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420c79e8c6b2070ca42d5999068073c58c61898c98c23438ee50472c0395b46a | Text | 497 | 8 | data taken from:
https://s3-us-west-2.amazonaws.com/telemanom/data.zip
labeled anomalies from:
https://raw.githubusercontent.com/khundman/telemanom/master/labeled_anomalies.csv
Corresponding paper:
Hundman, Kyle, Valentino Constantinou, Christopher Laporte, Ian Colwell, and Tom Soderstrom. "Detecting spacecraft anoma... |
ff40f24e381750312c06998f3ea79be8e2141a0c1dc7446f388dffabde44abb1 | Text | 498 | 18 | # Title of Dataset:
DR ATAC-seq
ATAC-sequencing raw data from mouse dorsal raphe nucleus sampled at zeitgeber time (ZT) points.
DR brain tissues were sampled at ZT00, ZT06, ZT12 and ZT18.
## Description of the Data and file structure
Datasets were processed as described (Kim et al., 2022 Neurotherapeutics doi: 10.1... |
a2c1213849e99c0683b50387edff7617ac487a482105997b0fc6176d461f9d9c | Text | 513 | 6 | # The `onavg` (OpenNeuro Average) template
The ``onavg`` surface template was created using high-quality structural scans of 1,031 participants from 30 [OpenNeuro](https://openneuro.org/) datasets.
Different from previous surface templates, the vertex locations of ``onavg`` are optimized so that different regions of t... |
3f48895de0f62e98d2981673f48736d3d07d3ec2164bfd9a67aa19b582d3265d | Text | 515 | 5 | The motor imagery experiment contain 50 patients of stroke. Every patients perform motor imagery instructed by a video.
We instructed participants to avoid swallowing and eye blinking during the trial period and to avoid any other movement.
If the participants were able to execute a movement, they went back to their... |
eca189937e6c42df10709f99a41c6e3496df981daae43110cf51970b5eebb285 | Text | 526 | 9 | # Morphological-WMNs
Codes (most for Matlab) and data for morphological white matter networks.
J. Li, S. Jin, Z. Li, X. Zeng, Y. Yang, Z. Luo, X. Xu, Z. Cui, Y. Liu, J. Wang, Morphological Brain Networks of White Matter: Mapping, Evaluation, Characterization, and Application. Adv. Sci. 2024, 11, 2400061. https://doi.... |
689f319ca3afe4cf66af42860e1f093f87851e99579c8671efa4300df12c9fc2 | Text | 542 | 9 | # Identify-bird-calls-in-soundscapes-BirdCLEF-2023
1. Firstly Mel-spectrogram images are created using the notebook : image-creation-128-x-256-from-audio-th.ipynb
3. After that, experimented with several models:
a. EfficientNet-B7 experimented with : fine-tune-efficientnet-b7.ipynb
b. EfficientNet-B7 embedded wit... |
a51ce62e9c88c7ed9cac9c665165183505b02e3736d3116865e72b45a84cdfe2 | Text | 543 | 5 | # TEM-equivariance
This is the code for the manuscript Classification of Viruses in Transmission Electron Microscopy Images using Equivariant Neural Networks. Provided is the code for the group-equivariant network, training on augmented BloodMNIST data. The file can be modified to use other symmetry groups, a baseline... |
e06e8d08d67040c27cc436938e1e12f3d2d2ff0e68ca678ab9e7ffc6ff21cdba | Text | 544 | 5 | # Robust Correlation Toolbox v2
The toolbox computes robust correlations as in [Robust correlation analyses: false positive and power validation using a new open source Matlab toolbox](https://www.frontiersin.org/articles/10.3389/fpsyg.2012.00606/full) and includes updates on multiple comparisons following [Improved m... |
840c636d946a5d00aa94dffc63074b449c5f3c3c496ce614b0ca138e22d68d55 | Text | 548 | 13 | # mgl Overview
Mgl is a suite of mex/m files for displaying visual psychophysics stimuli and writing experimental programs in Matlab. Runs on Mac OS X. Version 2.0.
# mgl Documentation
Full documentation can be found here: [http://gru.stanford.edu/mgl](http://gru.stanford.edu/mgl)
# mgl Citation
Gardner, J.L., Mer... |
c810edbc4ce9c7e11f19ddac8ed01e33235ac9d779271748981ef5ea29d7d884 | Text | 555 | 25 |
Brain age estimation from overnight electroencephalography with multi-flow sequence learning
Usage:
1. Adjust the _edf path_, _dataset_, and _psgID_ in the cfg of onekey_estimate_edf.py.
(It is recommended to test the HPAP1 data or the testset in swin_merge/prepared_data to prevent data leakage.)
2. Run onekey_es... |
828c307d98fe69bfe848d411d4f7d3db9614d5a42eae946bdf92491e61cb1ff1 | Text | 556 | 4 | # Huntington_midbrain_organoids
Code related to single cell transcriptomic analyses in the manuscript 'Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure'.
