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|---|---|---|---|---|
dbff57a09102cf1ea94d2b3891f514c14659d82743883a7386ca30443b7285f4 | Text | 1,791 | 46 | # Birds Solo-LTRs
Data and code used in research: "Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events".
## Citation
Chen, G., Yu, D., Yang Y. *et.al.* Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. ***Nat Commun*** 15, 3151 (2024). https:/... |
d9bce5822d2457304ccb8ada3d9b0b9620b50a496b7f32108e1fbbc82bf18a9e | Text | 1,804 | 23 | ## MouSee
Graphical user interface GUI to generate visual stimulation protocols of drifting/static gratings using Psychtoolbox and a DAQ (optional) to get the stimulation type and time in a voltage output.
This program uses two screens: one for visual stimulation and one for setting and controlling the visual stimulat... |
da6e1affce85dcb2dac5a62e8c2b9d9fed53203c5094992f877aa27603a5fa7c | Text | 1,825 | 52 | [](https://zenodo.org/badge/latestdoi/240048156)
# BioVoxxel_Toolbox
The BioVoxxel Toolbox is a suite which contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. The following plugins are hosted here:
... |
09f26f3b05c80325958f9e29fafbc15787290cbae749aa114e65cbe0ad0afa81 | Text | 1,832 | 73 | # NeuronBridge Python API
[](https://zenodo.org/badge/latestdoi/479832149)
A Python API for the [NeuronBridge](https://github.com/JaneliaSciComp/neuronbridge) neuron similarity search service.
See [this notebook](notebooks/python_api_examples.ipynb) for usage examples.
... |
00e300dce01b3900bdbaa4da26d45ba9ad15657f3ecbfa6a109e6e1ca8359d22 | Text | 1,838 | 8 | # Mouse_Brain_Heatmap
rmd with the framework to create Mouse brain heatmaps and analyze data generate by Nutil to useable (https://github.com/DaniellaDeWeerd/Nutil-To-Usable).
This code was written using SVGs downloaded from The Allen Brain Atlas http://api.brain-map.org/api/v2/svg_download/100883867?groups=28. Please... |
c8dfd7fe84b4e06f45938744c00b2ba6fad5b5b26596db26594148e0d9089d51 | Text | 1,844 | 76 | # NeuronBridge Python API
A Python API for the [NeuronBridge](https://github.com/JaneliaSciComp/neuronbridge) neuron similarity search service.
## Installation
This library is available [on PyPI](https://pypi.org/project/neuronbridge-python/), so you can install it like thi... |
4b7ec60142cc149ff69d1f0274c3bc7101b093cd2e59170dd4399c4cb457ee86 | Text | 1,868 | 56 | .. -*- mode: rst -*-
SESAMEEG: SEquential Semi-Analytic Montecarlo Estimation for MEEG
=================================================================
This is a Python3 implementation of the Bayesian multi-dipole modeling method and Sequential Monte Carlo algorithm
SESAME described in [1]_.
The algorithm takes in i... |
7554f1c55196dc3cee58aa36cd0bd58d6cc690c24c9f3af136802b770271acea | Text | 1,869 | 43 | # MeshLDDMMQP
Description: Repository for mesh-based alternating quadratic program and large deformation diffeomorphic metric mapping (LDDMM) optimization for mapping data sets across modalities and scales. Associated preprint: https://www.biorxiv.org/content/10.1101/2023.03.28.534622v1.
System Requirements:
1) Singl... |
af2f9cf6d98416fee85f38c9fb8b219319c7b129d55bf623d5ab1db36365aa0e | Text | 1,876 | 33 | # DeSMRRest-clustered-reactivation
Code for the publication "Clustered Reactivation During Retrieval"
This analysis was run with Python 3.9, but any version >3.8 should work.
### 1. Getting started
First install the requirements using pip `pip install -r requirements.txt`. It is recommended to run this in a dedicat... |
1317e1c686aea0c513c7b595c251f1c6797b9a0f130a24ce6ade65c3ea87174f | Text | 1,882 | 22 | # DELIVR Training pipeline
This is the official repository of the publication ["Virtual reality empowered deep learning analysis of brain activity"](https://doi.org/10.1101/2023.05.18.540970). This repository contains the source code to train DELIVR from scratch or retrain the existing cFos detection network.
## Insta... |
028c58ce7a5296a71e4febd4c432d6bc14b74c5cf71dd1c88f6a366767ded7a0 | Text | 1,887 | 8 | # 2023_Grant_Poor
Public respository for the manuscript: "Prolonged exposure to lung-derived cytokines is associated with inflammatory activation of microglia in patients with COVID-19"
Neurological impairment is the most common finding in patients with post-acute sequelae of COVID-19. Furthermore, survivors of pne... |
c428c582d020de48dd9fc10687b591d1e6153f3fb0a4134078cb7793a53902c3 | Text | 1,892 | 18 | # Hevesi_2023
1. System requirements
- All software dependencies and operating systems (including version numbers) are available in the [methods section][methods]
- Archived version of this repo has been tested on x86_64-pc-linux-gnu (64-bit) platform running under Ubuntu 22.04.1 LTS with R version 4.2.2 and Python ... |
e0caf36f3e63a7f5518764001e13cfc0fe0ceca8836c497e50896a44f756b8e3 | Text | 1,895 | 19 | # Convolutional Spiking Neural Networks for Intent Detection Based on Anticipatory Brain Potentials Using Electroencephalogram
### Authors: Nathan Lutes, Venkata Sriram Siddhardh Nadendla, K. Krishnamurthy
This... |
c87bcf8ed525305203f889c0f8b71c87d8f9baddbdd30917549dd6293c16b7d1 | Text | 1,897 | 18 | Here you find transcriptomic data of CA1 GABAergic neurons, together with analysis results described in the paper "Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics" by Kenneth D. Harris, Hannah Hochgerner, Nathan G. Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson... |
a50b555b8ef2e987acbe0ed3b73f99196da20ecc7c6592363f31ba08d8534f47 | Text | 1,926 | 48 | # ScanOMetrics
Welcome to the ScanOMetrics repository !
