sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
78d6fc433c73ae98afdc8e36de5008919d1d176ff224ea1ab799f01813a2aec5 | Text | 1,480 | 13 | # WindTurbineHighSpeedBearingPrognosis-Data
Dataset for "Wind Turbine High-Speed Bearing Prognosis" example in Predictive Maintenance Toolbox.
The data is sourced from http://data-acoustics.com/measurements/bearing-faults/bearing-3/.
The data is provided under a [Creative Commons Attribution-NonCommercial-ShareAlike ... |
1147efbcc63d7215cd7e1d49a185293599c2a0cb3c11a569791887907c1c1e52 | Text | 1,505 | 31 | # CEP-seg: Automatic Segmentation of Cartilage Endplate (CEP)
## About
This code performs automatic segmentation of L4-L5 and L5-S1 CEPs from **sagittal UTE** (**U**l**t**ra-short **E**cho Time) **spine MR images**<br />
Segmentation is performed via a U-net ([Ronneberger et al., 2015](https://arxiv.org/abs/1505.045... |
e7253608b2639b5a6efb0539aaf5ee83aeb5eb3da9963b9c4188d7710b56fb36 | Text | 1,510 | 38 | 
# CenFind
**Cenfind** is a command line interface written in Python to detect and assign centrioles in immunofluorescence images of human cells.
Specifically, it orchestrates the detection of centrioles, the detection of the nuclei and the assignment of the centri... |
a7c6a5e013f1ac6e04f7b19d85ba872996ebe908fe3ab49502fe6bae87fc2132 | Text | 1,550 | 38 | # LPF-Defense
The Code and Data for the paper ["LPF-Defense: 3D Adversarial Defense
based on Frequency Analysis"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0271388), by Hanieh Naderi, Kimia Noorbakhsh*, Arian Etemadi*, and Shohreh Kasaei.
# Prerequisites
This code depends on the following pack... |
985aca9c5ae35e54845ef3feafc1b194a1442e433ea83359493542e5ce32506e | Text | 1,553 | 22 | # Version information
This is the version used for https://doi.org/10.3389/fnins.2023.1074730 . The newest version is available in the matmri toolbox (https://gitlab.com/cfmm/matlab/matmri).
# Summary
The code in this repository is for performing a free-water elimination algorithm for the fitting of microscopic fracti... |
86532267c5b803575152e1ef68714f14c516ffae0f13287e59cbe95327516772 | Text | 1,558 | 43 | # EEG_vbcEnKF_mEI_est
[](https://zenodo.org/doi/10.5281/zenodo.10109708)<br>
There are sample scripts of model baseed E/I balance estimation method using vbEnKF in Neural mass model with parameter constraint.
<br>
<img src="./GraphicalAbstract.png" width=100%>
# Authors<br... |
4689b0f4521638aa2eaae43e825181955c7018f470ab0cbdc6c3c45f4b17ba33 | Text | 1,622 | 27 | ## README
This repository contains the simulation source code and example data analysis scripts for the following article:
L. Kang, J. Ranft, and V. Hakim, Beta oscillations and waves in motor cortex can be accounted for by the interplay of spatially-structured connectivity and fluctuating inputs, eLife (2023)
### S... |
93d989eca62e62601c51ae696c3f908ff1cb3e751db7e2b3a8330a2848169b8a | Text | 1,648 | 43 | # Spike-to-Fluroscence model of jGCaMP8 sensors
author: Ziqiang Wei
email: weiz (at) janelia (dot) hhmi (dot) org
## Introduction
This repo includes the codes for a variety of spike-to-fluroscence models and
fluroscence-to-spike models that were used to evaluate the performance of newly
developed [jGCaMP8 sensors](... |
87711015a0c649c5ccf4471d113d6a1cde53c0d6b0e6e686f55311c3381817b2 | Text | 1,656 | 45 | # MRI-DST
This project consists of two parts, Mask R-CNN based model and C3D-based-model. Mask R-CNN based model is used to segment the images. These segmented images is then fed into the C3D-based-model along with the remaining attributes to predict the probability of ≥3 linear stapler cartridges.
To protect patient ... |
cb57bb906d6a20617fd79e6170fb00dfa8e9b794a5d7b9997c7e59bcf4822398 | Text | 1,675 | 28 | # Supplementary Code
This directory contains supplementary code to the paper ["Longitudinal modeling
of age-dependent latent traits with generalized additive latent and mixed models"](https://doi.org/10.1007/s11336-023-09910-z). The actual data cannot be shared due to privacy, so we have instead created simulated dat... |
121d6aaa83748f2983a5cade2560fe014f154b6afa966acdd9b170bd3c084e5d | Text | 1,683 | 31 | # Installation instructions
## Installation requirements
hd-gliomouse only runs on Linux. You need a pytorch capable GPU with 4GB of GPU memory to run hd-gliomouse.