You can run the notebook using the data files from the related GEO repository starting from the dig... |
049529068e95ef6f16390905245bb5dc6d41442a9f58009b3429e03edc523d44 | Text | 569 | 15 | # Standard-Model-validation-using-3d-EM
Validation of Standard Model microstructure metrics using 3D electron microscopy
## Data
- 3d EM data, [doi:10.23729/bad417ca-553f-4fa6-ae0a-22eddd29a230](https://doi.org/10.23729/bad417ca-553f-4fa6-ae0a-22eddd29a230)
- dMRI data, [doi:10.23729/0f41bbec-78cc-43f0-b95a-9e9657... |
e94f234ceffa7c3b7fc4581c96f06869d182880e268bec362483b3777735b7ea | Text | 569 | 12 | # 1DCNNwP
#### 介绍
One-dimensional convolutional neural networks with a penalty network (1DCNNwP) is an innovative neural network-based approach for online fNIRS signals processing. The codes are related to the paper Real-time Motion Artifact Suppression using Convolution Neural Networks with Penalty in fNIRS. The addi... |
bde18424e7f54f8133460c1668b6d8677c5533a949ea35305e4d9a71bcb037ea | Text | 586 | 12 | 
# Neural General Circulation Models for Weather and Climate
NeuralGCM is a Python library for building hybrid ML/physics atmospheric models
for weather and climate simulation.
- **[Paper](https://arxiv.org/abs/2311.07222)**
- **[Documentation](https://neuralgcm.readthedoc... |
22bf0f57aefaa111f50251a27cf799ae35253b82e65530e41fcf1bb2c20be530 | Text | 593 | 9 | paintone_rsn
==========================
Laboratory for Predictive Neuroimaging - University Hospital Essen, Germany
This repo contains the main analysis steps related to develop and validate th RCPL signature (Resting-state functional Connectivity signature of Pain-related Learning).
Information about the study desig... |
e89d1f51359cde7df534251b801cba443238fd371651af755f2f635a9fb7cb73 | Text | 593 | 5 | # Model of Consequence-Based Decision-Making
Implementation in Matlab of the mathematical model published in Cecchini G., DePass M., Baspinar E., Andujar M., Ramawat S., Pani P., Ferraina S., Destexhe A., Moreno-Bote R., Cos I. A Theoretical Formalization of Consequence-Based Decision-Making. bioRxiv 2023.02.14.528595... |
ff3badc6fe2a61155a863801f4ae07edfcbc9d54a6e5e01be120debe6528596b | Text | 602 | 25 | # human-microglia
## License
This project is licensed under the terms of the MIT license.
## Description
This repository contains scripts used in Guvenek et al.
## TPM_count_SingleEnd.R
Script is used to count reads from bam files
## DESeq2 analysis.R
Script is used to do DESeq2 analysis for Figure 1b
## BulkR... |
0aa3ad4e570c4b2288b2edb0fb7aeb3c4a1061fb13a05846e8e952140d6fcbdb | Text | 608 | 27 | # Instructions
## XDF latency analysis of LSL data streams: Unity (triggered) vs EEG (measured)
### Situation
Every 500ms a beep sound is played and the background color changes one frame from black to white.
![Changing Background](https://raw.githubusercontent.com/mvidaldp/lsl_latency_analysis/master/img/backgroun... |
6d60a3746db115f8d54bfa6c414149ab45d3c5ead3398e341ce3c0641051fcac | Text | 613 | 24 | # Code for "Whole nervous system expression of glutamate receptors reveals distinct receptor roles in sensorimotor circuits"
[](https://zenodo.org/doi/10.5281/zenodo.12705826)
This repository hosts the codes for the paper *Whole nervous system expression
of glutamate rece... |
61c96af9249e15d87edd252c73f1c76548e2cc8f509352b0c0594e14720470b4 | Text | 624 | 6 | ## Multiple Sclerosis Patient Data Ontology (MSPD)
An ontology designed to represent patient data from the New York State Multiple Sclerosis Consortium, MSPD is being used to compare patient reported outcomes with clincial measures.
This project was originally funded via National Multiple Sclerosis Grant PP1970. It is... |
8f0c55941fceb59a27501e7ce738be0fca4d77424c9a3d0790645c03113cb613 | Text | 625 | 26 | # File Organization #
## Projects: Contains unique code used in specific projects
Amin - GCaMP
Boris - Photometry
- Pastry Tray Experiments
Calibration Investigation
Innovation Award Video Presentation
Ruth - Photometry Analysis
Siriram - MultiElectrode Analysis
## Tools: Contains gene... |
43615e1faf66ce3f71328e8dfdb81a4d061a783d661c6ad134ace759c69cfcb3 | Text | 633 | 11 | Analysis code for the snRNAseq data from Banner 101 samples, superior frontal gyrus.
Manuscript under review
A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease
Qi Wang, Jerry Antone, Eric Alsop, Rebecca Reiman, Cory Funk, Jaroslav Bendl, Joel T D... |
af80e9635af2a31e4041445503fdda1997ee8f74bd60358d62df2c2a8630f232 | Text | 647 | 12 | # Sensitivity-Suppression
The shared data and code is used in eLife2024;13:RP94198 DOI: https://doi.org/10.7554/eLife.94198.3
DAF data files consist of high gamma activity (70-150Hz) recorded with ecog during the production of words with 0, 50, 100, and 200 ms auditory feedback delay.
Data files are organized as tri... |
dc919cefff24626b6c8c2aab74ae8a4b8878f5e515c64fdcc1d552dc0fd2643d | Text | 648 | 11 | # GIMME Preprocessing Scripts
This set of scripts were used for preparing resting state functional MRI data for analysis using Group Iterative Multiple Model Estimation (GIMME) analysis. They should roughly be used in the order in which they're numbered. Quality control scripts are marked with a QC. These will by no m... |
6302722266a4445c3e55cd3e61d6cf886c97b4cd727d9b0024e1c1462703a6a5 | Text | 653 | 6 | # Kim2024_1-4xLPS
This repository contains the code and input data that was used for the analysis presented in the following publication:
Kim, J., Sullivan, O., Lee, K., Jao, J., Tamayo, J., Madany, A.M., Wong, B., Ashwood, P., Ciernia, A.V. (2024) [Repeated LPS induces training and tolerance of acute microglial respo... |
777d48e3059460a905bfb0b5edd4510d8472a0ee7af6390f109f28a9dd7195a0 | Text | 656 | 11 | # BrainAgingNet
This will contain the code of our publications about brain age estimation using deep learning.
