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fe73b5e8fb549047d3e5dfbe618d4af593897ddabeb136fa6f47f87bf47f4a58 | Text | 819 | 36 | Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex (Wei et al, 2021)
Code base for mouse V1 Neurpixels EAP data analysis
* Method is presented in Wei et al. (2021):
## Dependencies
* Python 3.6+
* AllenSDK
* pandas
* Seaborn
* Matplotlib
* scikit-learn
* SciPy
*... |
77fd3659041fa009794b8284611a0178d13da7a8f2f5ea31ad89acad8b41e445 | Text | 868 | 16 | # RL for navigation
## Overview
This is a repo for training reinforcement-learning agents is a gridworld, such that agents optimize for the shortest integrated Euclidean distance to rewards. Currently supported models:
- Tabular Q learning
- Tabular SARSA
- State-action Successor Representation
- Tile coding (w... |
66de60fb7c38ee94c0c690463708b14785d0a3715090f801fbbc40f4a790b695 | Text | 874 | 29 | # Near-lifespan longitudinal tracking of microvascular morphology, topology, and flow
## System requirements
The codes were developed and tested with MATLAB R2019a on Windows Server 2012.
Some of the codes have dependency on a shared library: https://github.com/optobrain/matlab-lib
No non-standard hardware is requi... |
7bb3106bc04e2c459be8917ef26026022a72752a6d4a358a63ad91341c905df8 | Text | 875 | 13 | ## Scripts
There four python scripts attached to the project and they can be found in "scripts" folder.
(1) "Creating-data-samples.py" : For creating raster samples and converting them to numpy arrays.
(2) "CNN-models-classification.py" : For training and testing CNN models based on data from across Sindh Provinc... |
c00264bfc3cf5a5a7d114aa0c7f9417b4a7ac900f08b47cb5645438e38a83f4a | Text | 876 | 30 | # 代码使用
## 数据
按顺序执行
- isruc_s3_preprocess.py :
- 预处理数据集
- 提取特征 然后编码
- 编码后使用stdp_graph.py中的方法生成邻接图 一并以npy的形式存入文件
- load_data.py :
- 读取数据，并对邻接图进行正则化，
- 使用dataloader类构建训练和测试数据
- 注意在这里使用conext_add 将每个epoch都添加上下文的数据 _**[batch, context, channel, EEG]**_
- layer.py
- 基础的网络层 一层GCN的实现
- models.py
... |
03a2f00369aa6867862fdefdb128916da1d052010540f82cd79c91de04375fe4 | Text | 901 | 11 | <!-- badges: start -->
[](https://zenodo.org/badge/latestdoi/489065058)
<!-- badges: end -->
# SCZ_PPI
Documentation for analysis scripts used in the SCZ PPI paper:
Hsu YH, Pintacuda G, Liu R, Nacu E, Kim A, Tsafou K, Petrossian N, Crotty W, Suh JM, Riseman J, Martín JM, ... |
6ef3291ccd93b210689694cb5b2a6ac6b27aadd24c9270a615ad6bdfdb975fe1 | Text | 903 | 38 | # DeepOM
DeepOM is a Python deep-learning software for optical mapping of DNA images to a genome reference.
See the [paper](https://doi.org/10.1093/bioinformatics/btad137) for details.
# For inference only: Running the example script
Ensure you use python >= 3.10
```bash
cd tool
python -m venv .venv
source .venv/bi... |
c1e3f286d5b15330a4afd6e867917b54878351bcb16467dd7c3e7a8b47ea3a2a | Text | 904 | 23 | # QTAB Twin Data Models
Example models for analysing the QTAB dataset
## 01_create_familywise_datafile.R
Example code to create a familywise dataset (i.e. one family per row) for use in OpenMx.
## 02_umx.R
Example code for running twin models using umx (a simplified version of OpenMx).
## 03_sat_covariate_OpenMx.R
E... |
b276d28b4901084e7b22d392dd795677d8f07cf2ab7a037d3badbf08a4c410a2 | Text | 911 | 13 | # Multielectrode-array
The code is an updated version of the old Kramer MEA code for retina spike analysis. It processes spike-sorted .xlsx files from Plexon sorter, and can utilize trigger time .txt files.
Use concatMEA to convert .mat files from Plexon to the .xlsx files for this code.
Cited in:
-
Cyclodextrin-assi... |
18f1440087434af3588cb8cbcd05f07c06d7424e1973a49627bd86cf7667d67f | Text | 935 | 37 | # Bounding Box Augmentation
Example of augmentating image with bounding boxes.
This code is based on [aleju/imgaug](https://github.com/aleju/imgaug).
Augmentable annotation format is Pascal VOC only.
