sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d94c3f1b2d5088fd67d21153aa742cde252f85d267857f98842b00915b9190e1 | Text | 914 | 23 | # Feature Selection - Framework Code
[](https://www.python.org/downloads/release/python-390/)
[](https://zenodo.org/badge/latestdoi/590997289)
Repo contains code used to generate the results and figures for the ma... |
1c7cfd204d6643ef75b2f2ded4efdcb0af01337997a324cb3e08c899ffa19bb0 | Text | 936 | 18 | # Transformer Time Series Prediction
This repository contains two Pytorch models for transformer-based time series prediction. Note that this is just a proof of concept and most likely not bug free nor particularly efficient.
* transformer-singlestep.py contains a single-step prediction model
* transformer-multistep... |
0797fed17c647b65bdeef519bc8ab5f50c6d0a4de48138c32874f26436cc01a7 | Text | 1,007 | 18 | # Glanz_et_al_2023
**Multicellular M1 Recordings and 3D Forelimb Position Data in Infant Rats**
[](https://zenodo.org/badge/latestdoi/586313842)
Matlab files for eight P8 and eight P12 rat pups are included. See [Glanz et al., 2021](https://www.jneurosci.org/content/41/3... |
ccf593b0168ab3a00f788d333385f4edff80c95ec2f8babaecfa408d72810a0d | Text | 1,022 | 26 | Demo codes for "Species-specific wiring of cortical circuits for small-world networks in the brain"
1. System requirements
- MATLAB (2021a is recommended.)
- Installation of Deep Learning Toolbox
- Uploaded codes were tested using MATLAB 2021a
- No non-standard hardware is required to run the codes.
2... |
0cf602af48a363de974ca413fa2f02cfc99f959ab6b7ecb9b1931ec6ad3af87a | Text | 1,034 | 38 | # DRS Dataset - Orthopedics
## File Name
DRS_meas_ortho.csv
## File Structure
5215 rows x 1532 columns
It contains all spectral measurements including Feature Names (i.e. Wavelength channel) and Class Labels, where
- Spectral measurements: 5215 x 1532
- Feature Name: 1 x 1531 (first row), which corresponds to wave... |
b6cebae67edb54fda0767b4ce2b1cf61d1bec5967cf652b4fd2dcea9c6bb4a7a | Text | 1,052 | 28 | Toric varieties of Picard rank 2
================================
This is a dataset of 200000 randomly generated toric varieties of Picard rank 2 with at worst terminal Q-factorial singularities, in dimensions 2 to 10.
The data consists of the plain text files "rank_2_dim_N.txt" where N, which is the dimension of the... |
2a0c412a243c27b29f4b0f71157bf55b91a42878c429ed7f238277875e859cb2 | Text | 1,089 | 51 | # Reverse engineering neural networks
[](https://zenodo.org/badge/latestdoi/266333834)
## Overview
This project involves MATLAB scripts.
<br>
Copyright (C) 2021 Takuya Isomura
(RIKEN Center for Brain Science)
<br>
2021-12-02
## bss
This is a supplementary material... |
a8a65d7b50b4762234879bb74709a6fe0f3c2fd543a286ecf2c881210ad907b9 | Text | 1,129 | 39 | # DRS Dataset - Orthopedics
[](https://zenodo.org/badge/latestdoi/591001156)
## File Name
DRS_meas_ortho.csv
## File Structure
5215 rows x 1532 columns
It contains all spectral measurements including Feature Names (i.e. Wavelength channel) and Class Labels, where
- Spec... |
54fc51523e10f4497348ee78beca00ff6a684b579210f052bc76a7aae5f05015 | Text | 1,197 | 34 | # A hybrid CNN-RNN approach for survival analysis in a Lung Cancer Screening study
**Note** Rearranging for public release
A hybrid CNN-RNN approach for survival analysis in a Lung Cancer Screening study
[[Link to Journal]](https://doi.org/10.1016/j.heliyon.2023.e18695)
DOI: 10.1016/j.heliyon.2023.e18695
## ... |
e34582b416bc9b49f75778d8643eb5e859afdfed5c8bc1787d78b120b3c88f2b | Text | 1,202 | 10 | # manifold-lin-dim
Code to calculate the linear dimension for manifolds from De & Chaudhuri (2023).
The directory structure of the code is the following:
Code for generating data from translation symmetric tuning curves are in the folder translation_symmetric.
circular_1d_uniform_tc_pca creates data from 1d trans... |
e69d614e167af86d07eb1e56774722d8ee34f324bb02f20b997c7f338224c666 | Text | 1,219 | 49 | # transmit
The aim of this package is to enable simulations of information transmission using Poisson processes and Bayesian inference as described [in this paper](https://github.com/tom-christie/transmit/blob/master/vignettes/Christie_and_Schrater_2019.pdf).
## Installation
```r
# Install the development version... |
a26f62d68623df68fd77c631808d4a26194994b9465e95e2ad11bdb5d423e690 | Text | 1,271 | 51 | # ProstateBrainMet_WGS_paper_figures
[](https://opensource.org/licenses/BSD-3-Clause)
This repository contains the code necessary for reproducing the figures and custom analysis in the following manuscript:
Evolution of Structural Rearrangements ... |
130519e0d14f10517c0861f7dd6da3c045c938ba57665d09b5e20aaed56157c5 | Text | 1,323 | 28 | # SEB3R Validation Dataset
## About
This repo contains all data used for the validation of MATLAB pipeline:
Whisker Nuisance test 3D for Rodents.