### Global-Local-Transformer.py
### Multi-scale-GLobal-Local-Transformer.py
- Sheng He, P.Ellen Grant, Yangming Ou, **Global-local Transformer for brain age prediction**. IEEE Transactions on Medical Imaging... |
cdcd6788e655617591cec5cff61daa6cef801827e1d4d7acf74c628544c4c648 | Text | 670 | 5 | # STAR Protocols
This repository contains the templates, files, and various resources utilized in "Hybrid Structured-light Three-Dimensional Scanning and Modeling of Human Postmortem Brain for Neuroanatomy Practice, Research, and Education" manuscript submitted to STAR Protocols journal from the Bieniek Lab at the Uni... |
68b9615fbbd8622f6f84a5cdc823495faab80fe013a047c09526fb4955bfe0ce | Text | 673 | 17 | # invitroTMS
MATLAB Code and Models accompanying in vitro TMS paper
<b>How Conductivity Boundaries Influence the Electric Field Induced by Transcranial Magnetic Stimulation in vitro Experiments</b>
Padmavathi Sundaram, Chunling Dong, Sergey Makaroff, Yoshio Okada
Brain Stimulation, Volume 17, Issue 5, September–Octo... |
e99aa0d061d738e9350e5cf12844bbb6e54fa70add2f75e2bb298c1a54481951 | Text | 675 | 8 | # SzCORE - Seizure validation Framework
This repository illustrates the flow to evaluate a seizure detection algorithm using the SzCORE methodology presented in [*Dan et al. "SzCORE: A Seizure Community Open-source Research Evaluation framework for the validation of EEG-based automated seizure detection algorithms"*](... |
f95d7ee33d5b3020b235b5a2dfc66689e851ea7702a48946c2a4422c14d974b3 | Text | 676 | 13 | # Stability Oracle: A graph transformer framework for identifying stabilizing mutations
## Model Inference
- To generate predictions, use the `scripts/run_stability_oracle.py` cli. Example commands are provided in `scripts/generate_predictions.sh`
- Datasets and predictions are provided in the data directory
- Due to ... |
baffb04c24f38b58e4c28c702758332acf18bba16b10e1160044e0e69ed227b2 | Text | 696 | 16 | # ProtCNNSim: Discovery of new protein family relationships with Deep Learning
## Data
Per-family embeddings and their Pfam labels can be downloaded from Zenodo [10.5281/zenodo.10091909](https://zenodo.org/records/10091910).
Pfam 35 family-to-clan mapping can be downloaded from the [Pfam FTP site](https://ftp.ebi.ac.... |
7e869acdca354a63052d5258a0f1cc67b428847fd45be692c2a5d11fbd2b5b5b | Text | 723 | 8 | # IntrinsicProperties
This code analyses the intrinsic properties, including 1 Input resistance, 2 Membrane time constant, 3 Sag ratio, 4 First spike latency, 5 Depolarizing hump amplitude, 6 AP amplitude, 7 AP threshold, 8 First AHP latency, 9 AHP half-width, of the recorded cells under current clamp configuration
It... |
4b3b945fa80a1576543d6a8961f7974e7beb6c86f66178b4dffbf3c80fd0acb9 | Text | 725 | 10 | # connectome_asymmetry
All the code, raw data, input files and stored networks used to generate the results in "Asymmetry in synaptic connectivity balances redundancy and reachability in the _C. elegans_ connectome".
_birari_rabinowitch_asymmetry_analysis_final.ipynb_ contains all the code used to generate the results... |
f29c244ce8cfb93d52ff6e01266ac2571fbdb7fbf7ba4ca872b25bad42ae1c13 | Text | 725 | 21 | # Factorial Mass Univariate ERP Toolbox (FMUT)
**VERSION**
0.5.1
**AUTHOR**
Eric Fields
**CONTACT**
e_fields2@uncg.edu
The Factorial Mass Univariate ERP Toolbox (FMUT) is an extension to David Groppe's Mass Univariate ERP Toolbox. The FMUT implements permutation and false discovery rate based m... |
655c44ef28250ec71e00a2a61428b69ddb7bb1a30bf2f06f418d3ca4f8d74fd0 | Text | 736 | 16 | # mgl Overview
Mgl is a suite of mex/m files for displaying visual psychophysics stimuli and writing experimental programs in Matlab. Runs on Mac OS X. Version 2.0.
# mgl Documentation
Full documentation can be found here: [https://gru.stanford.edu/doku.php/mgl/overview](https://gru.stanford.edu/doku.php/mgl/overvie... |
ae75d7c95e7955c87d27b0006d2aa97733edaa172245564256ded128c832c7dc | Text | 737 | 8 | # Pisanski2024
Custom code for data analyses used in figures 3,5,6 and supplemental .gifs from Pisanski et al, 2024.