About
=====
ScanOMetrics is an open-source software for normative modeling from MRI scans. Our tool currently provides a GUI for basic MRI
processing, statistical evaluation against a reference population, and visualization of results with 3D surface rendering a... |
87f027ad104efdf211e7becdd3fa8dafdd4be61a77c7d193117e211cb36f0bde | Text | 1,931 | 27 | # manuscript-binns_cortex_stn_comm
Code for the manuscript Binns *et al.* (Pre-print). DOI: [10.1101/2024.04.14.586969](https://doi.org/10.1101/2024.04.14.586969).
The repository has the following structure:
- [processing](processing) - location of scripts for (pre)processing of data (view [README](processing/README.... |
0d42f519eddd77229de548f579614564d201efb99216a2390479508e699493c4 | Text | 1,938 | 81 | # In-silico connected organoids
## Overview
Emulation of human cerebral organoids reciprocally connected with axons on Matlab using Hodgkin-Huxley neurons and conductance-based synapses.
_Maintainers_: Timothée Lévi (timothee.levi@u-bordeaux.fr)
_Authors_: Romain Beaubois (rbeaubois@u-bordeaux.fr)
## Features
| Fe... |
e51a4a815c1e8a1a8e365866d62705ee634251f23be2b6f6f344b4aa38b4ebfd | Text | 1,939 | 33 | # MelBrainSys_expression
Script for patient-matched melanoma metastases expression analysis
# Kraft et. al 2024, Workflow
**Personalized identification and characterization of genome-wide gene expression differences between patient-matched intracranial and extracranial melanoma metastasis pairs**
This is the pipeli... |
98bc4891dc60970b69062ce7671e96008c77236a34b42c24bda290a0ef02b980 | Text | 1,942 | 72 | # evomap
An R package for evolutionary mapping of continuous traits on phylogenies.
## Installation
```r
# install.packages("devtools")
devtools::install_github("JeroenSmaers/evomap")
```
## Functions
### Multiple variance Brownian motion (mvBM)
| Function | Description |
|---|---|
| `mvBM()` | Estimates rescaled... |
b5ecbdbdbcf4e8503061a72b269052cffb7beb47a99998836db4985514e8c12c | Text | 1,950 | 22 | # PTMPrediction
Supplementary scripts for the paper "Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of protein therapeutics"
## Rosetta documentation
Documentation for the Rosetta SimpleMetric can be found at [PTMPredictionMetric](https://new.rose... |
825c8508979b93dd4e0c987bb4093651e2c3f9937efa5a3c7e14bbb8539fda1c | Text | 1,953 | 33 | <!-- Hier Titel des Repositories eintragen -->
# Welcome to our repository of deep learning approaches for QSM!
<!-- Hier allgemeine Informationen über das Repo eingeben, zum Beispiel Autor, ... -->
<br/><br/> <!-- Am Ende des Abschnittes werden zwei leere Zeilen eingefügt um etwas Abstand zwischen den Unterpunkten zu... |
116fc931c0b1cff4f4fa17f61e1e928979ab5c11e67e28c797464ad2a6309577 | Text | 1,956 | 54 | # MutComputeX: A self-supervised 3D-Residual Neural Network for protein-X interface engineering
## X = nucleic acids, glycans, ligands, cofactors, other proteins
## To generate predictions on Norbelladine 4O-methyltransferase:
The models can be executed either natively, or from within a docker container. Regardles... |
2b1650027a66acabffd7b9ab004879f99a3e5a7d117fe8f55859f3ef7d0cab51 | Text | 1,959 | 38 | # Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features
Accompanying code and data for the manuscript: [https://doi.org/10.1021/acs.jcim.4c00127]
Copyright (c) 2024 Lhasa Limited and The University of Sheffield
## Respository structure
| Folder | Descr... |
3a9d9272436d22e23e95ca145e0230e96441a855b94d82eaeca91359f6f6fe3c | Text | 1,965 | 21 | 
[](https://pypi.org/project/dynast-release/1.0.1/)
], Sholl analysis has been a standard method to quantitatively assess the morphological complexity of neurons. It is performed by counting dendrite intersections in concentric circles emanating from the soma of a cell at a fixed radius interval. Diverse prog... |
98babc97075dcb48992a876ec4475953dc99e1f1ccc66dea6d219d173e11c9fb | Text | 1,983 | 51 | # WARN: Early Warning of Atrial Fibrillation Using Deep Learning
This repository contains the updated research code for predicting atrial fibrillation (AF) before onset from RR intervals using deep learning.