The script are available [here](https://gin.g-node.org/gchelini/SEB3R_pipeline).
**Note**: this dataset was generated through DeepLabCut and SEB3R! Original video track... |
b3433e61a90c863e0f107f13004c680f4bcb1519bf716e7b34d436cf8ec47413 | Text | 1,325 | 24 | ## FastQTL
This repository contains a modified version of the FastQTL QTL mapping software, with the following enhancements:
1. Options for filtering by minor allele frequency and minor allele sample count
2. Python wrapper for multi-threaded execution
3. Calculation of q-values (Storey) for FDR estimation (requires ... |
d0e6e96f8986ed649b8ead1a070a1c74558f7fb2f6fdbc8c1b0134922e36eb75 | Text | 1,326 | 66 | # Carbo-Tano_Lapoix_2023
## MLR stimulation in tail-free, head-embedded larval zebrafish
### Input data
* abf files with stimulation protocol
* avi file of larval behavior
### Analysis pipeline
1) Track larval movement using ZebraZoom
2) extractZZOutput.py
3) manualBoutSegmentation.py
4) fig2_3_syllabus
5) fig3_s... |
3793793759ec59d7d332b018b35e9b64947fa47dce9fbcfb6c2acd45d2be7b31 | Text | 1,347 | 17 | # A primer on Variational Laplace
This code accompanies the paper **A Primer on Variational Laplace** by Peter Zeidman, Karl Friston and Thomas Parr. <https://doi.org/10.31219/osf.io/28vwh>
## Standalone VL implementation and examples
A standalone implementation of the algorithm for MATLAB or Octave can be found in /m... |
256736066057251e669e9356e0c8cd6007978c35abe5f59ef322a89fd7b4bba5 | Text | 1,360 | 53 | # SONAR
SONAR is the algorithm of cell-type deconvolution for spatial transcriptomics
## Installation
#library(devtools)
devtools:: install_github("lzygenomics/SONAR")
## Dependence
- R version >= 4.0.5.
- R packages:
- this.path>=0.5.1; Matrix>=1.3.4; data.table>=1.14.0; Seurat>=4.0.3; matlabr=1.5.2; R.matlab=... |
24c01f7862fcdadd83ac2dda3ec3efffbd883fc820033b9b49093025c349eb90 | Text | 1,363 | 13 | This repository holds the data and source code for the following manuscript:
Mortberg MA & Gentile JE (equal contribution), Nadaf NM, Vanderburg C, Simmons S, Dubinsky D, Slamin A, Maldonado S, Petersen CL, Jones N, Kordasiewicz HB, Zhao HT, Vallabh SM, Minikel EV. **A single-cell map of antisense oligonucleotide acti... |
cb06538ffe56a2fc8bb4cb53af068338a6fc537fe0a91ff6fc6e1098aa09bb8b | Text | 1,366 | 26 | # In-vivo-Sholl-Analysis
Analyze in vivo sholl data from Imaris
Required software:
R and R studio: https://posit.co/download/rstudio-desktop/
Note this script was tested with R 4.0.0 and R studio 2022.07.1 Build 554. Updates to R may deprecate parts of the code. Please report an issue if so.
Required R packages:
ggp... |
8bd168e4b42ac4a2a5cb43fa2d33967233a96170ac67f5b6f86f60a9cdcdfc8f | Text | 1,410 | 27 | # nDeep for cancer prediction.
This repository contains the code for the paper "**A Study on Survival Analysis Methods Using Neural Network to Prevent Cancers**". ([Cancers](https://www.mdpi.com/2072-6694/15/19/4757))
Brief explanation of model architecture:
. Beyond L1 sparse coding in V1. PLoS computational biology, 19(9), e1011459. https://doi.org/10.1371/journal.pcbi.1011459
### Getti... |
f029e1dea0016f94b600e971eabeb4c933e5852bf3c837daa3f3401c7eb2c38c | Text | 1,436 | 22 | # kumar-sensorimotor-integration
## This is the code used to analyze the data presented in S. Kumar, A. K. Sharma, A. Tran, and A. M. Leifer, titled "Inhibitory feedback from the motor circuit gates mechanosensory processing in *Caenorhabditis elegans*".
The code is roughly divided into 2 sections: Real-time recordi... |
d99a91c1bca90afb453d4432ea43f6111d819f310b5756066d2e90c436411568 | Text | 1,437 | 33 | # Ubiquitous lognormal distribution of neuron densities across mammalian cerebral cortex
_Aitor Morales-Gregorio, Alexander van Meegen and Sacha J. van Albada_
___
This repository contains the code necessary to reproduce the figures from:
`A. Morales-Gregorio, A. van Meegen, and S. J. van Albada. (2023) Ubiquitous l... |
21bf54a1e04ec29108880e13976ff9b6abd79d85b2f9d09a516d4215f580c781 | Text | 1,452 | 54 | # ASD-DiagNet
This repository contains the implementation of ASD-DiagNet algorithm.
