transformer Model**
<img src="casanovo.svg" alt="Casanovo logo" width="300">
Casanovo is a state-of-the-art deep learning tool designed for _de novo_ peptide sequencing.
Powered by a transformer neural network, Casanovo "translates" peaks in MS/MS sp... |
5c32d827bd2eafda2199d1f347581fbad0fba0c5a91142d92aaae127b3cf22c8 | Text | 1,234 | 41 | # ConnectivityIndex
**Provides functions to calculate the connectivity index based on intertrial phase coherence**
Prepare data in steps 1-3 before using the code
Use "calculate_ConnectivityIndex.m" for algorithm
## Step 1: Preprocessing
1. Preprocess CCEP in similiar fashion to task data
2. Identify time of stimu... |
a16cd07d53f5388ad2032100f275e34a566295a2d38f73007c88f92b8c8a9f6d | Text | 1,234 | 20 | # Source code to ' Primacy of vision shapes behavioral strategies and neural substrates of spatial navigation in the hippocampus of the common marmoset'
This repository contains the source code to replicate the analyses that were done in this work (https://doi.org/10.1101/2023.05.24.542209).
Sample data will accompany ... |
3411bdbb94579a7a2343bbeb2711b2a5f05c3c5be88613cd6b01f3bcec559682 | Text | 1,247 | 37 | # Ishizu_et_al_2023
### 1. System requirements
All scripts were conducted to wrok on the MATLAB R2021a.
We tested to run the scripts by a normal desktop computer (64-bit Windows 10 Pro / Intel(R)Core(TM)i7-10700K CPU @ 3.8 GHz).
### 2. Demo
Expected outputs were the figrues and the relevant source data ... |
94bdabc2c7e85870df6cf31b43eeb45c4299b4c2076279fd65984ed4451005f8 | Text | 1,258 | 21 | # Chronic ingestion of soy peptide supplementation reduces aggressive behavior and abnormal fear memory caused by juvenile social isolation
## Summary
Raw numerical data and 16S rRNA sequencing data for the study 'Chronic ingestion of soy peptide supplementation reduces aggressive behavior and abnormal fear memory ... |
ea872703220b231ab8435afdf95e9e65ef46a0ff58128feec26dcf608cbf72af | Text | 1,259 | 28 | # Distributed and dynamical communication
Code for the paper "Distributed and dynamical communication: A mechanism for flexible cortico-cortical interactions and its functional roles in visual attention"
## Structure
`analysis` contains the functions and Python classes for data processing and analysis.
`connection... |
1f27aceb805ed3ce99bc15172278d1798684f51bcc1c661dde9bffb97b96c0d7 | Text | 1,266 | 19 | # Recall-tempo-of-Hebbian-sequences
Code for reproducing the plots of the manuscript "Recall tempo of Hebbian sequences depends on the interplay of Hebbian kernel with tutor signal timing"
To run the simulations, use run.py. This script takes a run number as an argument for the purpose of parallelization. For instance... |
d4c035f7f4dc9e56d37d5ce18c3b8cdc289398d2f40437657d8fbd0de7f05099 | Text | 1,281 | 19 | # StriatalLearning Library
Python Library to model learning of pattern classification task with striatal neurons.
Work done during PhD thesis of Gaëtan Vignoud (Inria and CIRB, Collège de France) under the joint-supervision of Laurent Venance (CIRB, Collège de France) and Jonathan Touboul (Math Dept., Brandeis Universi... |
e0363bf95e776a4cdac7b688c2716b13395115a1b00771c0508c4715085d2ccd | Text | 1,301 | 31 | # Code supporting the paper: "Distribution-informed and wavelength-flexible data-driven photoacoustic oximetry"
This code supplements the paper **"Distribution-informed and wavelength-flexible data-driven photoacoustic oximetry"**
by *Janek Gröhl, Kylie Yeung, Kevin Gu, Thomas R. Else, Monika Golinska,
Ellie V. Bunce... |
e594e0855074bf2ac4f8bf8532e5847bff065d33d619937bfa57c2d8a3df22d0 | Text | 1,304 | 34 | # Espaloma-0.3.0-manuscript
This repository summarizes the repositories to create and validate `espaloma-0.3`
## Manifest
- `01-download-qca-dataset/` - Download QM data from [QCArchive](https://qcarchive.molssi.org/)
- `02-refit-espaloma/` - Refit espaloma using QM datasets downloaded from QCArchive
- `03-geometry-be... |
8dfd845e1c589cd906402b5f68764fd5d500f7b8c8ec104a25db08c218d3f602 | Text | 1,306 | 44 | # IoSR Matlab Toolbox
A general purpose Matlab toolbox containing functions and classes for: auditory modelling, signal processing, sound source separation, statistics, plotting, etc. See [Contents.m](https://github.com/IoSR-Surrey/Toolbox/blob/master/+iosr/Contents.m) for a full list of functions/classes.