1) We strongly recommend you install hd-gliomouse in a separate python virtual environment. [Here is a quick how-to for Ubuntu.](https://linoxide.com/linu... |
d0a7207e6cbdd14041deadb522f493b81b39dd5a0350b29712228f27c7fbce70 | Text | 1,683 | 51 | # GRNOpt package for R
Gene Regulatory Network Inference Using Optimization
GRNOpt infers Gene Regulatory Network (GRN) from booleanized transcriptomic data and Prior Knowledge Network (PKN) using optmization methods. The package also includes methods for simulation and visualization.
## Installation manual
### D... |
4e8be948c3598c97c5f5c551d1b0f99bd6d86c39487dfb32dfa8e91ab36e2601 | Text | 1,687 | 31 | # Population Modeling and Mental Health Prediction: Replication Paper Code and Results
This repository aggregates the code and results data for the forthcoming paper:
"Population modeling with machine learning can enhance measures of mental health - Open-Data Replication" (2022). Ty Easley, Ruiqi Chen, Kayla Hannon,... |
f52c96496db6f6abd6a645c97a2373b5ea7659d3631a921276b3e0950902a6d8 | Text | 1,694 | 24 | # **Human-specific Genes with LncRNA-origin Encode Unique Human Brain Development**
## Introduction
Although gene duplication was considered as the predominant mechanism for the origin of new genes, we and other have proposed that new proteins can also evolve *de novo* from ancestral loci encoding lncRNAs. As mRNAs a... |
efb67e15e7e6dfc91f612317f3ff8faf8169f0190a4f2241d8953d7c40042511 | Text | 1,708 | 21 | # EyeEvaluationSourceCode_Extra
Additional Codes for Image Evaluation, Image Selection from Data Bases and Confusion Matrix Plotting
Image Evaluation (Optional)
-Check that the file 'netTransfer.mat' is in the working folder if it is not in the folder, look for it
-Load the test folder in the working browser... |
3d63e7f273db3f7204219a0e9383789ec5cc02ca9efacc39b8bf978c61e5a7be | Text | 1,711 | 29 | # Contrastive-Explanation-Method
Codes for reproducing the contrastive explanation in “[Explanations based on the Missing: Towards Contrastive Explanations with Pertinent Negatives](https://arxiv.org/abs/1802.07623)”
To find the pertinent positive (PP) of an instance,
```shell
python3 main.py -i 2953 --mode PP --k... |
6a91250b17d8075583f3070b4cd6b6936f62adf80e0d82661504993445a38dc9 | Text | 1,716 | 39 | # Object Detectors Involving a NAS-gate Convolutional Module and Capsule Attention Module
- This code is an official implementation of '*Object Detectors Involving a NAS-gate Convolutional Module and Capsule Attention Module*' base on the open source object detection toolbox [mmdetection](https://github.com/open-mmlab... |
0efa250feae27bd509848c19742f0eb6de8eb4643299c65794eaef83f95ee42b | Text | 1,730 | 43 | # Welcome to BrainGENIE!
```
Developed using
______
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
______
```
## Clone this repository with:
`git clone https://github.com/hessJ/BrainGENIE`
## Install dependencies for BrainGENIE with the command in con... |
5e21826c6364016c9d4ee5f194c9b8b06a35a8b89f448375396a7b1a5198d44c | Text | 1,734 | 56 | # gatk4wxscnv
Pipeline for WXS CNV using GATK4, based on https://gatkforums.broadinstitute.org/gatk/discussion/9143/how-to-call-somatic-copy-number-variants-using-gatk4-cnv
## Requirements
- Python3.6
- R and packages(`naturalsort`, `getopt`, `optparse`, `DNAcopy`)
- Java1.8
- GATK4
- Bedtools2
## Simple run
```bash
... |
6a8fb8efa87bc76f96aeda846c6177bab80f64a21417e2453383ecaf8edce4a2 | Text | 1,743 | 48 |
# rsRNASP
rsRNASP: A distance-dependent statistical potential based on residue separation for RNA 3D structure evaluation
The potentials were set to a high value of 30 kBT for atom pairs within 3 Å to exclude the structure candidates with severe steric conflicts; updated on July 23, 2024.
# Compilation and usage un... |
10d0e48cb5b1baa5aa946a4c72ad89ca5ec650645792d87365f488b42ad1fbfc | Text | 1,759 | 25 | # Eelbrain
[](https://zenodo.org/badge/latestdoi/3651023)
[](https://github.com/christianbrodbeck/Eelbrain/wiki/Installing)
| Stable | Pre-release |
| ------ | ----------- |... |
7d18f27fa6c100c7bce4b947f1da9ea671916d371c7ece26690c2bb5592c6e2b | Text | 1,768 | 45 | # FACEAI - Testing defacing tools
Code to test existing defacing tools with MRI/PET/CT in head&neck cancer patients.
## Datasets used
Here list of datasets from TCIA.
## Installation
Tools and dependences listed here below:
### Python environment
Run script setup.sh in software/external.