## Research article
Please cite the following paper if you use our work:
Taban Eslami, Fahad Saeed, Vahid Mirjalili, Alvis Fong and Angela Laird (2019) **ASD-DiagNet: A hybrid learning approach for detection of Autism Spectrum Diso... |
73fda012f7578bd8abe174f2f1dbdde6bf98a80e33651fbf3722c3aac6be034a | Text | 1,464 | 34 | # GPU_registration
this function perform drift correction of hyperstacks
# Parameters:
source path of the directory containing all the stacks you want to process (will all be processed in batch)
destination path of the directory to save all the registered stacks
Precision=1 or 2; % 1 means single precision for ... |
c02fed3542baa5a15c8d7711dae8d35ce862b053f32b137118acd1d9a0ba11bc | Text | 1,468 | 18 | ## OSC1Lite
**OSC1Lite is a 12 channel uLED stimulator board with precise and independent channel waveform control (currently only trapezoidal --custom waveform coming soon)**.
Request OSC1Lite and/or 2 sample [uLED probes](http://mint.engin.umich.edu/wp-content/uploads/sites/327/2019/08/PassiveOptoGen1Datasheet_V2.0... |
b9cbcaa87d4f54597be5573c20b658da925c249fd4ebcad16e8b3e8373511bf7 | Text | 1,472 | 21 | This repository contains the GWAS derived from modelA and model B using three different PD motor outcomes: MDS-UPDRSIII-TOTAL, MDS-UPDRSIII-LIMB, MDS-UPDRSIII-AXIAL
To open any of the following files, please unzip the folder, then use gunzip command line tool in linux to access the human-readable content
Each file ... |
f71b0de2da60039197d6844b6d3ae6e789800ca8d9577c5659416aa74eaf6088 | Text | 1,474 | 14 | # Different rules for binocular combination of luminance flicker in cortical and subcortical pathways (code)
These materials are a computationally reproducible version of the paper:
Segala, F.G., Bruno, A., Martin, J.T., Aung, M.T., Wade, A.R. & Baker, D.H. (2023). Different rules for binocular combination of luminan... |
96474e1b232dd3276490bcbe1223fc6ff9e33dcef441dc05bbd986bebeff339e | Text | 1,494 | 31 | # CxHp-2D
[](https://github.com/ScreenNeuroPharm/4Clusters/blob/master/LICENSE)
> The repository contains the data and the functions need to reproduce the analysis reported in the article "Multiple neuron clusters on Micro-Eelectrode Arrays as an in vitro mo... |
6b8ac6504c4c7d8c82ca1bf6123d08f7137daf5eaa139044d1d3f7b79dff773c | Text | 1,504 | 19 | # Brain model of associative recognition
This repository contains the model code associated with the following paper:
* Borst, J.P., Aubin, S., & Stewart, T.C. (under review). A Whole-Task Brain Model accounting for both Human Behavior and Neuroimaging Data.
In this paper we present a large-scale brain model (810k ... |
9adc728e9b4482e1cb5677e9ca115ccc034f01c678ad50f4b4691a42ff7d72ed | Text | 1,514 | 57 | ## NP Classifier
We typically will deploy this locally. To bring everything up,
you need docker and docker-compose.
### Local Server
#### Downloading NP Classifier Models
```
cd Classifier/models_folder/... |
10ddda282a8e75ee23abb73e30d2b0c1ca8ef24e21535a13e5493ec1bbf10a8d | Text | 1,551 | 25 | # Contractility Analyzer
The Contractility Analyzer is an open source ImageJ plugin designed to evaluate cell contractility experiments. It contains two modules.
## Spheroid Perimeter module ##
The Spheroid Perimeter module selects the largest cluster of connected pixels on a binary image sequence and returns its per... |
1f96f9951e0ad4ad16987908eff4625414217ddb7c442bf5149357b6d9d4a1d3 | Text | 1,580 | 83 | # Pycroscopy3D
---
[](https://doi.org/10.5281/zenodo.7660286)
Pycroscopy3D is a collection of tools for microscopy.
### Features
- Easy 3D-stack manipulation with [multipagetiff](https://github.com/mpascucci/multipagetiff)
- Straightforward extraction of... |
93ded300be0e16ea2cdee8bb2838a149e2da6291d2e84013709dcd3ccebd2ad5 | Text | 1,593 | 8 | This dataset contains experimental data from the mechanical testing of human brain specimens.
The data have been filtered (moving average and linear interpolation) and the load/unload curves averaged to approximate the hyperelastic material response for infinitely slow strain rates.
Every specimen folder contains data ... |
18de0566ca44a155d49670fd9696f3fa3aeb4bd9502ea78be954947ad9689017 | Text | 1,603 | 27 | # NeuronCounting
The code serves as a supplemental to our paper submitted to Frontiers Neurosceince. Please cite https://doi.org/10.3389/fnins.2023.1223226 if you find our method helpful.
The main code consists of several modules:
The first part defines parameters such as the path for the labelmap and classifier, th... |
1417ac5b8274f3738d536af4d2f115bf7bedfbf78579420e4c10dd0450b03d35 | Text | 1,625 | 49 | .. These are examples of badges you might want to add to your README:
please update the URLs accordingly
.. image:: https://api.cirrus-ci.com/github/<USER>/EEG-LTT.svg?branch=main
:alt: Built Status
:target: https://cirrus-ci.com/github/<USER>/EEG-LTT
.. image:: https://readthedocs.org/proje... |
e836f38b7f7d5cf5c3a383442471bb19ca1d95b1e2a0c1365d802007af1e0409 | Text | 1,628 | 71 | # Reverse engineering neural networks
[](https://zenodo.org/badge/latestdoi/266333834)
## Overview
This project involves MATLAB scripts.