The project processes ECG-derived RR interval signals, generates recurrence plots, and trains a neural network... |
c6aefcb7df7de26d53767324eebda5804790a8799b8ea0a025d52863c87e806c | Text | 2,001 | 46 | # PhyberSIM: Brain Fiber Bundle Simulator
## Overview
This code implements a brain fiber bundle simulator using spline curves for fiber representation. More information in this link https://doi.org/10.3389/fnins.2024.1396518
## Prerequisites
- The code has been executed on both Windows and Ubuntu platforms.
- Tested... |
3c3188238c9d0e946aa862c014fbe23203d7ca8c41258999a956c55dbfdc0fca | Text | 2,005 | 47 | # DeepGlyco
DeepGlyco is a framework for predicting fragment mass spectra of intact glycopeptides.
## Dependency
For model training, NVIDIA graphics cards with CUDA are recommended.
The following software and packages are required:
- Python (version 3.9.16, [Anaconda](https://www.anaconda.com/) distribution is recom... |
e689618fce897dfa8f1ee5957f4445b43af0b7f58e174ecebbb6f85af4f254d9 | Text | 2,005 | 57 | emcee
=====
**The Python ensemble sampling toolkit for affine-invariant MCMC**
.. image:: https://img.shields.io/badge/GitHub-dfm%2Femcee-blue.svg?style=flat
:target: https://github.com/dfm/emcee
.. image:: https://github.com/dfm/emcee/workflows/Tests/badge.svg
:target: https://github.com/dfm/emcee/actions?qu... |
35ea9a0efd2766699ac350127cdf1bd6fb235f6152fefe1841e56f64805135d8 | Text | 2,012 | 30 | <img src="https://raw.githubusercontent.com/berilerdogdu/SPIT/main/logos/spitting_llama.png" alt="spitting_llama" style="width:376px; height:200px; float:left;">
# SPIT
A statistical tool that quantifies the heterogeneity in transcript usage within a population and identifies predominant subgroups along with their... |
05bbf97f4523741d3f59c3a99cef8dc64806bb5cab6d6dba7bdec2f9e2f2586a | Text | 2,020 | 48 | ## run command:
before run the code, please visit https://github.com/nghorbani/human_body_prior to install the human_body_prior package
`python evaluate.py`
for evaluation
our data preprocessing is shown as `preprocess.py`
## data download
before running the code, you may need to download ckpt.zip and da... |
81bb330b24112848e657ca9cdf7268ba3fe1b060ceed15a008ea1ed9b1c8fc8e | Text | 2,022 | 60 | # BCI2000_DYNAP-SE
Code related to 'Robust compression and detection of epileptiform patterns in ECoG using a real-time spiking neural network hardware framework' [https://doi.org/10.1038/s41467-024-47495-y](https://doi.org/10.1038/s41467-024-47495-y)
### System requirements
Windows (for BCI2000 code)
- BCI2000: 3.6... |
b47e52b4260a8a655dcc7ea30bf04bad32adb451a44e27685f30b6daaea3dcb8 | Text | 2,034 | 53 | # robstat
Stata module to estimate robust univariate statistics
`robstat` estimates various classic and robust measures of location, scale,
skewness, and kurtosis, and, optionally, performs robust tests for normality.
To install `robstat` from the SSC Archive, type
. ssc install robstat, replace
in Stata. Stata... |
c597d796c22c415b4ef50e5da74752d54bcf6b8c4c3f7086aa0f1ca1d8668ebe | Text | 2,036 | 26 | # RDK_vMMM
### Random dot kinematogram data analysis using a von Mises mixture model
This code belongs to the paper "Psychophysics and computational modeling of feature-continuous motion perception" by [Töpfer, Barbieri](https://twitter.com/DecisionGuy) et al. (2022), published in the *Journal of Vision*. It consists... |
ce05ba7fde64c87dc1ca34558ccffafc4ad572c574c1163f0a1f340f0c87b8dd | Text | 2,037 | 35 | # aDFC
## Adaptive Delayed Feedback Control in Neuronal Populations
This application allows the user to run the Adaptive Delayed Feedback Control (aDFC) algorithm to control neuronal populations with electrical stimulation.
We developed this application to conduct the experiments for the publication:
*"Disrupting a... |
065e9bff283732f3a05d2ca664a4c8cb9012a6d35e7748e3d39adc168080b397 | Text | 2,041 | 31 | # LINGER
## Introduction
LINGER (LIfelong neural Network for GEne Regulation) is a novel method to infer GRNs from single-cell multiome data built on top of [PyTorch](https://pytorch.org/).
LINGER incorporates both 1) atlas-scale external bulk data across diverse cellular contexts and 2) the knowledge of transcription... |
5cec4118650ef69c91b34c5ace901bf83f5f53f43e1884fcef84990c860c758e | Text | 2,048 | 36 | # Combinato Spike Sorting
## Introduction
_Combinato Spike Sorting_ is a software for spike extraction, automatic spike sorting, manual improvement of sorting, artifact rejection, and visualization of continuous recordings and spikes. It offers a toolchain that transforms raw data into single/multi-unit spike trains. ... |
f2232511edd513995370d4978a26df219c2732525c066c6e7e538809a960f7e0 | Text | 2,050 | 37 | # CaimanGUI
A graphical user interface for visualizing CaImAn processed imaging data.