Citation:
Annette PisanskiMitchell ProstebbyClayton T. DicksonSilvia Pagliardini2024Mapping responses to focal injections of bicuculline in the lateral parafacial region identifies core regions for maxi... |
fc3793ef422d397dc9f933284594af6cca444e13e0ddc32a381f4aa566ec3419 | Text | 737 | 27 | # GRU-powered Sleep Stage Classification with Permutation-Based EEG Channel Selection
```
@article{moctezuma2024GRU,
title={GRU-powered Sleep Stage Classification with Permutation-Based EEG Channel Selection},
author={Moctezuma, Luis Alfredo and Suzuki, Yoko and Furuki, Junya and Molinas, Marta and Abe, Takashi},... |
735668307b3e00da934cb7720bb821d39d66c644e98062b4db96a723660efcf7 | Text | 745 | 20 | # object-detection-algorithms
This repository contains the MATLAB® source code used in my research project.
The datasets used are available in CaltechDATA at https://doi.org/10.22002/D1.20084 and https://doi.org/10.22002/D1.20085.
Results gathered by using this code might differ from the published results based on yo... |
17d15512ca06efe9f8b0e207da9d49ca4deea5afb6c1a79ec32dea958605625a | Text | 747 | 14 | # Fuzzy-AOI-EyeTracking
Perform area of interest measurements on eye tracking data recorded with an Tobii X300 during a series of experiments.
The scripts in this repositry are dependant on the I2MC-filter: https://github.com/royhessels/I2MC, be sure to add them to the Matlab path.
`eyetracker_HF_UL.m` contains the o... |
a86bcde8f0e9403eb2d4b1b7f0515fed44f1f54a82c2ede4aacb268816bbec40 | Text | 770 | 10 | # circularGraph
## Description
A **circular graph** is a visualization of a network of nodes and their connections. The nodes are laid out along a circle, and the connections are drawn within the circle. Click on a node to make the connections that emanate from it more visible or less visible. Click on the **Show ... |
1c46b8feafee77a0b659af3c7b8b3ec6d28f0b6de32ebd49b9cfccf72d1ffecf | Text | 775 | 7 | # Estimated-marginal-means
Estimated marginal (predicted) means from generalized linear mixed effect models in Matlab.
Requires the Stats toolbox.
The intent of these Matlab functions is to replicate (at least partially) the incredibly useful '<a href="https://cran.r-project.org/web/packages/emmeans/">emmeans</a>' pac... |
bbc28e991795f362afa19453ffd8825d9f8c775fac7e7de5e4b30aee6c22047c | Text | 778 | 27 | # WACV2018/TIP: Gabor Convolutional Networks
Official PyTorch implementation of Gabor CNN.
But all the results in the paper are based on [Torch 7](https://github.com/bczhangbczhang/Gabor-Convolutional-Networks).
These two implementations are sharing the same infrastructure level code.
## Requirements
- PyTorch 1.1.0... |
094a737e983e0747d9ef0f9442bce4526cdc93fd81582e17fa6f0ce43f95ffc2 | Text | 781 | 5 | # A machine learning artefact detection method for single-channel infant event-related potential studies
This repository contains the code behind the methods and analysis for the paper "A machine learning artefact detection method for single-channel infant event-related potential studies" (Marchant et al. 2024).
Anal... |
7bcb8540da7610c4ad0ced7a8faf594268a29d7d6cf8f56bb9df432b621ea170 | Text | 793 | 33 | # EEG-fMRI-replay
## Overview
This repository contains analysis code of "Replay-triggered brain-wide activation in humans".
Paper link: https://doi.org/10.1038/s41467-024-51582-5
## Usage
### Get data
1_behavior: behavior analysis
2_eeg_TDLM: EEG-based replay analysis in task and rest
3_feature_selection: featu... |
bd4204741e9216cf1c080e7c0dd6f0761afd0cd98862bd87baffb2d09dfd9350 | Text | 805 | 18 | Welcome to CereLAB v0.4!
This project uses copyrighted headers and libraries from Blackrock and borrows
heavily from this project to make the C++ wrappers:
http://www.mathworks.com/matlabcentral/fileexchange/38964-example-matlab-class-wrapper-for-a-c++-class
which is covered under this license:
http://www.mathworks.c... |
d0040754aa72810d435b2e64d2ab2610c41dd24f331bdd8a3efd4d0cdf67d812 | Text | 810 | 27 | # CSP-Research
The python code used for the publication ... .
It contains the results in /results and the source in /src
The source contains some patches for MOABB to speed up evaluation, but one will need approx. 50GB of main memory to run the scripts.
You can edit the config.py for changing the default calculation ... |
29a2b722826b43f82124eccd19f8b07015743ee051d9cb780eff7e0e9fc06aed | Text | 819 | 17 | # Description
This is the implementation of our paper: A novel detection and classification framework for diagnosing of cerebral microbleeds using transformer and language. Paper url: https://www.mdpi.com/2306-5354/11/10/993
# Private Dataset
Partial private Datasets can be found in: https://drive.google.com/file/d/1... |
cadc498ed6f09d4364fdb3f3cb5d828af43c9f138bc5083ac642bfcaaf2aabc5 | Text | 823 | 12 | # connectome_asymmetry
All the code, raw data, input files and stored networks used to generate the results in "Asymmetry in synaptic connectivity balances redundancy and reachability in the _C. elegans_ connectome".