<br>
Copyright (C) 2021 Takuya Isomura
(RIKEN Center for Brain Science)
<br>
2021-12-02
## bss
This is a supplementary material... |
d061465dc0ad819850403e414e6d9b0945eeb9eb74b5c990864f473cea744e78 | Text | 1,682 | 8 | ## Predicting the target-landscape of kinase-inhibitors using 3D convolutional neural network on densely covered chemogenomic data
Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J.P. de Esch, Bart A. Westerman
#### [Data](/data)
#### [S... |
9d09501b104fe9b425ab3d4cd789f2cf1013c20c882213ade00845a78c70712b | Text | 1,724 | 29 | # DEPRECATION WARNING
This repo is no longer under active development, and will be archived starting in January 2026.
For an up-to-date implementation of animal action segmentation algorithms see the [Lightning Action repo](https://github.com/paninski-lab/lightning-action/).
### daart: deep learning for animal actio... |
da7f1908ec097220dc7bb00984be6af9e92d0fc835258e19eb0ad19c246565af | Text | 1,724 | 11 | # Motor-Imagery
This database consists of 21 EEG signal collections from a single healthy adult male. The collections were performed on alternate days and each one consists of 60 trials of 8 seconds. In each trial, in turn, the motor imagery of the right, left or feet is performed. EEG data were collected through the g... |
51df8cf76e086034c7a9eeee37e9c557eade982057a96319f24431dcc7447370 | Text | 1,746 | 30 | # MANGEM
MANGEM (Multimodal Analysis of Neuronal Gene expression, Electrophysiology, and Morphology) is available for use
at https://ctc.waisman.wisc.edu/mangem.
MANGEM provides a step-by-step accessible and user-friendly interface
to machine-learning alignment methods of neuronal multi-modal data while enabling rea... |
ed51f2166285fe48581e7ab116e40ed1e3773b8d278c29277eb4f8b7fee770b8 | Text | 1,753 | 18 | # Diversity and evolution of cerebellar folding
Katja Heuer, Nicolas Traut, Alexandra A. de Sousa, Sofie Valk, Roberto Toro.
Data and code accompanying the manuscript "Diversity and evolution of cerebellar folding in mammals".
Neuroanatomical measurements and some complementary external data are provided in CSV file... |
00380d81bc01fda63f79744bfa759aa9dbed29e2e48c706686c8121364284a19 | Text | 1,778 | 51 | # Soruce code of DeepDendrite (built up based on CoreNeuron) and the demos in the paper.
src: source code of DeepDendrite and the modified NEURON simulator.
NOTICE: To perform AI tasks with DeepDendrite, we should use our modified NEURON simulator.
Figure5: Model used in Figure5 in the paper, i.e. spine-level hum... |
1211767d57d2dabf28090509cdf234c1740180ca4f237eef3d78ab33949fcc07 | Text | 1,804 | 29 | # transporter_density: vGlut transporter density in microscopy images
R tools for quantifying vesicular glutamate transporter (vGlut) immunofluorescence in two-channel microscopy images and reporting the results.
## How the quantification works
Illumination and imaging settings differ between recordings, so absolute... |
d1b090d684745609c39bdd089b99805f5952adb5472069012d8e1c5dc2f099bf | Text | 1,811 | 29 | # PF-SR
This repository contains an implementation of PF-SR, a 3D deep learning model for reduction of PF-related artifacts, and noise, and increase in spatial resolution of ULF MRI brain data.
Architecture of the 3D PF-SR deep learning reconstruction model
## Data preparation
Preparation of training data can be ... |
51506440081d17a63859932518de175035df6dbcd1e699d895ad3dafb6faa71c | Text | 1,859 | 29 | # EyeTracker
\
This MATLAB toolbox was created to work with SpikeGLX to detect the location and size of a pupil. It will run online pupil detection during video acquisition, and automatically synchronize videos by creating a lookup table that logs pairs of SpikeGLX timestamps with video frame numbers. It also provides ... |
ceb761dbb11c62918cb57f41e6254ead3f8d2e960ea393884755a4cdeaba91d1 | Text | 1,877 | 21 | # leafcutter
<img src="./docs/logo.png" width="200"> **Annotation-free quantification of RNA splicing.**
[Yang I. Li](http://web.stanford.edu/~yangili/index.html)<sup>1</sup>, [David A. Knowles](http://cs.stanford.edu/people/davidknowles/)<sup>1</sup>, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung ... |
511d9f1923e34de5eb7701acf9e751861cdd66317cf42de5cc0cef68cf873247 | Text | 1,929 | 44 | # MixfMRI
* **License:** [](https://www.mozilla.org/MPL/2.0/)
* **Download:** [](https://cran.r-project.org/package=MixfMRI)
* **Status:** [ has been published in Nature Communications!