## Install... |
2aad9cd51a92bf8fdeba3aabb891129a42293215b3d7a4e1546e6e32508c9a73 | Text | 1,313 | 21 | # dynamin_model
code and inputs for models of dynamin clustering
#Data folder
Excel sheet containing example parameter sets found for optimal agreement with experiment.
These are a sample. Sorted by isoform and D_{sol} concentration.
#Python folder
Python code that solves the ODE version of the model. There is a sepa... |
2ebc422026696f16ef2e54671e8bd6da296edebaf2117768e326c1b9dfa62695 | Text | 1,314 | 37 | # Feature Attention Graph Neural Network (FAGNN)
### Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer’s disease
Hae Sol Moon, Ali Mahzarnia, Jacques Stout, Robert J Anderson, Cristian T. Badea, Alexandra Badea
[... |
eb964310c1d0844dd3ae00f6cef4497bdf3435f480e34e11b5737a4c3ad707a7 | Text | 1,325 | 38 | # Self-Supervised Learning for CBIR in oral pathology
This repository contains code for training self-supervised learning models for oral histopathological images using PyTorch Lightning.
The code includes implementations of the SimCLR and TiCo models with ResNet18 as the backbone.
## Overview
The code provided tra... |
dd31937c3fdc50120d38923f5d4a708e81dc2061f5b79a3025cc243629c3cbec | Text | 1,329 | 19 | # Integrated-Photonic-Encoder-for-Terapixel-Image-Processing
Offical repository for "[Wang, Xiao, Brandon Redding, Nicholas Karl, Christopher Long, Zheyuan Zhu, Shuo Pang, David Brady, and Raktim Sarma. "Integrated Photonic Encoder for Terapixel Image Processing." arXiv preprint arXiv:2306.04554 (2023)](https://arxiv... |
dac22d207ed43ecfb048387e40c5f4b94ba34fb47b6a5ff9610cffa4f97d8aa2 | Text | 1,332 | 42 | # **factR v.2**
## Functional Annotation of Custom Transcriptomes in R
## General workflow
<p align="center">
<img src="man/figures/factR2.png" width="450"/>
</p>
**factR2** represents a substantial improvement over
[**factR**](https://fursham-h.github.io/factR/), providing users with
more powerful and user-frie... |
840ceb70a0541056aadac4319eca9cb8f9cdc336eb2a39ba00f6aa1348cae04f | Text | 1,337 | 22 | # A BERT-based pretraining model for extracting molecular structural information from a SMILES sequence
'datasetMake_pretrain.ipynb' is used to prepare input and target data for pretraining, it also creat a file for saving the dictionary of symbols.
'pretrain.ipynb' is used to conduct pre-training experiment.
'Propert... |
2f3234d0fc10f0b6679f1856d71f257dbb18b021bbbe32f98cdbfc0d382b533e | Text | 1,340 | 34 |
# PDneuralfingerprinting
Code associated with the with [this preprint](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934726/).