Activate environment wi... |
3459b9f2f494736cca7dd6ddaf1824b5ddeffe5f03b64dfc8fa37b16ccfdeec9 | Text | 1,822 | 39 | # Straw: rapidly stream data from .hic files
Straw is library which allows rapid streaming of contact data from .hic files.
This repository contains source code for the C++, R, Python, and MATLAB versions of Straw.
- For the Java version, see: https://github.com/aidenlab/java-straw/
- For the Javascript version, see:... |
80518242e39c6f2210fc0e492bbc78480848655a9b4fb5124a71a5c469688e92 | Text | 1,823 | 45 | connectome_analysis
==============================
Scripts to manipulate, process, and analyze the Drosophila larval brain connectome
Installation and setup
--------
The associated tools in connectome_tools_deprecated have been reimplemented in the connectome_tools repo with updated features, https://github.com/mwindi... |
a824682c95f0140f555de18aeac9220d0e17ce1f9c1d9737efb41b9cbcd2e003 | Text | 1,830 | 68 | # Codes that reproduce the computational model of Bilash et al manuscript.
Enter `_codes` directory.
## mechanisms
This directory contains all .mod files that are used in the hoc neuronal models.
## poisson inputs
Python script that generates theta-filtered poisson inputs.
## Python scripts
### `{cellname}_cell... |
62142899f1e2eb7a8bc07a5f57c4e609bf6cc05f0e4f5b62a73abe8752196eb3 | Text | 1,831 | 86 | # Psi Phi Quantum Mechanics (ppqm)
Simple bridge between RDKit and quantum chemistry (QC)
packages.
## Installation
```bash
pip install ppqm
```
## Example
All examples assume an RDKit molecule object with hydrogens and a 3D conformer:
```python
from rdkit import Chem
from rdkit.Chem import AllChem
molecule = Ch... |
9c782e52e531197c723f73b3d3da83f8312a15cb981e1deaf88e3952055d8f4f | Text | 1,837 | 13 | # Deep-Brain-Stimulation: when to go directional?
## Abstract
**Background:** Directional deep brain stimulation (DBS) allows for steering of the stimulation field, but it is currently unclear in which cases directional current steering might offer an advantage. Furthermore, extensive and time–consuming testing of al... |
06a99bf6fb7178109da0070a85489e7c49cd8dabb81dcaced110ac5e1d6fc93a | Text | 1,839 | 33 | # Stokes: create triangulated surface meshes and solve hydrodynamic Stokes equation
This is a collection of Python packages previously used to solve biological hydrodynamics problems, see references [3,4] below
- `FBEM`: routines to solve Stokes equation using a third-p... |
f863bed0e3436e343524f3ea3e61bd96d73481ed1abf4a152c1ee3baadd5fc30 | Text | 1,845 | 24 | # Roof-Type-Classification
Roof Type Classification with Innovative Machine Learning Approaches
Abstract
In this study, roof type classification was made with a small number of examples for training, in accordance with the one-shot learning approach and using the "Siamese Neural Network" method.
The images used for ... |
d00c4e90bb41e271f8405e3570ce7dea48cd7b6197303252a7738849267a105e | Text | 1,849 | 33 | # RasterUniqueCharacterizationCode
### Replicating figures
All original figures and results in Deshpande, Smith, & van Drongelen (2022, submitted) were created using [Matlab (Mathworks)](https://www.mathworks.com/products/matlab.html) R2021b, and can be replicated by running the appropriately named script in the `mat... |
addf10cde583dcc4431489912867d4dbacad9bf0fd2e5cba6cd37c817cea7045 | Text | 1,854 | 36 |
# scalable, interpretable Variational Autoencoder (siVAE)
siVAE is an extension of traditional VAE that learns feature embeddings that guide the interpretation of the sample embeddings, in a manner analogous to factor loadings of factor analysis/PCA. siVAE is as powerful and nearly as fast to train as the stan... |
9f0cef7a7d47d1c4701ca61820486c7741064714558217635c659cb3ac10c567 | Text | 1,858 | 29 | # polychrom
[](https://zenodo.org/badge/latestdoi/178608195)
## Open2C polymer simulation library
This library is designed to easily set up polymer simulations of chromosomes subject to a set of forces or constraints.
Polychrom is designed to build mechanistic models - ... |
e06ba72f9b9b9656128a570f219233d87d6017cb7d9560ebee6c408d9cf276bb | Text | 1,872 | 34 | # Description
Experiment and visualization code for the paper: "Parametrizing Analog Multi-Compartment Neurons with Genetic Algorithms" (in review).
The main part of the experiment is to find the appropriate inter-compartment conductance and leak conductance on the neuromorphic computing platform BrainScaleS-2 using ... |
ed59bd12bb6c40977268327f02826ade0f0e2b26f9ac6158bd1a0998b948b369 | Text | 1,876 | 48 | # Hierarchical Depression Symptom Classifier
This repository contains the implementation of the model used in [Towards Automatic Text-Based Estimation of Depression through Symptom Prediction](https://www.researchsquare.com/article/rs-2096670/v1).