# Requirements
Please download the dataset at https://doi.... |
9ce9410bb1bbb225dd9648fd8f1a4425d90359deeed479f8ba85e028ff2a7c1a | Text | 1,961 | 19 | # ECG-Synthesization
**Synthesization of P waves and QRST segments of simulated data**
The code combines separately simulated P waves and QRST segments to an ECG segments of 10 seconds (main function: synthesize_P_QRST_timeSeries). To achieve this, both the distance between the P wave and QRST complex and the dista... |
05453f9f1ad9f383988de090b29b2208416157238eb43f5c73551d36bfa73c67 | Text | 1,973 | 41 | # Benchmarking-the-Autoencoder-Design-for-Imputing-Single-Cell-RNA-Sequencing-Data
This repository contains the R and Python code to create the result in the paper 'Benchmarking the Autoencoder Design for Imputing Single-Cell RNA Sequencing Data'. The data used in this study is available at [Zenodo repository](https:/... |
2acc2e1ab042ed80fcd04647396b429031c5ab905132028364f084c5a6359a52 | Text | 1,984 | 38 | Copyright (C) 2023 Marjorie Xie and Ashok Litwin-Kumar
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distrib... |
15a7b551b1e063d4dff9b2cdc681a4a25516b05444cffccca9853ac883d0f942 | Text | 2,005 | 59 | # Automatic evaluation of atlantoaxial subluxation in rheumatoid arthritis by a deep learning model
This code is for [Okita, Y., Hirano, T., Wang, B. et al. Automatic evaluation of atlantoaxial subluxation in rheumatoid arthritis by a deep learning model. Arthritis Res Ther 25, 181 (2023)](https://doi.org/10.1186/s130... |
68aacbb577b12764b368cac8ddd41110f4a88a1cff6b4789312ba2faf26a0abd | Text | 2,047 | 26 | :bangbang:
**NOTE:** The CoreNEURON is now [integrated within NEURON](https://github.com/neuronsimulator/nrn/tree/master/src/coreneuron) simulator at the source level and hence all the latest development happens under the main GitHub project [neuronsimulator/nrn](https://github.com/neuronsimulator/nrn). To use CoreNE... |
72fc1fc416d2724adff6f4cd3fee8c1c14ccfd7072e6dfa8a27ad3442a1d1fd2 | Text | 2,081 | 53 | <!--
* @Author: ----
* @Date: 2022-04-09 11:57:47
* @LastEditors: GhMa
* @LastEditTime: 2023-05-02 19:35:49
-->
# Noisy Spiking Neural Networks
 to edit ridge and ravine lines on a surface. The curve and surface files are in VTK format (see "example" directory)
Ridge and ravine lines can be generated using [Crest Lines]... |
6077789b054d98d5522955f3ff4950a65bad24b93085239e55cfea6ca4a8f172 | Text | 2,120 | 78 | .. image:: https://travis-ci.org/wiseman/py-webrtcvad.svg?branch=master
:target: https://travis-ci.org/wiseman/py-webrtcvad
py-webrtcvad
============
This is a python interface to the WebRTC Voice Activity Detector
(VAD). It is compatible with Python 2 and Python 3.
A `VAD <https://en.wikipedia.org/wiki/Voice_a... |
27fc7eac8024202e9078454f288f7c2f9fcee2504195bf7b6aac17994513557a | Text | 2,134 | 81 | # Hybrid inference: Inferring fast and slow
[](https://opensource.org/licenses/MIT)
## Getting started
To install the relevant packages:
```bash
pip install -r requirements.txt
```
... |
a3d51563f20abe01633ae4d638c28548b841097fa1d310de04f452cc2cae218c | Text | 2,164 | 16 | # WHODAS 2.0 functionality prediction from digital biomarkers
Functional limitations are associated with poor clinical outcomes, higher mortality, and disability rates, especially in the elderly. Continuous assessment of patients’ functionality is important for clinical practice; however, traditional questionnaire-bas... |
d50df4b0c5c2d8228dd77044e1695f04fb7a59a6074647bf61976e0687e2f755 | Text | 2,220 | 27 | ## Variational Log-Gaussian Point-Process Methods for Grid Cells
Rule, M. E., Chaudhuri-Vayalambrone, P., Krstulovic, M., Bauza, M., Krupic, J., & O'Leary, T. (2023). Variational log-Gaussian point-process methods for grid cells. Hippocampus, 1–17. [doi: https://doi.org/10.1002/hipo.23577](https://doi.org/10.1002/hipo... |
7b049a721702e255baac9a08379f590342d08d91093a783a8c964b1feffdb330 | Text | 2,250 | 44 | # Perfusion-NOBEL
Pre-clinical DSC-MRI perfusion map generator written in Python. Optimized for the analysis of brain disease models in rats.
## Getting Started
This repository is a work in progress. Both the repository structure and source code are subjected to changes in order to make everythin more comprehensive... |
0f24c10ed01f7c96697aad9e0eb93ea24321a9823eb2b47d3195e05bbea126af | Text | 2,312 | 61 | Description
Codes for training and evaluating topographic neural network models (convolutional neural network and self-organizing map) and for analyzing the feature maps of the models.
System requirements
Operating Systems
Windows 11 Home
Software dependencies
Python
py... |
f6a059310c5a2ffaca3e1b1dddddaaaa2b6a18dcb9855fd8aa2c3622f2c5ac55 | Text | 2,334 | 44 | # Serial Section ET
Here we report an intelligent workflow for sub-nanoscale 3D reconstruction of intact synapses from serial section electron tomography.