# Information
Contains codes to i) perform fingerprinting analyses, ii) compute relative contribution of fingerprinting features (i.e., ICC analysis) iii) run regression and decoding analys... |
cdf557abdab9253c058eacd895237c13bcb955d65c02679dd02710466de55d46 | Text | 1,353 | 36 | # kmerPMTF
# Usage
1. Download dataset from here: https://figshare.com/articles/dataset/kmerPMTF-data/24916023
2. Clone kmerPMTF into your platform:
```git clone https://github.com/Weihankk/kmerPMTF.git```
3. Move dataset to kmerPMTF directory and decompose it:
```
mv data.tar.gz /your/dir/kmerPMTF
... |
1b1a9c8689726324637c18a6df4dc8de75363ee4c1e9fd81ff6689337ab1b752 | Text | 1,366 | 30 | # Distributed and dynamical communication
Code for the paper "Distributed and dynamical communication: A mechanism for flexible cortico-cortical interactions and its functional roles in visual attention", Ni, S., Harris, B. & Gong, P., Commun Biol 7, 550 (2024)
## Structure
`analysis` contains the functions and Pyth... |
b28e457daf2516e28bc6a481052adef3a83fe509a4abcb079830433661846800 | Text | 1,374 | 20 | This repository contains the data used in [Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology](https://elifesciences.org/reviewed-preprints/91398).
The data consists of dissection photographs of patients with neuropathological disease collected from two sites-.
1. Massac... |
40a67ee7d800d24018686ce567f0ede878845c666a119cdefbb7476f9bfd933f | Text | 1,378 | 28 | # article-belief-hierarchical-spatial
This repository contains data and code supporting the following paper:
Katayama et al., "Belief inference for hierarchical hidden states in spatial navigation"
FigureX.R files will generate the specified plots from the paper.
Unthresholded group-level statistical maps supporting... |
b26aa97603270f61a64f7a245e292e6fe9947fa6a33c65fe90a98170f6fa8bf9 | Text | 1,381 | 25 | Codes for training RNNs with Short-term plasticity mechanism to control both temporal and spatial scales of neural dynamics and sensorimotor behaviors.
Optimization is implemented in TensorFlow 2.3.
For details please see 'Unified control of temporal and spatial scales of sensorimotor behavior through neuromodulation ... |
45d57546ef4d8854f141a2767ec17feade87e40b65ff3b82f9887011557dab2c | Text | 1,389 | 29 | # EI_clustered_network
## Overview
This repository contains simulated data to reproduce the figures in "Spiking attractor model of motor cortex explains modulation of neural and behavioral variability by prior target information" ([Rostami et al. (2024)](https://doi.org/??)).
## Data Files
### Files without endi... |
4667affde418e93147a2da9c7b9b1aa6156792d35c7fad9fa3dcb8e225896ec6 | Text | 1,392 | 35 | Original release date : 2/28/18
Reference #1 : "prDeep: Robust Phase Retrieval with Flexible Deep Neural Networks"
Authors : Christopher A. Metzler, Philip Schniter, Ashok Veeraraghavan, Richard G. Baraniuk
Questions/suggestions/comments: chris.metzler@rice.edu
Primary Contents
-------------... |
91eb22ade1f228e86a83cfa522927c1cceb6dbba57926996e7d88db72c45031e | Text | 1,397 | 14 | Jay_Plugins
===========
ImageJ plugins from Jay
This code is licensed under the GPL. Please read the license.txt file for more details. I recommend using the Stowers Fiji update site or my website (http://research.stowers.org/imagejplugins/) for download and update.
This code is organized roughly according ... |
8bf748284005d0724d600d36178c3e794e1952340ac56a837b29e46916d20c7e | Text | 1,406 | 6 | Data for Figures shown in Gonzalez-Islas et al 2024 eLife study "GABAergic synaptic scaling is triggered by changes in spiking activity rather than AMPA receptor activation". Also included is the burst detection program used to do the spiking analysis.