_birari_rabinowitch_asymmetry_analysis_final.ipynb_ contains all the code used to generate the results... |
2f3b5a7bb1358a97bfcf76a60121cad4e6be90d1b6e6ae7ef62fbf04d6b346e4 | Text | 828 | 4 | # LIF-STDP-SP
## Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity
To investigate the impact of different types of plasticity mechanisms, we combine a network of excitatory integrate-and-fire neurons with different synaptic weight and/or structural plasticity mech... |
2454299f87a10b36bfb6ed70a8eeaaad004168d9a60a953257bbc0a61ce481d9 | Text | 835 | 12 | # GIMME Preprocessing Scripts
This set of scripts were used for preparing resting state functional MRI data for analysis using Group Iterative Multiple Model Estimation (GIMME) analysis. They should roughly be used in the order in which they're numbered. Quality control scripts are marked with a QC. These will by no m... |
c99915df55c7916aabfb3eddaaa23b15b42d4d39daa9ba4b50c10ddc535e2f0d | Text | 836 | 4 | # Shiozaki_2024
Code related to Shiozaki, Wang, Lillvis, Xu, Dickson, and Stern (2024) Activity of nested neural circuits drives different courtship songs in Drosophila
This code collection was used to creating figures in the publication "Activity of nested neural circuits drives different courtship songs in Drosophil... |
23d398193ab773a32ac67471a79a253f8b9ceaed3f261f147ce19ed346ac4037 | Text | 844 | 6 | # open-field-analysis
This python script takes raw open field analysis data in an excel spreadsheet and calculates the average metrics for velocity, rotations (both clockwise and counterclockwise), and distance moved.
You can access the excel files containing the raw data and the analyzed output data in the data folde... |
4e0944e4ff578fe6db80287638ce8b6c3a6de3f08b65f36082dd5fbbf9fe0aaf | Text | 853 | 19 | ### Slow wave sleep drives sleep-dependent renormalization of synaptic AMPA receptor levels in the hypothalamus
#### Jianfeng Liu ¶, Niels Niethard ¶, Yu Lun, Stoyan Dimitrov, Ingrid Ehrlich, Jan Born * , Manfred Hallschmid *
This repository contains Matlab scripts used for the analysis reported in the paper *"Slow W... |
b805ddd98ed72b4277118af4cd99c880ccfb5ce4007a3f9e5416862a75e52b85 | Text | 858 | 11 | [](https://zenodo.org/doi/10.5281/zenodo.12706763)
# scrattch
## **S**ingle-**c**ell **R**NA-seq **a**nalysis for **t**ranscriptomic **t**ype **ch**aracterization
This is the umbrella package for the `scrattch` suite of R packages from the Allen Institute for Brain Scienc... |
8522a974251ebb6f9119e3588dd294bb32e65d12cad83862fac982eed800b38e | Text | 859 | 13 | # iSpeech: speech and music processing with sEEG recordings
te Rietmolen et al. eLife 2024 "Speech and music recruit frequency-specific distributed and overlapping cortical networks"
This GitHub provides the codes to reproduce the results and figures of the manuscript with Python.
The conditions of our ethics approval... |
84dd094be31fe3f5a34255693aa74e6e618c9cadc0fb2327985548e47f206825 | Text | 862 | 30 | Heterogeneous neighbor contrastive graph attention network(HNCGAT)
====
This repository contains the author's implementation in Pytorch for the paper "HNCGAT: heterogeneous neighbor contrastive graph attention network for metabolite-protein interaction prediction in plant".
Environment Requirement
===
The code has bee... |
26a20b89b467b0ae337ecc36f8cbf2ad4f617cbaaf7e6498f43137b028b9cc13 | Text | 879 | 7 | # A machine learning artefact detection method for single-channel infant event-related potential studies
This repository contains the code behind the methods and analysis for the paper "A machine learning artefact detection method for single-channel infant event-related potential studies" (Marchant et al. 2024).
Anal... |
98a0124b6cf1dcb90710a27d12517773688602c85717eb49667d05299136fec2 | Text | 890 | 10 | # Pregnancy-Loss-Genetics
R codes to study genetics of pregnancy loss in horses. Multiple samples from 256 product of conceptus (POCs) underwent chromosomal microarray analysis (CMA) and short tandem repeat profiling using multiple STR markers. Ploidy status were also confirmed using 30X whole genome sequencing and 10X... |
82ef76752365b0bb499741bd499819a77ca5d8da511d3c12e459120ee62f2b2e | Text | 894 | 25 | # PSP Whole Genome Sequencing Analysis
The analysis pipeline for Progressive Supranuclear Palsy (PSP) whole genome sequence data.
## Dependencies
- [Manta v1.6.0](https://github.com/Illumina/manta/releases/tag/v1.6.0)
- [Smoove v0.2.5](https://github.com/brentp/smoove/releases/tag/v0.2.5)
- [Strelka v2.9.10](https://g... |
937e406989e55bf33b2db7e5782b90767d48e1ded7343a89d83a69d0b2befa09 | Text | 895 | 27 | # Decoding dynamic visual scenes across the brain hierarchy
This is the code and data of **Decoding dynamic visual scenes across the brain hierarchy**
## Preparation
Download the training data example from [Google Drive](https://drive.google.com/drive/folders/1SAaq6XAOt6bayl_9PdR7vdASDFMliyYN?usp=drive_link)
Download... |
5b6575a4840439d37a836ce017dc5cbd5a7f5544d475837c626599d86b2efa10 | Text | 907 | 9 | # ISC_NarrativeRoles
Heroes and villains: Opposing narrative roles engage neural synchronization in the inferior frontal gyrus (2024)
The codes for the main analysis are written in Python and adapted from the Dartbrains tutorial: https://naturalistic-data.org/content/Intersubject_Correlation.html
The neuroimaging da... |
efde875664464d72fa6be921c03e28e22eeff2c42038a62ed537e1e88427e42a | Text | 924 | 1 | The provided code offer a comprehensive approach to anomaly detection and classification tasks using machine learning algorithms. Starting with anomaly detection, the Isolation Forest algorithm is applied, covering data preprocessing, model implementation, and visualization of results. Subsequently, various anomaly det... |
dbdb8658ffa5dd38cb032d21c82e9350f0da1e6b2d70a36be3fe23bd53e25caa | Text | 925 | 28 | This repository has been archived and is no longer maintained.The code is provided for historical reference and may contain unpatched or unknown vulnerabilities. It should not be used in production systems.