Our workflow contains rapid ROI locating, automatic alignment, volume reconstruction, and semi-automatic synapse reconstruction.
Multiple intact synapses in wild-t... |
eb6ee1dbcf43ace9ff2f2c508fc9a76ae9f83a7327e70cf5ae2c5b79fe266d93 | Text | 2,365 | 63 | # Enhanced Fusion Convolutional Neural Network for Cross-Subject EEG Motor Imagery Classification
## Dependencies Required
-------------------------
* Python 3.7
* Tensorflow 2.1.0
* Pywavelets 1.1.1
* SciKit-learn 0.22.1
* Gumpy (https://github.com/gumpy-bci/gumpy)
* SciPy 1.4.1
* Numpy 1.18.1
* mlxtend 0.... |
2ffaa317bfc6c6fc4b63eaebaedcb3903b44083bf6333add834bfaae45cc11be | Text | 2,379 | 36 | <!-- [](https://github.com/mackelab/sbi/blob/master/LICENSE.txt)
[](https://doi.org/10.21105/joss.02505) -->
# Simulation-based inference for computational connectomics
This reposit... |
48fcd19113b54febff519534b89e92e933cb02bf58cd6539e12f6554a98db16c | Text | 2,382 | 73 | ## Capturing dynamical correlations using implicit neural representations
<img width="1368" alt="Screen Shot 2023-03-21 at 11 15 28 PM" src="https://user-images.githubusercontent.com/39596225/226817874-f7c4009e-f892-4563-afff-4a8265b3639a.png">
---
## Installation
1) Make a new local folder and clone the repository... |
af7b1033d3308cd8f9f9083f5d917381ba9afa9d27628f20d20722bfcec2e05b | Text | 2,397 | 43 | # Machine Learning methods for regional yield forecasting
Training various Machine Learning algorithms on satellite and meteorological data time series for regional yield forecasting.
Methods described in the paper [Yield forecasting with machine learning and small data: what gains for grains?](https://doi.org/10.1016... |
5e25c52044f0d87683553f2c206925673a95c687f4459a7dc7da4377f558a13e | Text | 2,492 | 31 | A. Quick Overview
- synthetic_2_5spk.tar: Synthetic dataset with 2-5 speaker mixtures
- aug_dataset3_5_spk.tar: Augmented dataset (i.e. real-world collected dataset + synthetic dataset) with 3-5 speaker mixtures. Real world mixtures are collected in anechoic and reverberant environments. No objects are placed on the t... |
f20a2de7461db38134a1fcb800c17ea317ff330536e722d7e794130e3744f997 | Text | 2,578 | 57 | # TorchMD
## About
TorchMD intends to provide a simple to use API for performing molecular dynamics using PyTorch. This enables researchers to more rapidly do research in force-field development as well as integrate seamlessly neural network potentials into the dynamics, with the simplicity and power of PyTorch.
Tor... |
da90f36ec47f7ce9afd62721ac6f013a1ba05efdb8bca8c9492277fbf8e66084 | Text | 2,586 | 71 | 
# Pando <img src="man/figures/logo.png" align="right" width="180"/>
Pando leverages multi-modal single-cell measurements to infer gene regulatory networks using a flexible linear model-based framework. By modeling the relationship bet... |
95528fdef8062564b39eb8c22ad9d470e8cf3c0f13d2ec04c5c0ef45a6a6a1aa | Text | 2,639 | 58 | # AI-enhanced numerical solvers
Updated! TODO!
By [Zhongzhan Huang](https://dedekinds.github.io/), [Mingfu Liang](https://www.mingfuliang.com/), [Shanshan Zhong](https://zhongshsh.github.io/) and [Liang Lin](http://www.linliang.net/).
The offic... |
41b02d74454dd9b4d466556258d51a1a5a1fddcc490cf81d10391e1effb9a528 | Text | 2,642 | 80 | # Polar Star
This code analyzes the read depth along long-read contigs and finds outliers.
## Dependencies
The Polar Star pipeline installs several common bioinformatics tools:
1. Htslib
2. Samtools
3. Bedtools
4. Vcflib
5. Minimap2
These codebases have serval system library dependencies. There is a shell scri... |
ab817dca2caede821069365eb3a61241ac00b551af014f7dabb76c295e761f06 | Text | 2,683 | 40 | # |openvibe repository| |README|
[](http://openvibe.inria.fr/)
[](http://openvibe.inria.fr/documentation/latest/)
[, [Hui Qu<sup>1*</sup>](https://github.com/huiqu18), [Yikai Zhang<sup>1*</sup>](https://github.com/hazaiisme), Mert ... |
3cd691b4696685b0047e9dab6dcf87be86898109bbfbaa5b062f8539b1973471 | Text | 2,746 | 48 | # LampreyBrainAtlas
## A comprehensive single-cell atlas of the sea-lamprey brain
This resource allows to interactively explore the single-cell atlases of the adult and larval sea-lamprey (*Petromyzon marinus*) brain obtained using scRNA-seq.
The atlas can be accessed here: [lampreybrain.kaessmannlab.org](https://lamp... |
fd4ea92b794189a0edecb50cb798136e960b19876b17944162bc9a3ba1d0eb84 | Text | 2,826 | 75 | # Lean Temporal Convolutional Neural Network for yield forecasting
Training temporal Convolution Neural Networks (CNNs) on satellite image time series for yield forecasting.