Burst Detection App (BurstDetection_V3.mlapp) for identifying burs... |
a25d9853c2eb517b25be6af4a951452a355ac5b656f61252185d8c517a84a7e8 | Text | 1,407 | 9 | # Matlab-scripts-for-Calcium
Scripts for Analyse of Calcium oscilations
Analyse_Calcium_Data.m For determination of peaks of all waves and turn them into binary data. In detail, algorithm determined base line of wave by 9 fixed points and smooth with “Loess” method with 30% point windows around each point. Point to poi... |
19f49e2983bf86e0dd77654a81873769b7cff0a9553517930b11352fafc75feb | Text | 1,410 | 25 | # dn_networks: Repository holding the code for the paper "Networks of descending neurons transform command-like signals into population-based behavioral control"
Jonas Braun, Femke Hurtak, Sibo Wang-Chen, Pavan Ramdya 2023
The bioRxiv paper can be found [here](https://www.biorxiv.org/content/10.1101/2023.09.11.557103... |
b98c7b77b6563ca6dd8f60bd5c4b528fcc45a96f6aa887ee3cda6144163e3060 | Text | 1,417 | 55 | # Reinforcement learning on a chemoatic cell
**On the integration of spatial and temporal information**
[](https://arxiv.org/abs/2310.10531)
<p align="center">
<img src="https://github.com/kirkegaardlab/chemoxrl/assets/38870744/d31bccfe-0... |
8539dcc86eb7851517278738086eecaa97df698544bd74ddfde7f21de3902b8c | Text | 1,425 | 20 | # Demixing fluorescence time traces transmitted by multimode fibers (Python)
NMF analysis for Demixed Fiber Photometry
Python codes for the Non-negative Matrix Factorization (NMF) results shown in: **C. V. Rimoli, C. Moretti, F. Soldevila, E. Bremont, C. Ventalon, and S. Gigan - 2024 - Demixing fluorescence time trace... |
bf4da560b5de62b10566cac1da5d2423121c7d0d9f2e60740ef8b6e29043efc1 | Text | 1,428 | 65 | # DeepSP
**DeepSP** is an antibody-specific surrogate model that can generate 30 spatial properties of an antibody solely based on their sequence.
# How to generate descriptors (features) using DeepSP
---
## Pipeline Workflow
### 1️⃣ Feature Preparation
Prepare a CSV file named:
```
DeepSP_input.csv
```
This fil... |
f116735a07f199c11fc1f5cde07fcd90927c9cdd5b8cb8078aef4de117893bf2 | Text | 1,428 | 20 | # Integrated-Photonic-Encoder-for-Terapixel-Image-Processing
[](https://zenodo.org/doi/10.5281/zenodo.10819457)
Offical repository for "[Wang, Xiao, Brandon Redding, Nicholas Karl, Christopher Long, Zheyuan Zhu, Shuo Pang, David Brady, and Raktim Sarma. "Integrated Phot... |
e8da8b5131b59eb110da312ddfc3083da35f47316a69539e9a645df7b205a515 | Text | 1,430 | 12 | # EEG_OPMMEG_HealthyAdultStudy_YoungEpilepsy
Data and code for simultaneous EEG and OPM-MEG experiments conducted in healthy adults at Young Epilepsy, UK
Data are stored on the Open Science Framework. Project link: https://osf.io/z6w2t/
These data are 'pre-processed'. OPM-MEG data have had homogeneous field correction... |
2ccc32cee8eead1304efe59c943f76fa6ecf74789f63ee541c740eed87ce4fed | Text | 1,442 | 19 | # Computed Tomography Reconstruction Using Deep Image Prior and Learned Reconstruction Methods
In this paper we describe an investigation into the application of deep learning methods for low-dose and sparse angle computed tomography using small training datasets. To motivate our work we review some of the existing ap... |
39d99c670ba2d9d47ecd8d05aad3634d0bc0f43525d52a25200c3589c70be078 | Text | 1,455 | 37 | # LE/LI recurrent network model
## Description
A recurrent network linear rate model with local excitation/lateral inhibition (LE/LI, also known as Mexican Hat or Difference of Gaussian)
connectivity, used to model the effect of stimulating the network with different input patterns.
## Getting Started
### Depende... |
c9bb4870b7845a2273fdf15724ada0f8c35790cfbad387dc6ff14c3cc04aed8e | Text | 1,457 | 27 | This is the case study application of batch effects analysis protocol,
mostly implemented using `proBatch` package.
Here we investigate batch effects and their correction in three datasets:
1. InterLab study [1];
2. PanCancer study [2];
3. AgingMice study [3].
Each dataset analysis is stored in its own folder, and i... |
7eff6eb2f79b8af47b9b61b209aa678b5e3c10e9b0adac34ca712f3bd42ae45e | Text | 1,463 | 28 | # Publication 2023 - Learning the effective order of a hypergraph dynamical system
## **This Repo is still under construction! Not all features are currently available**
In this repository, you can find the code used in the paper "Learning the effective order of a hypergraph dynamical system". You can find the paper ... |
1894e6bd7982118416b0caa4943d13e8743ec5406416189b111008e205e94bc6 | Text | 1,471 | 40 | # JRCLUST
## Note
**JRCLUST is no longer being actively maintained.**
If you still want to use JRCLUST, we recommend using the [latest release](https://github.com/JaneliaSciComp/JRCLUST/releases/tag/v4.1.0) or cloning from `main`, rather than `master`.