Before you can run the model, you have to obtain the DAIC-WOZ corpus. ... |
32d0dc8a560f9c0179380a38bbe1b210c4b9fd00d038c6c49439e1e58324a938 | Text | 1,878 | 56 | # WMHpypes
Nipype implementation of WMH segmentation pipelines.
## Interfaces
* ### sysu_media
the winning method in MICCAI 2017 WMH segmentation challenge orginal work repository: ([wmh_ibbmTum](https://github.com/hongweilibran/wmh_ibbmTum))
## Installation
### As a python library (pip)
```
conda create -n wmhpyp... |
5aaeb5233cb49f00da4948702359d226096f4f7ded524fe930af78e51db690ef | Text | 1,886 | 19 | # CFAS-ranking-code
CFAS Neuropathological Assessment of Dementia Using Machine Learning Feature Selection (Python Code Scripts)
### Two folders are included:
1. Data: two main files are need to run the scripts (CFAS_NeuropathologyData May 2018.xlsx) and (CFAS_ClinicalData.csv) and the rest of files are already in ... |
54f2d96433a7936c8853c7f47fed02ac62e25f3cd1c29bb39488da9ecb3f0868 | Text | 1,890 | 26 | # Self-supervised End-to-End Landmark Detection and Matching
Code for the paper *[An end-to-end deep learning approach for landmark detection and matching in medical images](https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11313/2549302/An-end-to-end-deep-learning-approach-for-landmark-detection/10.111... |
79138cbdb110e865ed900e420b219f935ba6419ff7aed2bbd6f4b0e063899a58 | Text | 1,919 | 25 | # Reversible inactivation of ferret auditory cortex impairs spatial and non-spatial hearing
Stephen M. Town, Katarina C. Poole, Katherine C. Wood and Jennifer K. Bizley
Ear Institute, University College London, London, UK.
## Get started
### 1. Read the paper
The full report is included with this repository as a [... |
6f98bdfcdd26758db61bcbd9a8482904867e25f43e859ca7e0c64d346a1cb7b9 | Text | 1,941 | 49 | Dendrify
========
*Introducing dendrites to spiking neural networks*
.. image:: https://img.shields.io/pypi/v/Dendrify.svg
:target: https://pypi.python.org/pypi/Dendrify
.. image:: https://readthedocs.org/projects/dendrify/badge/?version=latest
:target: https://dendrify.readthedocs.io/en/stable/?badge=stab... |
b9bb8366f365e6e78e075134be5b810997dc993f1c6b9d0a5f93fb7be029fe48 | Text | 1,941 | 54 | # NIRSimple
> fNIRS signal processing simplified
*NIRSimple* is a Python 3 package for fNIRS with a focus on signal processing. It gives control on preprocessing and processing, enabling to adjust parameters and use different methods from the scientific literature.
This package handles data as numpy arrays. It can b... |
cb684643be0f86505c68f5eb279093dd68f61fb0bcd02f582c0bf86000f6385f | Text | 1,948 | 46 | # mnl_ccepAge
This repository contains the scripts and functions necessary to reproduce the analyses and figures in this manuscript:
- **Developmental trajectory of transmission speed in the human brain.** D. van Blooijs*, M.A. van den Boom*, J.F. van der Aar, G.J.M. Huiskamp, G. Castegnaro, M. Demuru, W.J.E.M. Zweip... |
13f1cee5b09f83b23132778ab76180bbc9b2bd82bd2a67431700dd5a5426ef30 | Text | 1,965 | 52 | # EphysAFM
## Description
This is a python package written to analyze atomic force microscopy and electrophysiology data collected in tandem from the manuscript "The energetics of rapid cellular mechanotransduction". An example analysis pipeline can be found in the Jupyter notebook file "EphysAFM.ipynb".
![EphysAFM](... |
c25700b7611448f31fc58bb61f9df4bc4bc267c8c36903f9dfe440b274a38481 | Text | 1,965 | 25 | For plotting figures, download data: "Figure_Souce_Data.mat";
For plotting Supplementary figures, download data: "SupFigure_data.mat";
_____________________________________________________________________________
For analyzing partial correlations (fig.7)
1. download data file: "Fig7_PartialCorrelation_example.mat"
2. ... |
19454a0bde43292cee8cf779558f681f12f42a67d9ae672fc1e8c09b2a9247c4 | Text | 1,966 | 50 | # Kong2022 ArealMSHBM Parcellations and FC
References
==========
+ Kong R, Yang Q, Gordon E, et al. [Individual-Specific Areal-Level Parcellations Improve Functional Connectivity Prediction of Behavior](https://doi.org/10.1093/cercor/bhab101). Cerebral Cortex. In press.
----
Data
====
In this study we utillized HCP ... |
47a708b2e6bc28c3685603934665a5ee39228ca0e49398fa10eaf125c03cbf0e | Text | 2,006 | 25 | # PredictionOrientationSelectivityMouseV1
The underlying code for the manuscript :
Expectation violations enhance neuronal encoding of sensory information in mouse primary visual cortex.