[CaImAn](https://github.com/flatironinstitute/CaImAn) is a powerful computational software to process one-photon and two-photon imaging data. Here, CaimanGUI provides complementary visulizing functionalities that help neuroscientists... |
ae011ec130e3b0fde90494c99cbff526bce5ba38ba4e174f7d229dacf59ff840 | Text | 2,055 | 30 | # Neuromorphic one-shot learning utilizing a phase-transition material
This repository contains code and data to reproduce the results in _Galloni et al. (2024)_
"**Neuromorphic one-shot learning utilizing a phase-transition material**". The full final version of this paper is available at
[PNAS](https://www.pnas.or... |
5ee0db37836b10afc22cd4057c78a4c7e2aa49b9e274972a4bae0619eeb5af56 | Text | 2,078 | 43 | # Insect Navigation Sinusoidal Optimality
A sinusoidal activity profile in a circulant ring network doing path or heading integration has some nice properties - it is noise resistant and self-stabilising with a Hebbian learning rule.
This code performs the analysis and figure generation for the paper ["Theoretical pr... |
f6b22597e7321c6173bf224260130f17932661cb17c2f3dccd0be6b653422ff7 | Text | 2,079 | 27 | # Princeton Multi-Voxel Pattern Analysis (MVPA) Toolbox #
The MVPA Toolbox is a set of Matlab tools to facilitate multi-voxel pattern analysis of fMRI neuroimaging data.
The aim is to create a set of open source functions in a widely-used language to facilitate exploration of multi-voxel pattern analysis techniques a... |
6695ff860017e77f654535674f7c2f59fe3fc57557ac9d7692380b440d03da54 | Text | 2,086 | 48 | # GeoFind_SHC
Howdy Stranger!
__If__ you get here through an Apendix A link,
Then congratulations! You are at right place!
__Else__
You may be lost in TimeSpace.
This is an underconstruction space about a Thesis In Electrical Engineering, with a published work.
__Endif__
## Open repository for G... |
cd533ba0c044636e15f1badcaf1cd7ee48eae1622ab443f6d8f3950532d42af4 | Text | 2,089 | 43 | # TurkicASR
This repository provides the recipe for the paper [Multilingual Speech Recognition for Turkic Languages](https://www.mdpi.com/2078-2489/14/2/74).
## Pre-trained models
You can download the best performing models below.
|model|
|---|
|[turkic_languages_model.zip](https://drive.google.com/file/d/1GtK-OrH... |
4e0e667f4c0134671316b8962534b0ba6188c5b17335fc95069922c89d9223c4 | Text | 2,098 | 50 | # Knowledge Graph Neural Network
This is our implementation for the paper
> Xuan Lin, Zhe Quan, Zhi-Jie Wang, Tengfei Ma and Xiangxiang Zeng. KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction. IJCAI' 20 accepted.
<img align="center" src="Figure1.png">
Figure 1 shows the overview of KGNN. It tak... |
b216c4bab43636af63999ceeea1508f98647966f42794c66691d2665add835a3 | Text | 2,100 | 15 | # NeuroConnectivity
Most neurological disorders share a phenotype of synaptic dysfunction. High-content microscopy is indispensable in the drug discovery process but the sensitivity relies on the accuracy of mature synapse detection. We present a workflow whereby synchronous calcium bursting is measured in GCaMP6f-tran... |
0c71e0812405381fac07e7b2491ed12b53efc7c168e1e6347f4110f57d62f983 | Text | 2,126 | 31 | # tau-spread
Code to reproduce all network analyses in Lubben et al. "LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread". Scripts are modified versions of those found in https://github.com/ejcorn/tau-spread.
## Requirements:
- Tested with R 4.2.1
- Requisite packages are... |
43a8b19a4d5f72d4d2a7ec3a20180d39484a2262444df107a5e57a3e1e83dcc4 | Text | 2,131 | 62 | # BCI2000_DYNAP-SE
Code related to 'Robust compression and detection of epileptiform patterns in ECoG using a real-time spiking neural network hardware framework' [https://doi.org/10.1038/s41467-024-47495-y](https://doi.org/10.1038/s41467-024-47495-y)
[](... |
39fc7fd63be4c1f81a72f3d565165dc14f0bb6099ba6cae473b749e520e5b3d4 | Text | 2,138 | 69 | |ShapeOut2|
===========
|PyPI Version| |Build Status| |Coverage Status| |Docs Status|
**Shape-Out 2** is the successor of
`Shape-Out <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut>`__,
a graphical user interface for the analysis and visualization of RT-DC data sets.