JRCLUST is a scalable and customizable package for spike sorting... |
8db536b0e12852353ea8ab40c87938f64b4df27e6c6f860706f500f45b55bb15 | Text | 1,472 | 18 | # Toxo_delivery_Bracha_et_al_2024
Code and links to data for Bracha et al, 2024
In the codes you can find:
1. CellProfiller piplines for image analysis of the infected HFF and infected LUHMES neurons datasets.
2. Codes for the analysis of the image analysis outputs. The results from this are presented in figure 4 (ki... |
ad66ac517b9a20fdd8716bf90ce9cd80f00828d4c5213dd1657fc89661a3ffd5 | Text | 1,503 | 8 | # Petelski-Guenzel-et-al-Synergistic-olfactory-processing
Analysis scripts for Petelski & Günzel et al.; Synergistic olfactory processing for social plasticity in desert locusts
## Summary
Desert locust plagues threaten the food security of millions. Central to their formation is crowding-induced plasticity, with soci... |
e8d4d4355257df137b52c948af16d84ac3bcadb5b2f77067f3780048140e6d46 | Text | 1,503 | 44 | # ssREAD
scREAD (version 1 archive): https://bmbls.bmi.osumc.edu/scread
Dev server: https://bmblx.bmi.osumc.edu/ssread/
---
This repository serves as the front end part of ssREAD, it also contains ssREAD workflow in the /script folder.
[ssREAD](https://bmblx.bmi.osumc.edu/ssread/) (A single-cell and spatial RNA-seq... |
5fd669030ab1fddd6e227abda04c4f2ff8c4c2442e6d50fcd9dd4f49264b2469 | Text | 1,512 | 16 | # Foxp1-SPN-Development
**FOXP1 promotes the development of glutamatergic synaptic input onto spiny projection neurons and induces gene expression reversal with reinstatement.**
Long-range glutamatergic inputs from the cortex and thalamus are critical for motor and cognitive processing in the striatum. Transcription ... |
40d54a25e6d50973b54a9e2d78e2227ce4fb9eec4cfb7f553e4ee4f84e6869c8 | Text | 1,531 | 44 | # A-hybrid-CNN-SVM-model-for-enhanced-autism-diagnosis
****
## Dependencies
List the main dependencies required to run the project along with their versions, including installation methods.<br />
matplotlib==3.7.1<br />
numpy==1.22.4<br />
pandas==1.5.3<br />
scikit_learn==1.0.2<br />
shap==0.41.0<br />
torch==1.11.0<... |
7a6e97ebc360f4d7b7c5e4c60106e8d61e5f3c656e3889898b2165a16414bbc8 | Text | 1,537 | 46 | [][fex]
superbar
========
Make bar charts rammed full of extra features:
- in full technicolor, with a unique colour for every bar
- showing errors on the values using errorbars, with many styles available
- with statistical signific... |
6c71d9ad483c08f1f1c5426b0ea96b3bed2151f77d2b385aff750e3b2a62faa7 | Text | 1,549 | 21 | # whisker_tracking
[](https://doi.org/10.5281/zenodo.4315318)
Unsupervised whisker tracking in freely behaving mice/rats
This repository includes a copy of ConvNet by Sergey Demyanov ( https://github.com/sdemyanov/ConvNet ) - if you'd rather use a recent... |
8ea10d08a430084b1879de39baefbd054e8a70ecebfcce4c69232c57f52ee0d9 | Text | 1,555 | 23 | [](https://zenodo.org/badge/latestdoi/449755672)
# SPRiNT: Time-resolved parameterization of aperiodic and periodic brain activity
Code for simulating dynamic neural time series, spectrogram parameterization (using SPRiNT), and generating figures from the SPRiNT preprin... |
08061616dcc1ccaca3124b3dbae0d2f71ee096403178d36be8ce1a7545645c7b | Text | 1,564 | 39 | [](https://doi.org/10.5281/zenodo.10892426)
# LE/LI recurrent network model
## Description
A recurrent network linear rate model with local excitation/lateral inhibition (LE/LI, also known as Mexican Hat or Difference of Gaussian)
connectivity, used to... |
3c435261c71a86a129899e13292631d325c81619b277b924e8571b8f94aaf914 | Text | 1,581 | 29 | # Overview of Brain.GMT:
This repository contains the public release of our curated brain-related functional gene set file (Brain.GMT) and associated code to accompany the publication:
"Resource: A Curated Database of Brain-Related Functional Gene Sets (Brain.GMT)"
by Megan H. Hagenauer*, Yusra Sannah, Elaine K. Hebd... |
007d9fbbd1d3697d23251ce74adae437fb0319c0145a66c17161da23a9aa9cd6 | Text | 1,589 | 39 | # About e3nn_Unet
Segmentation networks based on e3nn O3 and SO3 equivariant convolutions.