Authors: Matthew F. Tang, Ehsan Kheradpezhouh, Conrad C.Y. Lee, J. Edwin Dickinson, Jason B. Mattingley, and Ehsan Arabzadeh
Cit... |
b5feb625113954d74aa4931d3523654e3afb98009cbae9cbe825d524b8bb83bb | Text | 2,006 | 37 | # PfAbNet-viscosity
This repository accompanies the manuscript "Low-Data Interpretable Deep Learning Prediction of Antibody Viscosity using a Biophysically Meaningful Representation." The code and notebooks in this repository can be used to train PfAbNet-viscosity models, generate test set predictions and reproduce all... |
78781cc00fb8caa66c8f2f5fbcb752c4cfa1f6955ddc2d9d3098a41acf9e6659 | Text | 2,052 | 42 | connectome_tools
==============================
tools to analyze connectomics data from a CATMAID instance; includes modified scripts from neurodata/maggot_models by bdpedigo and from mwinding/connectome_analysis
Installation and setup
--------
connectome tools can be installed via pip:
```
pip install git+https://... |
902bc5a7d745b9838a6d66e89837b82c0e22105181a12730ff501679fb33256f | Text | 2,056 | 76 | # Synaptic-Self-Organization-of-Spatio-Temporal-Pattern-Selectivity
This repository contains the codes to implement the model described in the manuscript "**Synaptic Self-Organization of Spatio-Temporal Pattern Selectivity**".
**To reproduce the results, follow the steps below:**
Extract the Folder.zip into the ... |
b3422e6a1f7f5e0b2d02b35921eefe1da60c419871a694733fcb104de27660a0 | Text | 2,067 | 26 | # SAFER (Socially-Aware Fake News Detection Framework)
This repository contains the official code for the paper [Graph-based Modeling of Online Communities for Fake News Detection](https://arxiv.org/abs/2008.06274)
## Abstract
Over the past few years, there has been a substantial effort towards automated detection of ... |
784a3f3e2a6cba4a86956c05f6547ad7a1314d37803ecdef93fe5763b1ca923e | Text | 2,094 | 53 | # Using Graph neural networks to predict single neuron firing rate responses in in-vitro networks
This repo stores both computing scripts and data used to generate results in the paper: https://www.frontiersin.org/articles/10.3389/fninf.2022.1032538/full
# Installation
An exact copy of conda environment is provided... |
0b9d07ff661062de4d6860c7629591bdcd54f32316938f768a0c8d3c9311e33d | Text | 2,101 | 94 | # ECOSYS
The ECOSYS model for terrestrial ecosystem biogeochemistry
The code is developed by Professor Robert Grant at University of Alberta.
Jinyun Tang (jinyuntang@lbl.gov) helps maintaining the code on github.
# Download
git clone https://github.com/jinyun1tang/ECOSYS.git
You can also make a fork using the for... |
49736f64c914b60663ef7e99c34492a5adc72d23492aa011e2d762f577bdddc0 | Text | 2,103 | 19 | # vhlab-TwoPhoton-matlab
VH Lab tools for analysis of calcium imaging data
`RRID:SCR_023369`
## Papers
(Not an exhaustive list)
1. Li Y*, Van Hooser SD*, Mazurek M, White LE, Fitzpatrick D. Experience with moving visual stimuli drives the early development of cortical direction selectivity. Nature. 2008 Dec 18;456(... |
0846747dd764db3376fdd9c8a2f88da8a5d3c186899cc283e8d8d4ee1954ca64 | Text | 2,118 | 12 | # Neuronal-Network-Inference-with-Reservoir-Computer
Code to build and train a reservoir computer to infer neuronal connectivity from calcium fluorescence time series data of *C. elegans* neurons.
This repository contains a MATLAB code (elegans_network_inference.m) demonstrating a minimal example of a Reservoir Comput... |
a5cb08993eb2f6e74f2a27a6d2037894c80ab26bbec52968152b26267b57715a | Text | 2,138 | 67 | # Finnish Parliament Data Tools
[][license]
[][tests]
[
[Publication in Scientific Data](https://www.nature.com/articles/s41597-023-01974-x)
# GraphXAI
As explanations are increasingly used to understand the behavior of graph neural networks (GNNs), evaluating the qua... |
c42b6d00414ac959350cd4c0c396ae647d11cf4da2234c6275c70380c652b3fb | Text | 2,180 | 59 | # Rand and adjusted Rand index for MATLAB
[](https://github.com/cmccomb/rand_index/actions/workflows/tests.yml)
`rand_index` measures agreement between two cluster assignments. It returns the
Rand index by default or the adjus... |
7e16cc6cf8962eda0648e1147ec8dedb75091cea5a2c9d41bd2cb999bf5c037f | Text | 2,185 | 45 | # New second generation model available
We have published a new model called sciLaMA that extends and outperforms siVAE, to be published in ICML 2025, preprint available here:
https://www.biorxiv.org/content/10.1101/2025.01.28.635153v2.abstract
The associated GitHub repo is here:
https://github.com/microsoft/... |
1d70ee596bda2cc59898bcd1a61ff39e8ea62ceaab00911c71ddb56aaf8fefc8 | Text | 2,204 | 39 | # EASI-FISH Nextflow Pipeline
[](https://www.nextflow.io/)
[](https://www.docker.com/)
[![Run with Singularity](https://img.shields.io/badge/run%20wi... |
73ae0c480ebfc72148052019a1a516e0902738e87de6343c334d12d76915e175 | Text | 2,205 | 15 | # Overview
Code for analyses presented in "Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications".