### Table of contents
* [Prerequisites](#prequisites)
* [Technologies](#technologies)
* [Setup](#setup)
 measurements from an auditory oddball task with an ITI of 2 s (session 1) and a luminance task in which discs with different shades of grey were presented. Also included are task inform... |
c737d1738790365b2b8c6b8e2af36d8ed602e2eeb5b275f4e1bc08bc92c0b3e4 | Text | 2,882 | 22 | # 2023-Eval-POCUS-ONSD
This repository contains the code and notebooks used in: Moore BT, Osika T, Satterly S, Shah S, Thirion T, Hampton S, Aylward S, Montgomery S. Evaluation of commercially available point-of-care ultrasound for automated optic nerve sheath measurement. Ultrasound J. 2023 Aug 2;15(1):33. doi: 10.11... |
3c8c1e20c083a43a70954e204d565d27ba97f2efbe09460af7e02e2e0b5cbb33 | Text | 2,886 | 53 | # Neuronal Cell Body Segmentation using Swin Transformer
This repository contains the official implementation of [Mohammad Shafkat Islam, Pratyush Suryavanshi, Samuel M. Baule, Joseph Glykys, & Stephen Baek. (2023). A Deep Learning Approach for Neuronal Cell Body Segmentation in Neurons Expressing GCaMP Using a Swin T... |
2cc57919c5487e359643740c711a5ad519c015ffac88c5623b97875b494d21fa | Text | 2,901 | 46 | # FIM_Eikonal
Extension of SCI-Solver_Eikonal by Fu et al. for simulation of anisotropic wavefront propagation in the heart. See `SCI-Solver_Eikonal/README.md` for a description of the Fast Iterative Method, references to the detailed papers, and author information for the original code.
tetFIM uses the fast iterative... |
fc71a11ccca74df86960bd8b826251b7d7cb5e2a573318a6a4a3fe98b9929f32 | Text | 2,918 | 55 | # MVLM-DTI: Multi-View Linear Manifold for Drug-Target Interaction
Official implementation of our manuscript detailing the **Multi-View Linear Manifold (MVLM)**. This repository provides the source code and inference engine to align pre-trained chemical and proteomic latent spaces for highly accurate, mathematically i... |
ba6bd68b7db0cf19571384bb05469b3db034ec8fa84ccf06871910c54d8b3f1c | Text | 2,995 | 82 | # SONAR: A Probabilistic Framework for Cell-Type Deconvolution in Spatial Transcriptomics
> **Important update:** This repository is kept as the original MATLAB-backed SONAR archive. A MATLAB-free R/Rcpp version is available at **[SONAR_R](https://github.com/lzygenomics/SONAR_R)**.
SONAR is an algorithm developed for... |
3ca4bc6b6498d5e92ca83a5330579d139c4bebc47249b6111a079ea00c764d2d | Text | 3,064 | 32 | # Code for replicating reported findings on: "Developmental Emergence of Neurogliaform cell Diversity"
#### Due to GitHub file storage limitations, source data for replicating this work is only accessible at https:... |
df9d8c3a3fb35520cfa2506b9a5d8c0ae492ac59b7a97a6feda634bfd57ab16c | Text | 3,068 | 65 | **ReactionDataExtractor** is a toolkit for the automatic extraction of data from chemical reaction schemes.
## Features
- Automatic extraction of chemical reaction schemes
- Segmentation of reaction arrows, conditions, diagrams and labels
- Optical recognition of chemical structures and text, parsing of reaction cond... |
80a8eb2d95bc0262b7290a497e8119ad286b56141cc0a89e1d9acaa176f4b16c | Text | 3,176 | 66 | # Allen Institute Visual Coding Dataset Saccade Analysis
*Primary Author: [Chase King](https://chaseking.me)*
This is the code used for the paper:
Saccade-responsive visual cortical neurons do not exhibit distinct visual response properties
Chase W. King, Peter Ledochowitsch, Michael A. Buice and Saskia E. J. de Vries... |
0f9d1c9b197ab241b36002e95b2ff7fd5c6c8cf267c28b325d6ff033dc6f5f95 | Text | 3,234 | 93 | # Histomic Atlases of Variation Of Cancers (HAVOC)
HAVOC is a versatile tool that maps histomic heterogeneity across H&E-stained digital slide images to help guide regional deployment of molecular resources to the most relevant/biodiverse tumor niches
## Cloud usage
Explore HAVOC on https://www.codido.co to run on th... |
26688b46ec427c62eee3d10b81ec97da271afc8992516fc433247c76cd2542a1 | Text | 3,243 | 71 | # ET-Tox
Adapted from https://github.com/torchmd/torchmd-net
## Installation
1. Clone the repository:
```
git clone https://github.com/torchmd/ET-Tox.git
cd ET-Tox
```
2. Install Mambaforge (https://github.com/conda-forge/miniforge/#mambaforge). It is recommended to use `mamba` rather than `conda`. ... |
81499aad0373a91f9572cc2b8808a5bffe07ffa1576170c04dc4f3af9b2c405f | Text | 3,281 | 59 | # TouchCog
## Hardware Requirements
Computer with 64-bit Windows, MacOS, or Linux Distribution (Debian, Ubuntu, Raspbian, etc.). ChromeOS Linux also supported.