The networks allow for scalar, vector or tensor inputs, user-defined number and
type of downsampling operations, type of equivariance, and number of hidden
irreps.
## Installation
```bash
git clone https://github.com/SCAN-NRA... |
74a7c1bebcbc994de5654a29c907cdadd318e62000e309931494e3855d45a9fc | Text | 1,590 | 25 | # rexgen_direct
Template-free prediction of organic reaction outcomes using graph convolutional neural networks
Described in [A graph-convolutional neural network model for the prediction of chemical reactivity](https://pubs.rsc.org/en/content/articlelanding/2019/sc/c8sc04228d)
# Dependencies
- Python (trained/tested... |
7233a6c4497e1b984a82e361ddadb67fe1359821edf40f8f98c394b334418cc7 | Text | 1,606 | 25 | # Demixing fluorescence time traces transmitted by multimode fibers (Python)
NMF analysis for Demixed Fiber Photometry
- [](https://doi.org/10.5281/zenodo.12125030)
Python codes for the Non-negative Matrix Factorization (NMF) results shown in: **C. V. Ri... |
1bec6cceb1d43b597c9fe4fef146422357f2588e65ea77ff958f403afd807bf3 | Text | 1,613 | 41 | # STEP
Data and code for STEP (Siamese Twin deep sequence Embedding of Proteins) approach.
## Relevant files
1. ''ppi_finetuning.py'' tackles the finetuning and prediction for use case 1 (brain tissue-specific ppi prediction)
2. ''ppi_virhostnet_finetuning.py'' tackles the finetuning and prediction for use case 2 (sar... |
5faf29ea8a72cd0963232a80e9189f22e4bb4d46ce3e5210d16ee58e5ee4b589 | Text | 1,625 | 18 | # DeepIDA-GRU
Biomedical research now commonly integrates diverse data types or views from the same individuals to better understand the pathobiology of complex diseases, but the challenge lies in meaningfully integrating these diverse views. Existing methods often require the same type of data from all views (cross-se... |
c5a95641a9a64867517da2855df494333a374241abe105e8f957fcc1d925d92d | Text | 1,627 | 33 | [](https://app.travis-ci.com/CINPLA/edNEGmodel)
# edNEGmodel
edNEGmodel is an implementation of the KNP continuity equations for a
one-dimensional system containing six compartments: two representing a neuron, two representing extracellula... |
cf01c67b08f7785f6eba06f8d86a6b77d04f325e134188fb5acd7ab12546c12f | Text | 1,632 | 37 | # Demixing fluorescence time traces transmitted by multimode fibers (Python)
Python codes for the Non-negative Matrix Factorization (NMF) results shown in:
**C. V. Rimoli, C. Moretti, F. Soldevila, E. Bremont, C. Ventalon, and S. Gigan - 2024 - Demixing fluorescence time traces transmitted by multimode fibers** arXiv:... |
cf8437b1c316771701aafd5a5bb3ac053c94429d126216cfed451462314f8c9b | Text | 1,632 | 42 | # Chainsaw
Chainsaw is a deep learning method for predicting protein domain boundaries for a given
protein structure.