# Data availability
Processed data is available at https://www.synapse.org/TFBSglioma
# Abstract
Gliobla... |
6d3fcd3f1c044ca9a6d843e2e6dd3633e04e1f589ed5a99aa518d8dbb551c30b | Text | 2,219 | 67 | # rescoss_logp_ml: Machine intelligence models for fast, quantum mechanics-based approximation of drug lipophilicity
[](https://github.com/cisert/rescoss_logp_ml/actions/workflows/build.yml)
[](https://github.com/psf/black)
[](https://github.com/Pugavkomm/cgtasknet/actions/workflows/main.yml)
# cgtasknet
## Table of Contents
[Ab... |
dc17561c61cf7f92a7601432da611ac45637774dcb874fb1a1e5c83d4e01702a | Text | 2,250 | 67 | # rescoss_logp_ml: Machine intelligence models for fast, quantum mechanics-based approximation of drug lipophilicity
[](https://github.com/cisert/rescoss_logp_ml/actions/workflows/build.yml)
[ (yes, we changed the name!) for an up-to-date version with new and improved features.**
](https://travis-ci.org/bonej-org/BoneJ2)
# BoneJ
BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology. It provides free, open source tools for trabecular geometry and whole bone shape analysis. This repository hosts the modern inc... |
b1d38fb3d20da9f35ebc0c0120ac7c0c967239c5e5a95c0dc402e4aa8c9ee400 | Text | 2,286 | 71 | # scPrisma
scPrisma is a spectral analysis method, for pseudotime reconstruction, informative genes inference, filtering, and enhancement of underlying topological signals.
<!-- Manuscript -->
## Manuscript
[Karin, J., Bornfeld,... |
a57dab0b6302b497bfb03a34425ef25f915fcb3ff8a9945e9c4615ad06257153 | Text | 2,302 | 24 | # abcd_fmriprep-analysis
Download ABCD MRI data convert the DICOM data to BIDS format, preprocess the BIDS data with fMRIPrep, and denoise it with 3dTproject.
## Download
`download/` contains scripts to download ABCD magnetic resonance imaging (MRI) data and convert the DICOM data organization to fit the Brain Imagi... |
6095351feb14a0948da0b43336fbf1d9c67cb732aebc10664655dc99a1ef8a41 | Text | 2,337 | 43 | # Tracking_Functional_Network_Connectivity_Dynamics_in_the_Elderly
This is code repository for the paper: "Tracking_Functional_Network_Connectivity_Dynamics_in_the_Elderly", mainly for the results visualizaiton
***There are 6 .py in this repo, each of which respectively corresponds to the 5 steps in the flowchart ab... |
7f99497ee43e83d7925add48ea39210794af1e29a7067ccce254cf795b8ed7d9 | Text | 2,337 | 22 | [](https://github.com/bonej-org/BoneJ2/actions/workflows/build.yml)
# BoneJ
BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology. It provides free, open source tools for trabecular geometry and whole bone shape anal... |
d33693186af9316cfb7e10007192b7b650ba1d6af09ade39567968883a91b151 | Text | 2,344 | 55 | Connectome topology of mammalian brains and its relationship to taxonomy and phylogeny
==============================
## Paper abstract
> Network models of anatomical connections allow for the extraction of
quantitative features describing brain organization, and their comparison
across brains from different species.... |
400bf6898cbcf3eab1099280c8c79d8baf86c99dad5836c6f5294ac86efd6462 | Text | 2,377 | 39 | # Rethinking Gradient Operator for Exposing AI-enabled Face Forgeries
Zhiqing Guo<sup>1</sup>,
Gaobo Yang<sup>1</sup>,
Dengyong Zhang<sup>2</sup>,
and Ming Xia<sup>1</sup></br>
<sup>1</sup> Hunan University, China;
<sup>2</sup> Changsha University of Science and Technology, China</br>
<img src="GocNet.png" alt="dem... |
1caa682a1823da42d34115cb5d73f41bc7fc25ba3299ea99cd10a619f0ca1d0c | Text | 2,379 | 48 | ## Predicting Phenotypes From Novel Genomic Markers Using Deep Learning
NovGMDeep is a one-dimensional deep convolutional neural network model for genomic selection. It predicts phenotypes using novel genomic markers to reduce the curse of high dimensionality of SNP data. The model avoids overfitting by applying the c... |
db3db249a2a1b401b16fd31ff9d4f2e50b09ae1ee9a097c39a5b73740767e5ce | Text | 2,429 | 24 | # TQIP
Code accompanying the paper "Assessing the Utility of Deep Neural Networks in Dynamic Risk Prediction After Trauma"
We have published five Jupyter notebooks:
* [Data preprocessing](https://github.com/alexbonde/TQIP/blob/main/1_Data_preprocessing.ipynb)
* [Pre-Hospital Model](https://github.com/alexbonde/TQIP/b... |
bc4608bc87184870842eaa36424707d3e8071db4732165e11996fff3c0255b45 | Text | 2,442 | 44 | # Information-Bottlenecks-in-Rapid-Motor-Behaviour
Analysis and figure generation code for the paper "Capacity Limits Lead to Information Bottlenecks for Ongoing Rapid Motor Behaviour."