LyChI (Layered Chemical Identifier)
===================================
This directory contains code for BARD/G... |
fbd45678ccc517fc37bb7a6b9d589eb1f68faf0aff78c773642710f6f45355cf | Text | 925 | 26 | # EfficientBayes
Code used for simulations in paper: **'Signatures of Bayesian inference emerge from energy efficient synapses'**
- Data for figures 2, 3, 5 and 6 can be found in folders:- *data-_*
- Simulations for figures 2, 3 and 5 can be replicated using *sims-_.py*
- Plots for figures 2, 3 and 5 can be replic... |
4c36fcc78e397fff461c5016583edf38e2f15f992534c6e91d8dcebbdc3520f5 | Text | 927 | 24 | # A universal material model subroutine for soft matter systems
When using, please cite
**"A universal material model subroutine for soft matter systems",
M. Peirlinck, J.A. Hurtado, M.K. Rausch, A. Buganza Tepole, E. Kuhl,
Engineering with Computers, 2024**,
[DOI/URL](https://doi.org/10.1007/s00366-024-02031-w)
... |
fcd8e305096e6c3900a615f92a0918ee801607f71dba341cdb496ec8a113dc8e | Text | 942 | 12 | # University of Salento Grapevine Yellows dataset
Dataset to for detecting Grapevine yellows in Vitis vinifera. Augmented with other categories chiefly from the Plant Village dataset.
# Citation
If you find this data useful please cite the following:
- A. Cruz, Y. Ampatzidis, R. Pierro, A. Materazzi, A. Pan... |
870ec623e8f19799cd12d6541acf8610a9af1b6d6eb4109b5e4fd5339028ea8e | Text | 954 | 27 | Training and prediction of atomic polar tensors using the e3nn framework implementing E(3) equivariant neural network on top of torch.
Note that the code is working and tested on liquid ambient water (see publication below), but still in beta. It is therefore not optimized and might be subject to change in the future. ... |
3dce211a771e8bbcf937c2cac43907a04a5357f2232f3ef23e32f995d639de83 | Text | 957 | 12 | ## NeuralGeometry-BehavioralDiffs
This repository contains 4 main directories with python scripts and datasets. Each aims to reproduce the main behavioral and neural analyses from real and artificial datasets.
1. "behavior" directory: it contains the 'behavior_main.py' and the behavioral data from 2 subjects. To r... |
24baff76dee83b17bdf128956b41fdc4811ebf7ff3a03dc1d16c819aa25306a2 | Text | 969 | 12 | ## LERCause: Deep Learning Approaches for Causal Sentence Identification from Nuclear Safety Reports
A repository of dataset and source code for the publication paper of causal sentence classification from nuclear safety reports
# How to use files
1. To get the results described in the paper, all the code was implement... |
118ec9cb6579c84f51fe1732b954ad699ae8a9968cbd2f0f1caf13c1c26d92c9 | Text | 976 | 22 | Code for the surrogate model in the paper [The deep latent space particle filter for real-time data assimilation with uncertainty quantification](https://www.nature.com/articles/s41598-024-69901-7).
Reference for citing the work:
*Mücke, Nikolaj T., Sander M. Bohté, and Cornelis W. Oosterlee. "The deep latent space p... |
c0680bfd2f9b47b385560699736bd01c2791d0931e7af5751ef80199f0c1f74d | Text | 976 | 9 | # Intersections
These matlab codes can read the morphological infos of a biocytin-filled neuron from a .swc file generated by Neuromantic or other softwares and analyse the number of intersection against vertical or horizontal axis with function of translation and/or rotation.
Firstly, run "changeextension" to copy t... |
2e74d92d162380d5daf0024905af49e19c1379ff66c290e6ecb9e6cb98637871 | Text | 979 | 5 | # Code and instructions to reproduce: Rodent Automated Bold Improvement of EPI Sequences (RABIES): A standardized image processing and data quality platform for rodent fMRI.
In this repository are found the scripts and associated instructions required to reproduce results reported in the manuscript. These consist of th... |
b8a8881d1b24584eaa86cdee63e91b9371abd145181ff01a76d9507a213a9328 | Text | 990 | 27 | # DeepRVAT
Rare variant association testing using deep learning and data-driven burden scores
[](https://deeprvat.readthedocs.io/en/latest/?badge=latest)
## Installation and usage
Please consult our [documentation](https://deep... |
747f0e43429d5f39e12d1e1f48bad1aead27e3392a7514825a500c0a655275ad | Text | 991 | 22 | Code for the data assimilation in the paper [The deep latent space particle filter for real-time data assimilation with uncertainty quantification](https://www.nature.com/articles/s41598-024-69901-7).