For more information please visit https://zellm... |
0f769da6c929dad417f6f54ff42a5b14285152de89b1f01144ffd0e3609f61ad | Text | 2,141 | 32 | # Computational Scoring and Experimental Evaluation of Enzymes Generated by Neural Networks
## Colab notebooks
| Notebook | Description |
| -------- | ----------- |
| [ESM-MSA sampler](https://github.com/xzfu/protein_scoring/raw/refs/heads/main/colab_notebooks/scoring-protein-2.4-alpha.3.zip) | uses the ESM-MSA mod... |
f469a45fab8c6d297457ccb1eab43c07feb7b1d9bbde148c75d1c380c065e8d9 | Text | 2,164 | 14 | # ORF-RATER
ORF-RATER (Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.
The software was created at [Jonathan Weissman's lab at UCSF](http://weissmanlab.ucsf.edu/) and ... |
a6e6261c41abe1d69b9a7018f8dccdc8606c654d2d6e70c73f77b61ed6a46310 | Text | 2,170 | 43 | This dataset comprises four main directories, below is a detailed description of each directory and its contents:
1. [OneDCNN]: Contains preprocessed EEG epochs that are artifact-free, aligned either with the decision-making onset or the feedback onset. The EEG epochs within each '.mat' file are concatenated by partic... |
8f78da267f6fe1ccdef7d7e55da1f8647b86e82310f3a8fc9877548f5ddf286b | Text | 2,171 | 84 | # qqman: An R package for creating Q-Q and manhattan plots from GWAS results.
[](https://cran.r-project.org/package=qqman)
[](https://doi.org/10.21105/joss.00731)
](https://pypi.python.org/pypi/gradec/)
[](https://pypi.python.org/pyp... |
cd8e8e6dbd62c7adbed7a65ab49651016d87603754c98b98083d8810793f75fc | Text | 2,177 | 35 | # Matlab Code for the study ‘Bange et al.: Subthalamic stimulation modulates context-dependent effects of beta bursts during fine motor control’.
The function _determineThresh.m_ defines the beta amplitude threshold (defined as 75 percentile of the amplitude distribution).
The function _betaBurstFeatures.m_ extract... |
4cf2dcde22ecfbe2866b6fb10d5b718aa6793f351d996824a4b680d5788f42b0 | Text | 2,204 | 35 | # Matlab Code for the study ‘Bange et al.: Subthalamic stimulation modulates context-dependent effects of beta bursts during fine motor control’.
The function _determineThresh.m_ defines the beta amplitude threshold (defined as 75 percentile of the amplitude distribution).
The function _betaBurstFeatures.m_ extra... |
50aedc8963b7b5a9689319a79aa464c302ac12ea26da97b814be49de89829460 | Text | 2,205 | 65 | # ICADCML 2021 Paper A Novel Approach to Encrypt Data using Deep Neural Networks
<div align="center">
![Build mkdocs](https://github.com/oke-aditya/template_python/workflows/Build%20mkdocs/... |
cadac3f477e62a6a6e9e207d1cf1c0adef78b06617270a3d48efca62b5207fe8 | Text | 2,206 | 63 | ## Project title
Sodium salicylate improves detection of amplitude-modulated sound in mice
------------
## Description
This is the code to generate Figure panels for the manuscript "Sodium salicylate improves detection of amplitude-modulated sound in mice" by Van den Berg et al, 2024.
--------
## Authors
- Maurit... |
1cec500b44bac8c3b0f50ba09419758470f84f1c4dbc2f3334b1972a4322f703 | Text | 2,215 | 47 | ## 3D fetal MRI altases of craniofacial features
This repository contains 3D fetal MRI atlases of the fetal head / craniofacial features cretated at King's College London from 3D SVR reconstructed images.
-----
### Structural 3D T2w MRI altas of fetal craniofacial features at 1.5T
The fetal head atlas was created ... |
3e43ecff3fc79033a5613bbab94c153da3d2d620d6e9782dc338b1d4df615a50 | Text | 2,221 | 29 | # Global_FAPAR_250m
Land potential assessment based on 2000--2021 FAPAR monthly time-series at 250 m resolution
Preliminary global maps of monthly FAPAR time series, FAPAR long-term trend and potential FAPAR predictions at 250 m spatial resolution are available at Zenodo.
Please cite as:
- Hackländer, J., Parente, L... |
4657be0a198e8f7734aaff605a6f105cedd3c0c12e6a76d8dc64457ad7ba54c5 | Text | 2,222 | 24 | # singlecell-sporocysts
This repository contains the scripts used for the analysis of single cell RNA-seq data from S. mansoni sporocysts.
1. ###QC_sporos.R: QC of sporocyst samples. This script was written and run by cdsoria (https://github.com/cdsoria)
2. ###Analysis_sporos.R: Inital analysis of sporocyst samples. T... |
95c464ea9ad4f1f54eb8f14cbd65cf9b535e4419fe3760bc52f784700fa06cc3 | Text | 2,231 | 47 | # Dragnet
Dragnet (Directional \Delta G Neural Network) is a python package for modeling binding free energies and other properties of ligands and proteins.
## Getting Started
#### Environment
It is strongly recommended that you install this package in some kind of virtual environment (like a conda environment).
Cr... |
74c4a802a09a31636b8974c059433deaa48c82ef11f1ddc4d8940b3b1c4659d0 | Text | 2,243 | 50 | # WindSeer
This repository contains the tools to predict the wind using a neural network.