[](https://doi.org/10.5281/zenodo.6326269)
## Note about licenses
Th... |
9f524d3e169b85bbd1206b693b44a10b8166bd6f9f7376194ca0f62d64efa375 | Text | 2,447 | 45 | # Brain Data Standards Queries
A repository for the Brain Data Standards Ontology services, queries and dumps. These queries are utilized to build dumps of the BDS ontology in json format. Provided dumps are indexed to the Solr and can be queried by the provided RESTful services.
* Dumps can be found in the [dumps](du... |
113fb241e0f60181d0d2d83a8c607d0060f0b9b26906bf984ddafbe1819bedac | Text | 2,457 | 84 | # VCD-Net
High-efficiency light field microscopy reconstruction for VCD-LFM. *todo: add reference*
### This package contains:
1. /datapre: Matlab scripts (GUI interface provided) for VCD-Net training dataset synthesis
2. /vcdnet: Source code for deep-learning based light field microscopy reconstruction
### Require... |
4dbcfa4d3f62cf6d91356b574c37222bb1cd644319fe35be6706a720201cef87 | Text | 2,458 | 51 | # MesoNet
You can find here the implementation of the network architecture and the dataset used in our paper on digital forensics. It was accepted at the [WIFS 2018 conference](http://wifs2018.comp.polyu.edu.hk).
> We present a method to automatically detect face tampering in videos. We particularly focus on two rece... |
5fb903b105a05cd64c3a4557fc941dbe2043ec56d706aca22f7ef150d68889cc | Text | 2,464 | 40 | # epsych
## NOTE THAT THIS REPOSITORY IS FULLY DEPRECATED AND HAS BEEN REPLACED BY EPSYCH2 [https://github.com/dstolz/epsych2](https://github.com/dstolz/epsych2)
This Matlab toolbox is designed to facilitate behavioral experiments with/without simultaneous electrophysiology using Matlab with Tucker-Davis Technologies... |
2fb542829295463b5964cf43151c52158338f8304b7444038adbc05887824bf4 | Text | 2,467 | 42 | # Targeting succinate metabolism to lower brain injury during mechanical thrombectomy in ischemic stroke
The notebook contains:
Metabolomics data of patients/mice from the brain tissue at different timepoints after ischemia (0min, 5min, 15min, 30min, 60min, 120min) that were analysed by liquid chromatography-mass spec... |
81da61c5526332a3906c7bb299ff6ec3f6be2bc1db85771c78fa535bf080a73c | Text | 2,470 | 41 | # aug_accuracy
This package contains a set of tools to train and test classification neural networks.
The structure is inspired by msd_pytorch package.
Data loader includes standard augmentation techniques implemented without transforms from torchvision.
Model combines architectures from torchvision with a scaling ... |
27eb9b7c2b0498f364b6b4751f6997f59d8e1214ad26a3a4b1ceeb78fb9a1983 | Text | 2,486 | 80 | <div id="top"></div>
<!-- PROJECT LOGO -->
<br />
<div align="center">
<!-- <a href="https://github.com/minjeejang/useqfish_analysis">
<img src="images/logo.png" alt="Logo" width="80" height="80">
</a> -->
<h1 align="center">USeqFISH Analysis</h1>
<p align="center">
Ultrasensitive, sequential flouresc... |
8004d4e3cab5d2641f32bf7965bd989c021008f392dd84cd4310bcba4d12a145 | Text | 2,500 | 56 | # Force field-inspired molecular representation learning for property prediction
This is the official implentation of FFiNet: "Force field-inspired molecular representation learning for property prediction". In this work,we construct a force field-inspired neural network (FFiNet) that can utilize all the interactions ... |
41e43225022a42b2abfbb400bb535b1fd7de2b9fff6f546b149711ef9788bea7 | Text | 2,511 | 35 | # Virufy COVID-19 Open Cough Dataset
<p align="center">
<img width="200" src="https://virufy.org/img/logos/virufy-logo.svg">
</p>
Virufy is a volunteer-run organization uniting the world to build a global artificial intelligence (AI) database of crowdsourced cough sounds to identify patterns that signify respirator... |
a69138c8a9e7b8fcc7ae33590b128f97480e4e3c2baf010435693ad5c89d17c3 | Text | 2,527 | 36 | # CNS-paper
<p align="center">
<img src="https://user-images.githubusercontent.com/17041165/214026426-fbfa324e-29ea-46f6-a19e-759aee6a4336.png" width="500">
</p>
[](https://zenodo.org/badge/latestdoi/590467204)
Provides code for FEM, optic flow and generating kymographs... |
eaac0f747e0a942cb596930ef5c2e9b28e5afc34c180c160ebf784faff9dd221 | Text | 2,528 | 73 | PyTorch DGCNN
=============
About
-----
PyTorch implementation of DGCNN (Deep Graph Convolutional Neural Network). Check https://github.com/muhanzhang/DGCNN for more information.