Reference for citing the work:
*Mücke, Nikolaj T., Sander M. Bohté, and Cornelis W. Oosterlee. "The deep latent space... |
3e8441d7301ee16959dd08e86ccd2508ee2836f80b8152e57717dd40e1ff1e03 | Text | 995 | 38 | # PepCA
Unveiling Protein-Peptide Interaction Sites with a Multimodal Neural Network Model
## Installation
Clone the repository and Install requirements
```bash
git clone https://github.com/cloudaner115/PepCA.git
cd PepCA
pip insatll -r requirements.txt
```
You can use this one-liner for installation, using the late... |
6808feb426bdadd6b0d7f205b106fa7d558801ba5fe76d938336f8d51f8d94cc | Text | 1,000 | 9 | The folder "Dendritic_domains" contains the data tables, Matlab and Python code and Jupyter Notebooks that were used to generate the figures of the manuscript "Clustered synapses develop in distinct dendritic domains in visual cortex before eye opening" by Leighton et al..
The individual notebooks are related to spe... |
9e9dfcde4a85ba07ad7749afe079f7e01026b8380d45b74ae11357b9ebca6cc6 | Text | 1,000 | 18 | # POST_COVID_REST
Raw resting-state EEG data (in "Raw_EEG" folder) and extracted MSE (Multiscale Entropy in "MSE_Data" folder) and SPD (Spectral Power Density in "SPD_Data" folder) data for the following manuscript:
Title: Resting-state neural dynamics changes in older adults with post-COVID syndrome and the modulato... |
deacaddaad8b7b2bf7c1fe74d2a2c80fc76247aa2a923a7c3c1de407ab87d8fe | Text | 1,010 | 13 | <h1><b>Delta Latent Space Vectors</b></h1>
Implementation of paper "Exploring molecular heteroencoders with latent space arithmetic: atomic descriptors and molecular operators" by Xinyue Gao, Natalia Baimacheva and Joao Aires-de-Sousa
<b>Prerequisites:</b> CDDD (https://github.com/jrwnter/cddd)
<b>Files:</b>
- dls... |
44d1099a70ca08ac871997e568c11b57fb6fb794b29fbcf7f6ca30586d8fd01d | Text | 1,011 | 18 | [](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest)
neuron_morphology
===========... |
b889c22c299adbd5ed51d2ceff07d64ece7eb37b27ad7f7bdd82e5db543c780f | Text | 1,024 | 25 | # Sensory_Adaptation
MATLAB code that generates the figures from Colins Rodriguez _et al_., 2024. "Sensory adaptation in the barrel cortex during active sensation in the behaving mouse".
Related data is published as
Loft, Michaela S. E.; Colins Rodriguez, Andrea; Maravall, Miguel; Schiessl, Ingo; Petersen, Rasmus ... |
f0a5e652477ea84ce514271141568f8bdf5f16c9cdc67d9991b1df6b4acc0c5e | Text | 1,026 | 1 | The code showcases a series of visualizations aimed at understanding and comparing the performance metrics of various systems under different conditions. The bar charts illustrate how average response times vary across systems concerning the number of users, devices, and transactions. These comparisons provide valuable... |
fb460e43c295264573468ef665687193c4103e343020aba2f3fe5b9fa271ac1e | Text | 1,030 | 15 | These scripts will exactly reproduce the images in `figures/`. This includes several figures which were not used in the correponding manuscript.
Note the dependencies listed in `dependencies/`.
The `datasets/` folder will be shared separately as it is 1.8TB in size.
To run the full scripts, first extract each tar fi... |
47539ab3d510b5e02269c17cbee257034eb2584b6d389359f3562b1b0e6e0f49 | Text | 1,043 | 15 | # E-P-INAnalyzer
E-P-INAnalyzer is a Python-based toolkit for understanding enhancer-promoter interaction networks from RNA-Seq, ATAC-Seq, and ChIP-Seq datasets. E-P-INAnalzyer allows researchers to reveal substructures, integrate transcription factors, locate disease-associated variation, and perform enrichment analys... |
e03d3294c65c206d84102f954250606428fc5b5e86391ae7216c6f3a7fcb369c | Text | 1,059 | 25 | # MultiSpineModel
Python package for the submission of "Competitive processes shaping multi-synapse plasticity along
dendritic segments".
Included is the jupyter-notebook to generate the figures and a file to fit the model to the dataset.
# System requirements
The codebase uses python and the jupyter-notebook archite... |
48ea1c57a7c95455101e6193689083bd757be1b2ba119aabb33f6135a2332ff4 | Text | 1,065 | 20 | # LiC_et_al_MR_crosstalk
Bidirectional_MR
------
Code for bi-directional MR analysis between m6A and epigenome (DNAme and H3K27ac) implemented by R package TwoSampleMR (v0.5.6). TwoSampleMR is available at https://mrcieu.github.io/TwoSampleMR.
SMR
------
Code for summary data-based Mendelian randomization (SMR) tests ... |
ed6cf024030e3d7e2f348e4acf7c629f030e16edf3f03a2ffc7e0dce4565c6a3 | Text | 1,075 | 22 | # Tooley2023_prenatal_env_cortical_network_dev
**Author**: Ursula Tooley, 2023-2024
This repository contains code for the analyses described in our paper:
"Prenatal environment is associated with the pace of cortical network development over the first three years of life.""