If you are viewing a downloaded copy of this repository (ZIP archive), consider obtaining the latest version online from https://github.com/ethz-asl/WindSeer.
## Structure
### Benchmark Planner
The planning benchmark tools used... |
3272da5fa854ffb1dcdd56ecb3cf036acd78f02129b3f437553cf93271e3de1e | Text | 2,252 | 54 | # Resources:
+ README.md: this file.
+ data: GDSC dataset
### source codes:
+ preprocess.py: create data in pytorch format
+ utils.py: include TestbedDataset used by create_data.py to create data, performance measures and functions to draw loss, pearson by epoch.
+ models/ginconv.py, gat.py, gat_gcn.py, and gcn.py: p... |
f1c20168c3fa5740d08a653f11c16601f9e0ad3337f7585f427a017f199785e8 | Text | 2,262 | 62 | # ichseg
An interactive tool and GUI for segmenting and annotating volumes stored in DICOM, VTK, or NIFTI-format
## Example screenshots
## General requirements
- Hardware: A GPU supporting at least OpenGL 4.1
- OS: Windows 10 or Ubuntu 18.04+ (not tested on macOS... |
b8e3cfbbead3f9850bec506f454b25aebde589e96f9c4282355b2550e3dce032 | Text | 2,282 | 41 | # OIA-DDR
A General-purpose High-quality Dataset for Diabetic Retinopathy Classification, Lesion Segmentation and Lesion Detection
You can download OIA-DDR from either Baidu Drive or Google Drive.
- OIA-DDR on Baidu Drive: [DDR dataset](https://pan.baidu.com/s/1560JK2pzxTN9Ny1TcmNasQ "悬停显示") PWD:ue0t
- OIA-DDR on Go... |
9cf7b236b391b602d2de739cc4ac8d42632b58b20ef8ba64a631c5374a6bc7a7 | Text | 2,283 | 37 | # NiMARE: Neuroimaging Meta-Analysis Research Environment
A Python library for coordinate- and image-based meta-analysis.
[](https://pypi.python.org/pypi/nimare/)
[](https://pypi.python... |
2d0d3f628d63d66cd91746c3f2484cb2586735a3c0f41eb1f2506c988aaa2a42 | Text | 2,287 | 53 | # <img src="http://imgur.com/NKyhO5c.png" height=30px> PyBehaviour
## Description
Software for control of stimuli presentation, recording of responses, and delivery of associated consequences in associative learning (operant conditioning) behavioural paradigms.
## Screenshots
... |
de963253ad7541a1cb6ee3775f43c48ac55846e32f193c34593963e8fa17d33d | Text | 2,287 | 54 |
# Enhanced Spatial Fuzzy C-Means Algorithm for Brain Tissue Segmentation in T1 Images
This repository contains the implementation code and dataset for the paper titled "Enhanced Spatial Fuzzy C-Means algorithm for brain tissue segmentation in T1 images". In this paper, an enhanced spatial Fuzzy C-Means (FCM) algor... |
0e0567fe71ae9d837f662ba6dd37ffd80219cf6d64f250ea8e7a88277d97aba0 | Text | 2,288 | 30 | # deepMRI: Deep Learning Methods for MRI
**Authors:** Yang Gao, Zhuang Xiong, Xuanyu Zhu, Samiha Prima, Hongfu Sun
This repository is a collection of deep learning tools for MRI reconstruction and quantitative mapping. Each method lives in its own standalone repository (linked below). Each subfolder here contains a s... |
02654bb6a5172c0b7e8ae55c3a4742a32de7f571cc7b69f3a3493f8bcfec87a1 | Text | 2,300 | 33 | # README: takemura_hgf
[<img src="https://img.shields.io/badge/DOI-10.1186/s41232--024--00322--9-FAB70C?style=flat&logo=doi">](https://doi.org/10.1186/s41232-024-00322-9)
[<img src="https://img.shields.io/badge/PMID-38475915-326599?style=flat&logo=pubmed">](https://pubmed.ncbi.nlm.nih.gov/38475915/)
[](https://pypi.python.org/pypi/nimare/)
[](https://pypi.python... |
e85b24e5a83dcb23442f9525a3073e57f6b07c3d2bf842effd571dd50ac94791 | Text | 2,326 | 32 | ## MouSee
Graphical user interface GUI to generate visual stimulation protocols of drifting/static gratings using Psychtoolbox and a DAQ (optional) to get the stimulation type and time in a voltage output.
This program uses two screens: one for visual stimulation and one for setting and controlling the visual stimulat... |
8278827e86921d95b1708100315e3d3450b29237c69f5b51a8a821f12ee12b74 | Text | 2,344 | 30 | # manuscript-binns_cortex_stn_comm
Code for the manuscript Binns *et al.* (Pre-print). DOI: [10.1101/2024.04.14.586969](https://doi.org/10.1101/2024.04.14.586969).
The repository has the following structure:
- [processing](processing) - location of scripts for (pre)processing of data (view [README](processing/README.... |
7a7ee5da86bd51d9939f79aafab6c9a440d08c65eaeadaaaabfcc2e1f12d495f | Text | 2,358 | 41 | # MultipleComparisons
# About
MultipleComparisons allows to calculate and process extended (e.g., n-ary) similarity indices.