For touch input, the system must utilize touchscreen technology (e.g. capacitive, IR, etc.)
## Software Requirements
In order to run the scripts, you will ne... |
e7d8ffc37f2aa684759fcaaa16298f45832ce5c53a425bebcd51e5494fa3bb8e | Text | 3,295 | 98 | # TriNet
## 1.Making predictions for sequences
### 1.1 Description
TriNet is a tri-fusion netural network for anticancer and antimicrobial peptides recognition. By inputting the peptide sequences and PSSM profiles, this software can use the pre-trained model to identify anticancer and antimicrobial peptides.
### 1.2... |
08048048e2c7a143f2f60ddaa48358194e7deb65d105265b489cd25c8258e7f3 | Text | 3,338 | 39 | <div align="center">
<img width="400px" height="100px" src="https://github.com/lutzroeder/netron/raw/main/.github/logo-light.svg#gh-light-mode-only">
<img width="400px" height="100px" src="https://github.com/lutzroeder/netron/raw/main/.github/logo-dark.svg#gh-dark-mode-only">
</div>
Netron is a viewer for neural netwo... |
7ae6c806fc622a7355d5c6785c29fe05f635d0948e09059d37e3171fa6673914 | Text | 3,370 | 68 | # Python implementation of STOI
Implementation of the classical and extended Short Term Objective Intelligibility measures
Intelligibility measure which is highly correlated with the intelligibility of degraded speech signals, e.g., due to additive noise, single/multi-channel noise reduction, binary masking and vocod... |
070ae1185fe54e7b4680676a900a53661d0f297fbfe9a001b92da1821985512e | Text | 3,457 | 95 | ### PatMap: Identifying Pattern Completion Neurons in Neuronal Ensembles
Darik A. O'Neil, Alejandro Akrouh, & Rafael Yuste.
PatMap contains code and a simple graphical user interface for detecting pattern completion neurons using the approach utilized in [Identification of Pattern Completion Neurons in Neuronal Ens... |
8ff762e755f833b46e01af411483be00da334c2a9af3b159e57d6dbd6d0c61e7 | Text | 3,488 | 70 | # Flystim is now deprecated and unsupported
We recommend switching to [stimpack](https://github.com/ClandininLab/stimpack), which includes and expands flystim functionality.
# flystim
[](https://travis-ci.com/ClandininLab/flystim)
**flystim... |
58d765327c7171599eee110fedfcfccdc7e2dc9be56bac8cff0c7074a857a991 | Text | 3,545 | 123 | # BoNE
Boolean Network Explorer
## Table of contents
* [General info](#general-info)
* [Systems requirements](#systems-requirements)
* [Installation guide](#installation-guide)
* [Demo](#demo)
* [Instruction for use](#instruction-for-use)
## General info
BoNE is a free, open source software
that can be used analyze b... |
2c59e0d9f3c6ebcd359c6a6f9969afc5f4cbb7e3f6d7ee67b8d3499eec0d947e | Text | 3,554 | 118 | --------------------------------------------------
# QuickNATv2
Tool: QuickNAT: Segmenting MRI Neuroanatomy in 20 seconds
-----------------------------------------------------------
Authors: Abhijit Guha Roy, Sailesh Conjeti, Nassir Navab and Christian Wachinger
The code for training, as well as the Trained Models a... |
4cb9b9546b921c0ff7b08619dabe57e9a2635042ea080f21ef5bbe49a3650b6a | Text | 3,573 | 24 | # Overview
Decoder-FFPE-seq is a dendrimeric DNA coordinate barcoding design for FFPE tissue-adapted spatial RNA sequencing by integrating RNA-to-DNA probe conversion with blotting-assisted barcoding, which establishes a robust, high-resolution, and accessible framework for sensitive ST profiling in fundamental and t... |
c6675d3f536318541983232fb8da1d330b8e9b071c2cda210a9842b20bb1ca6a | Text | 3,576 | 39 | # PUB-FeatureSelectionSuppl
# Supplemental Material
## File Name
1. fig_DRS_Spectra.tif
2. fig_OVR_Balanced_Accuracy_Compare.tif
3. fig_SHAP_Feature_Importance.tif
## File Description
1. Diffuse reflectance spectra measured from bone cement, bone marrow, cartilage, cortical bone, muscle and trabecular bone showing (... |
60a64be819044dc4eb0b3039879052b2908fcd844292acacc5b389dd7bfa2caa | Text | 3,600 | 86 | # YORO: Pipeline for LTR-Retrotransposon domains detection and classification using Deep Neural Network YOLO inspired
## Genomic Object Detection: An Improved Approach for Transposable Element Detection and Classification Using Convolutional Neural Networks
## Installation
<a name="installation"/>
We highly r... |
74131797f72dfafa87555119e9026a650a7c2905f5fd25b824cb3c9a923961eb | Text | 3,633 | 39 | # Structural differences in adolescent brains can predict alcohol misuse ([medarxiv link](https://www.medrxiv.org/content/10.1101/2022.01.31.22269833v1))
**ABSTRACT:** Alcohol misuse during adolescence (AAM) has been linked with disruptive structural development of the brain and alcohol use disorder. Using machine lear... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.