Requirements: python 2.7 or python 3.6; pytorch >= 0.4.0
Installation
------------
This implementation is based on Hanjun Dai's structur... |
0f512a04ae91a8279f223cda85bd5f4a1ac444139842fbaeb149363c9c22af97 | Text | 2,535 | 23 | # Whole-brain mapping and analysis codes
The following method was used in Weinschutz Mendes et al. (2023) to analyze whole-brain confocal z-stack images of 6 dpf larval zebrafish brains immunostained for active (pERK) and total (tERK) neurons. In Weinschutz Mendes et al. (2023), this method was used to identify brain ... |
641370fe15cfe0aaef71aaf2c4f9eda68801a025de1d4c7a037f4a3db43b73a5 | Text | 2,623 | 24 | # Whole-brain mapping and analysis codes
The following method was used in Weinschutz Mendes et al. (2023) to analyze whole-brain confocal z-stack images of 6 dpf larval zebrafish brains immunostained for active (pERK) and total (tERK) neurons. In Weinschutz Mendes et al. (2023), this method was used to identify brain ... |
6467a2c660e0950a80539ea9a3a95d6f88659049737f5ce23e312759b9b86b27 | Text | 2,663 | 31 | # flexsim
This package can be used to reconstruct scanned objects, change the internal structure and reproject the augmented volume. The goal is to generate new X-ray projections similar but not identical to the acquired data
# Installation
CT reconstruction and forward projection uses flexbox that has to be installed ... |
11437023aa5e47f80a26b9e8a05fd3087091f5a30e8514f979f865efaa300bf9 | Text | 2,665 | 62 | # Optical Lever Sensitivity Calibration
## Description
This app is written in Python and uses Streamlit. It is used to calibrate the inverse optical lever sensitivity. The piezoscanner position is determined using the manufacturer calibration and the applied voltage. The photodetector vertical difference signal (V) is... |
32f83675109d1be2b0cf8311e9542614b2f6538b3a9760808b499adf7721ca0f | Text | 2,676 | 41 | The vised_marks extension for EEGLAB is the concatenation of two previously independent plugins for EEGLAB.
VISED
The VisEd extension for EEGLAB adds editing functions to the native eegplot data scrolling figure. Specifically, it allows adding/editing event markers, flagging channels/components, flagging time periods ... |
a4885c786ef38b7c03a2ff67e7985aecbdd15d6dfb8b04145c0dfc0920c3b506 | Text | 2,701 | 67 | # Central-Asian-Food-Dataset
In this work, we propose the first Central Asia Food Dataset, containing 16,499 images across 42 classes.
<img src="https://github.com/IS2AI/Kazakh-Food-Dataset/blob/main/figures/samples.png" width="750" height="700">
The dataset is unbalaced. The statistics across all 42 classes is sho... |
66e5b8048a93463677494e384d46c6cef389907dcc33b8110c2ef6f2cba76d64 | Text | 2,712 | 28 | # ChemPropPred
Repository for predicting conductivities through Arrhenius parameters for polymer electrolytes using a modified version of the original chemprop model described in [Analyzing Learned Molecular Representations for Property Prediction](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00237) and available a... |
65b76606ab4084db7ad544f1f2d31e35678858a2da3b196e81a378f5b6143cfc | Text | 2,758 | 71 | # Palmari
[](https://palmari.readthedocs.io/en/latest/?badge=latest)
[](https://python.org)
[
**Piecewise Quadratic Neuron (PQN) model** is a spiking neuron model designed to faithfully reproduce a variety of neuronal activities with limited computational cost.
In addition, the PQN model... |
c060424a1d317d2bf0d600df539f140e3450d58043fbb0d590deb0abc91bb7cc | Text | 2,799 | 70 | # Questionnaire-free machine-learning method to predict depressive symptoms among community-dwelling older adults
Sri Susanty a,b, RN, PhD; Herdiantri Sufriyana c,d, MD, PhD;
Emily Chia-Yu Su c,e,f,\*, PhD; Yeu-Hui Chuang a,g, \*, RN, PhD
a School of Nursing, College of Nursing, Taipei Medical University, 250 Wu-Xin... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.