The basic theory is detailed in: "Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics", R. A. Miranda-Quintana, D. Baj... |
01898e51702590c9f3f35b6a5fcd529ad1d881f84782c7bdb48ea1240140dce1 | Text | 2,369 | 45 | ## HMMER3Di - This is a fork of hmmer3.3.2 and easel 0.48 patched to support the Foldseek (3Di) alphabet
This program was used in the work:
Johnson, Sean R., et al. “Sensitive Remote Homology Search by Local Alignment of Small Positional Embeddings from P... |
ba8bb54fcc3f2985100b222f85e7c2ad28b3482fd6f3c3c742e445b491511b1b | Text | 2,397 | 43 | # About
This is the mathematical model for epithelial transport along the superficial nephron, specifically focusing on magnesium and calcium transport which is implemented in Python 3. The models account for sex differences, providing a better understanding of nephron functionality. Related research papers are listed ... |
5fb6baadaa7ea37dd28ae8f8950dd6e64b50b3565e1545614858e41b7074536d | Text | 2,416 | 44 | # **wave**: spatiotemporal analysis of noisy multisite data #
**wave** is a MATLAB toolbox for unsupervised analysis and visualization of noisy multisite data. Originally developed for multichannel recordings in neuroscience, where both optical imaging and multielectrode data are increasingly common, the functions in ... |
918653f693d2125590d42e5fdcc7d56fe01f8956228dd25e42313e691d6e5f92 | Text | 2,418 | 11 | # SCZ_Training
This is the data and R script for the manuscript:
"Video game training increases clinical well-being, attention and hippocampal-prefrontal functional connectivity in schizophrenia"
Authors: Maxi Becker, Djo Juliette Fischer, Jürgen Gallinat & Simone Kühn (2022)
Abstract:
Recent research revealed that ... |
33ee2e0c3178e144af68c8e8c741a227373304151a6b53660c8542306fffb0d4 | Text | 2,436 | 38 | ---
language: en
tags:
- exbert
license: mit
widget:
- text: "[MASK] is a tumor suppressor gene."
---
## MSR BiomedBERT (abstracts + full text)
<div style="border: 2px solid orange; border-radius:10px; padding:0px 10px; width: fit-content;">
* This model was previously named **"PubMedBERT (abstracts + full text)"**.... |
8b60fa8104922d48ec15a7296ff94850c54881926488d4afd793a8622972995f | Text | 2,446 | 48 | # emergent_transitive #
Code and human behavioral data for "Emergent neural dynamics and geometry for a transitive inference task". Pre-trained models presented in the study are available at datadryad (https://doi.org/10.5061/dryad.83bk3jb0v). Contact Kenny Kay (kaykenneth@gmail.com) any clarification or requests.
... |
cda2deecf7c8f8e221237c2069b92522aad21deb07381f440340062af6273b3a | Text | 2,465 | 37 | [](https://mybinder.org/v2/gh/ale-tom/MEG_LBA_PD/HEAD)
# Parkinson’s disease impairs cortical sensori-motor decision-making cascades
This repository contains code and data to reproduce the figures in the article [“**Parkinson’s disease impairs cortical sensori-motor deci... |
a0b7a384015c89a6dc43ec1b8d28fe76d45ea174d516e4cd35935f759b2b8e80 | Text | 2,472 | 51 | ### Spike Predictor
Module designed to predict action potential events and stimulate N milliseconds before the occurrence of the spike.
Please, if you use this module cite:
Alicia Garrido-Peña, Pablo Sanchez-Martin, Manuel Reyes-Sanchez, Rafael Levi, Francisco B. Rodriguez, Javier Castilla, Jesus Tornero, Pablo Varo... |
1ae0343308fe8c7e6e679cd12688df7586aa87df286be19d8bb2969b8abcac64 | Text | 2,495 | 38 | 
# Noto Emoji
Noto Emoji (Stands for No Tofu) is an open source (Open Fo... |
0b383504c9b1f5a2c9c215b8e7e5121d07fa9e3f67d07e0b3d18c6a60845d04a | Text | 2,506 | 23 | ## Code for GRN construction
### Overview
Scripts in this repository provide an example of GRN network construction from single-cell/single-nucleus data corresponding to the manuscript entitled "BHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer’s disease and other disorders of lipid-rich ti... |
fa976e2748e632897ca0820bee6bdf69aba6961577fb325c2363fbe8c1438dd7 | Text | 2,507 | 51 | # Benchmark denoising strategies on fMRIPrep output
[](https://doi.org/10.55458/neurolibre.00012)
The project is a continuation of [load_confounds](https://github.com/SIMEXP/load_confounds).
The aim is to evaluate the impact of the denoising st... |
ede28cc2176254948b8c8d12611d30b9302476bd30d079b0e9a64b3c343c0df8 | Text | 2,527 | 29 | # Gomorphological classification
This repository contains the code and results for “[Explanation of the influence of geomorphometric variables on the landform classification based on selected areas in Poland](https://www.nature.com/articles/s41598-024-56066-6)” article.