Preprint available [here](https://doi.org... |
4bdd5a94a839e9cb5224dee9530740d34adf87c945e72ab3f3f7178fd2d6f8bd | Text | 1,079 | 34 | # ANN-for-Lattice-Structure
This is the data set and the python & Matlab code for *Prediction of Mechanical Properties of Lattice Structures: an Application of Artificial Neural Networks Algorithms*
### 文件夹框架
MachineLearningANN
|__ data 机器学习之前所有txt格式的数据文件
|__ lib 静态库
|__ AbaqusModelCreate.py ABAQUS模型批... |
fca50b65fa319faee7fa0a16f9ea1454362b02d3f510bb3ee7760b303e68ba82 | Text | 1,089 | 26 | # Source data and code
This repository contains the source data and code to regenerate figures for "Concept and location neurons in the human brain provide the what and where in memory formation"
## Matlab version
This code was developed on Matlab R2019b, but should also run on later versions. Minor adjustments may ... |
90d79ec00b55e6a6b5a8f8bc66cbc1d4d9966ce486142c63bcf37b0ab158defa | Text | 1,090 | 37 | 
# PPI Origami
Tools for processing and analysing PPI datasets
## Installing
You can install PPI origami using pip
```bash
pip install -U ppi-origami
```
## Documentation
Information for usage and installation is available from the documentation site https://emad-combine-lab.git... |
da2391386b0b96ecf6f010babc9a16255433d74b3b835d2de858af071166b51c | Text | 1,095 | 17 | # Astrocytes enhance plasticity response during reversal learning
This repository hosts the code used to produce and analyze the results of the paper:
Squadrani, L., Wert-Carvajal, C., Müller-Komorowska, D. et al.
*Astrocytes enhance plasticity response during reversal learning*.
Commun Biol 7, 852 (2024). https://... |
1f84e55da19bd0a7d2adb2636cf5f35c485ee6bc7ad847c67c530819f7b4ea40 | Text | 1,100 | 27 | ### Vital parameter forecasting in the ICU
This repository contains the software
behind the paper entitled **Short-term vital parameter
forecasting in the intensive care unit - A benchmark study
leveraging data from patients after cardiothoracic surgery**.
- The _R_ folder contains code in the R statistical
progr... |
5d011081e19bc0f46750a6713fe1277400cc651dc746e790b3e18c4e27239c5b | Text | 1,114 | 15 | # deeprvat-analysis
Code for generating all plots for the paper 'Integration of variant annotations using deep set networks boosts rare variant association genetics' (building on https://github.com/PMBio/deeprvat/)
To run the code, the DeepRVAT conda environment is needed and DeepRVAT has to be installed. Additionaly,... |
d5cb0be7b1bde3e68af6def0abdf7d6e007e569f8f5b34955928936afe0f7936 | Text | 1,130 | 11 | # Scripts for quantitative spatial analysis of basal ganglia annotations across atlases
This repository contains the code used for the quantitative comparison of basal ganglia annotations in Brain Maps and The Rat Brain in Stereotaxic Coordinates with regions in the Waxholm Space rat brain atlas. This analysis is part... |
1b0aafaa2cafcfc08020e47343c83abe421cdc65cf765781238740b7a8316c8a | Text | 1,131 | 30 | # Parkinson-Progression-Subtyping
This is implementation of our manuscript "Identification of Parkinson PACE subtypes and repurposing treatments through integrative analyses of multimodal clinical progression, neuroimaging, genetic, and transcriptomic data"
### 1_data_preprocessing
Code for PPMI data extraction and ... |
c117f2e9d50b1516fcdd897c4df266448070759c635d9b7b84ef4a59125f2784 | Text | 1,143 | 17 | # Modularized Physical Incorporated Neural Network for Future Building Energy Modeling
This repository proposed a Modularized Physical Incorporated Neural Network (SeqPINN) for Future Building Energy Modeling, which can be used for 1) load prediction, 2) dynamic modeling, 3) retrofit and 4) energy optimization.
The "... |
8ba82f202dd2bc39b81e2a9f034a7d6ab4c882a4cd9ebc58d3c1585133c80b08 | Text | 1,162 | 25 | # Difficulty in chirality recognition for Transformer architectures learning chemical structures from string representations
Investigation on procedure of Transformer learning chemical structure.
## Publication
- [peer-reviewed publication](https://www.nature.com/articles/s41467-024-45102-8)
- [preprint](https... |
1033f257aab05c1c704c5bb0382522c077e8c903a58de138da2130b37297895e | Text | 1,173 | 29 | # PPI.bio
[](https://zenodo.org/doi/10.5281/zenodo.10652229)
This is the codebase for PPI.bio, the software that powers [PPI.bio](https://ppi.bio).
A server for protein-protein inference using the RAPPPID and INTREPPPID algorithms.
## Documentation
You can read the docu... |
59de8c561e43c08a8130a09f778576d5a15760727909d922b9ae5eef74a9e147 | Text | 1,179 | 25 | # Prediction of Freak Waves from Buoy Measurements
Thomas Breunung and Balakumar Balachandran
Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
# License
This software is made public for research use only. It may be modified and redistributed under the terms of the MIT Lic... |
69d13c689c08adbfd64fb728081269beaa8053b44ece8a2964dec7ce3786e5d1 | Text | 1,182 | 29 | pSCNN
===
The pSCNN repository includes all materials for the prediction of the normal melting points of ionic liquid. It contains the trained models via five-fold cross-validation (model_[0-4].keras), a package with zscore standardscaler and 209 Mordred molecular descriptors(for-external.pkl), one package with all da... |
f170c7dcaa7457a2f35afb77f4a4caa749b06d42bf41e5cfd88a3c7780b25275 | Text | 1,189 | 40 | 
# PPI Origami
[](https://zenodo.org/doi/10.5281/zenodo.10652233)
Tools for processing and analysing PPI datasets
## Installing
You can install PPI origami using pip
```bash
pip install -U ppi-origami
```
## Documentation
Informati... |
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