If you find Chainsaw useful in your research, please cite:
**Chainsaw: protein domain segmentation with fully convolutional neural networks**
Jude Wells, Alex Hawkins-Hooker, Nicola Bordin, Brooks P... |
bbb0b9abc87f76484ad97f662dad83e72649f2b21d81843b4f925d46b8b4176c | Text | 1,644 | 38 | # Transfer learning on PINNs for tracking hemodynamics
The source code and data for the article [M. Daneker, S. Cai, Y. Qian, E. Myzelev, A. Khumbhat & L. Lu. Transfer Learning on Physics-Informed Neural Networks for
Tracking the Hemodynamics in the Evolving False Lumen of Dissected Aorta. *Nexus*, 1(2), 2024](https:/... |
fd28e2c5f006683fbf530b4d08a5adc6db09a942420ce30ec27ac74917d37265 | Text | 1,649 | 42 | # Kalman filtering to reduce measurement noise of sample entropy: An electroencephalographic study
This is the matlab code implementation of our paper "Kalman filtering to reduce measurement noise of sample entropy: An electroencephalographic study"
## Datasets
The data used in this study includes the [sleep signals... |
fe3b03b61b667c42e132550569fdc5b0c35027f6be37525084897ef4e52ea192 | Text | 1,652 | 33 | =====================================================================
MRdataset : unified interface to various neuroimaging dataset formats
=====================================================================
.. image:: https://img.shields.io/pypi/v/MRdataset.svg
:target: https://pypi.python.org/pypi/MRdatase... |
dcc8aefa0bde8193f748d965f39179d1fc3bd677b29a036de07c96afbc8701d4 | Text | 1,664 | 72 | # scREAD-backend
This is the API server for [scREAD](https://bmbls.bmi.osumc.edu/scread/). Ther server builds on top of Koa.js and connects to a MYSQL database. The server is developed by [Bioinformatics and Mathematical Biosciences Lab (BMBL)](https://u.osu.edu/bmbl/)
## For new users
You can directly use the scREA... |
8b87042806142e95de980b8b102b2b2ac1d691e324e57d89a99d50889a6fbf09 | Text | 1,708 | 32 | Representational similarity modulates neural and behavioral signatures of novelty: Model simulations
##########################################################################################
Authors: Becker, Sophia [1] (ORCID: 0000-0002-9574-0727), Modirshanechi, Alireza [2, 3] (ORCID: 0000-0002-7870-8602), Gerstne... |
b9a326a46373566d2a18327d1fac05831dd3a4bdbcb06286ab5aa94fa8b84c12 | Text | 1,713 | 39 | # Measures of Effect Size (MES) Toolbox
The Measures of Effect Size (MES) Toolbox is a set of Matlab functions which compute a wide range of effect size statistics. The four main toolbox functions cover common analysis designs, including two-sample-, oneway- and twoway- ... |
eabfc483d6bff3e5534ed401b95f9d645eeb93ec4ae2b6866d66a73da9ca47cd | Text | 1,724 | 33 | [](https://app.travis-ci.com/CINPLA/edNEGmodel) [](https://zenodo.org/doi/10.5281/zenodo.10775264)
# edNEGmodel
edNEGmodel is an implementation of the KNP continuity equations for a
one-dimensi... |
8ebc56145f90e9243935a74a147d0b92d3f53a7ce14cadc5f02d23b55aa5a07e | Text | 1,728 | 33 | # ABCD_relief
This repository stores code and analyses for our recent commentary in ImagingNeuroscience entitled
> Removing scanner effects with a multivariate latent approach - a RELIEF for the ABCD imaging data?
[Read the paper here!](https://doi.org/10.1162/imag_a_00157)
* This works builds upon Zhang et al (2... |
3b3aae1106cd4e5daec2dce9a88918d9e9d568f79e0c2a02d932a1fe732349be | Text | 1,752 | 60 | # RostSpace
RostSpace visualizes embeddings in 3D and 2D space and colors them by groups, provided throug a CSV file. Dimensionality reduction can be performed with UMAP, PCA or t-SNE. Additional features for biologists are implemented, to display molecule structures by providing PDB files.
## Installation
RostSpace ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.