Reference geomorphological maps are available f... |
75fda9c22ad37cd4dc35569e702029781b07eb50e2c44c8d5ecc9dda49c995d9 | Text | 2,528 | 9 | Included are raw neuroimaging and preprocessed neural recording data from "The neural basis of resting-state fMRI functional connectivity in fronto-limbic circuits revealed by chemogenetic manipulation" (see Related Works section; citation will be updated after publication). Please cite this paper if you use any of the... |
7f40bb88abf4b2579d5594dcb5e1ecef84b4250ac6b6bbb82927ed6256676f81 | Text | 2,533 | 32 | # Automated Hate Speech Detection and the Problem of Offensive Language
Repository for Thomas Davidson, Dana Warmsley, Michael Macy, and Ingmar Weber. 2017. "Automated Hate Speech Detection and the Problem of Offensive Language." ICWSM. You read the paper [here](https://ojs.aaai.org/index.php/ICWSM/article/view/14955).... |
83008be38ff9776ca31092578c6a92ed5e42881e9e252b45f5166e1ecb0f13dc | Text | 2,534 | 42 | # High-precision regressors for particle physics
<h3>
<p>
<a href="https://inspirehep.net/authors/1279838">Fady Bishara</a> (<a href="https://inspirehep.net/institutions/902770">DESY</a>), <a href="https://inspirehep.net/authors/1209756">Ayan Paul</a> (<a href="https://inspirehep.net/institutions/946076">Northeaste... |
e9023e138e6bd8854fdbb6b305291c0ad2134087b6c3fa4b6ce96552fec5f5a7 | Text | 2,554 | 33 | # AD_genetics_stratification
## Description
Code repository for the paper entitled ["Genetic-based patient stratification in Alzheimer’s disease"](https://www.nature.com/articles/s41598-024-60707-1). The repository follows the methodology and results presented in the mentioned work.
... |
c4c6f9a7f3183cb644bf7d528850e04bea9749edc4baca03a146d28ae7cb9c4b | Text | 2,558 | 46 | # The GLM-Spectrum: Multilevel power spectrum analysis with covariate and confound modelling.
This repository contains the scripts and software to run the simulations and real data analysis published in:
Andrew J. Quinn, Lauren Atkinson, Chetan Gohil, Oliver Kohl, Jemma Pitt, Catharina Zich, Anna C. Nobre & Mark W. Wo... |
18b6f83e0d7061f668aa1e6e3a855f44de300a2d6aa4c2c09394751e9ad78cd3 | Text | 2,582 | 44 | # Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells, by Sefora Conti et al.
This repository contains the code for the paper Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells, by Sefora Co... |
ff181f9b3825d7aba20348ddbdfac7e84ea747dbf1ce4037703d6eda8c50732f | Text | 2,637 | 70 | [](https://mybinder.org/v2/gh/IBM/rgan-demo-pytorch/main?labpath=examples/nonlinear/uniform_prior.ipynb)
This repository provides pytorch source code for demonstrations associated with our _(DOI)_ preprint publication, "Novel and flexible parameter estimation methods for d... |
6039bd052964b33557de857d90ed9c2ba7b5e82b413a91a965f82e53186afba7 | Text | 2,643 | 55 | <p align="center">
<img src="https://raw.githubusercontent.com/pyushkevich/greedy/master/utilities/logo/greedy.jpg" alt="Greedy" width="600">
</p>
# Greedy
Greedy is a tool for fast medical image registration, developed at the
[Penn Image Computing and Science Laboratory (PICSL)](https://picsl.upenn.edu) at the
Uni... |
70cc04b216ecb63444eee3d222634d826a3cafe7265e06988da45a326ad7c4f4 | Text | 2,651 | 73 | # `AIgarMIC`
## Introduction
`AIgarMIC` is a Python package and collection of commandline scripts designed to facilitate the automation of agar dilution minimum inhibitory concentration image interpretation.
`AIgarMIC` has the following features:
* Automated image processing of agar dilution plates in the following... |
bf666c7d32897296d028b655fdc0a3f16d7309cc69af11e93d3473218c2b00f2 | Text | 2,681 | 46 | ---
language: "en"
tags:
- fill-mask
license: mit
---
# ClinicalBERT - Bio + Clinical BERT Model
The [Publicly Available Clinical BERT Embeddings](https://arxiv.org/abs/1904.03323) paper contains four unique clinicalBERT models: initialized with BERT-Base (`cased_L-12_H-768_A-12`) or BioBERT (`BioBERT-Base v1.0 + Pu... |
1caa8e2c8bba9823955f4d5aa25e8fa3f650ef9168d28979d4ea6baed40912a5 | Text | 2,692 | 14 | # Wang-Spindles-in-Axons
Read Me
The goal of this project is to create MATLAB code capable of detecting the spindle within the hippocampus and generate plots based on the result.
The “FD_Generation.m” is to generate a data structure recording the feed direction for each axon based on the previous study. The structu... |
4cf953a9a94896aaf60b6ce9798e9e577b47c427b21981da8e06fa3a1318dc92 | Text | 2,724 | 91 | # UNNT (Utility for comparing Neural Networks and Tree-based models)
UNNT enables users with structured (tabular) data to compare CNN and XGBoost models by providing a utility to train both models
### Installation
UNNT requires [Anaconda](https://docs.anaconda.com/free/anaconda/install/index.html) to run.
#### Cr... |
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