## Examples
Above image can be augmented to the following images.
| Example 1 |... |
3c81fa1ec24769edd3fdfa04c4441e8938682d3884239ddb6c530c5b46a48cb0 | Text | 967 | 28 | .. image:: https://img.shields.io/pypi/v/bouter.svg
:target: https://pypi.python.org/pypi/bouter
.. image:: https://github.com/portugueslab/bouter/actions/workflows/main.yml/badge.svg
:target: https://github.com/portugueslab/bouter/actions/workflows/main.yml
.. image:: https://codecov.io/gh/portugueslab/b... |
fcbf34a7db68f423cf283b11fa135bfb1dd4c8b69acece969060af9d6e06ca92 | Text | 978 | 40 | # Bond-type embedded crystal graph convolutional neural network (BE-CGCNN)
# Installation
This project required Pytorch and Pymatgen
# Usage
For training and test, you need a dataset consist of structure files (cif format) and related properties data (id_prop.csv) in same directory (data_demo). Then, you can run... |
48afb0b52338411fd7b0de166703ec9a4c402005da41181f24594937d1762779 | Text | 986 | 20 | # Mesoscale two-photon imaging with the 2p-RAM
[](http://mybinder.org/repo/sofroniewn/2pRAM-paper)
Notebooks and data acquired with the two-photon random access mesoscope (2p-RAM), accompanying
A large field of view two-photon mesoscope with subcellular resolution for in vivo ... |
8346e3cfba5d1189bff9756e3306e74751b64d448ce6f250cd92743bad929176 | Text | 999 | 18 | # Li-CellTypes-2023
This repository accompanies our article:
**Li, YT and Meister, M (2023). Functional Cell Types in the Mouse Superior Colliculus. ELife.**
## Contents of the repo
This repo contains the data and code needed to reproduce the figures in the paper.
* `/manuscript.pdf`: Preprint version of the arti... |
534f3ba70cefd91cd77ac0befb97ac68cf73beb1d9e8e93f63bc98930c278c17 | Text | 1,011 | 11 | ## Neural spiking for causal inference and learning
Ben Lansdell and Konrad Kording 2023
**Abstract:** When a neuron is driven beyond its threshold, it spikes. The fact that it does not communicate its continuous membrane potential is usually seen as a computational liability. Here we show that this spiking mechanism... |
94612b65e5588d0d5f5b00f0863919b99855bacae3ed60f7a98a29fa7e36de00 | Text | 1,031 | 12 | # Code used to extract features
The code available here may be used to customize the feature extraction and tailor it to a target task.
### Input file for batch processing
The script "batchpyradprep.py" creates a CSV file with the paths to the images and masks and adds a line for each label in the image. It produces ... |
cec1ad24c9c675ff7a70559928fa59a6cb804e0edeecb2781ea3d117a565b8fc | Text | 1,080 | 26 | # Multilayer Modularity for Multi-frequency EEG Network Analysis
This repo includes codes to run multilayer modularity based community detection in multi-frequency EEG networks as described in [[1]](#1). Although the paper's focus is EEG networks, the method can be applied to any type of multilayer networks. Here, a m... |
d2450324df5e773f74e5f4f60f089e95fd02888c094383bc1a48e0d53c5a27f5 | Text | 1,116 | 29 | # DSB_GNN
Requirements:
Python >= 3.6
PyTorch>=1.6
Numpy>=1.16.0
torch-geometric>=1.6.0
pandas>=0.24.0
scikit-learn>=0.20.0
# GraphMaker
Save the NHEK datasets in the data directory, run the graphmaker.py file, and the running instructions are:
`python Graphmaker.py`
The generated file... |
24a3ec5607b7cd19fe5ab462fab0d908d7fabcf6cc0099e759942aef9b622d70 | Text | 1,133 | 15 | # QPN_SpeechAnalysis
MEG data processing and spectral deviation computation for manuscript: Aberrant neurophysiological signaling underlies speech impairments in Parkinson’s disease (Wiesman et al., 2022)
# Author & Affiliation
Alex I Wiesman [neuroSPEEDMcGill, McGill](https://www.mcgill.ca/bic/research/neurospeed-neu... |
0eba4e27cfdf23d6bea4ebb63d79b4817831f3c7050a9d099b80a2dfcd1dbe09 | Text | 1,163 | 13 | # MiraBest
The MiraBest Batched Dataset is a labelled dataset of Fanaroff-Riley (FR) galaxies drawn from [Miraghaei and Best 2017](https://academic.oup.com/mnras/article/466/4/4346/2843096). At present, the dataset consists of FRI, FRII and hybrid FR sources, labelled as either confidently or uncertainly classified, a... |
bd150d4a9463db9bc5e06d5184e1092689b5bbdde5732e944ec6671bd1c5bdb3 | Text | 1,165 | 19 | # Koch *et al.* 2023 Code Repository
Code for simulation and figure plotting for "Loss or Gain of Function? Effects of Ion Channel Mutations on Neuronal Firing Depend on the Neuron Type" by Koch *et al.* 2023. [https://doi.org/10.3389/fneur.2023.1194811](https://doi.org/10.3389/fneur.2023.1194811)
Modelling on the effe... |
f09c2cc1fa912db5d9b55a73f1f982a1ef3e565cda127621ebe6bf38b3e5e804 | Text | 1,166 | 23 | # Signal novelty detection as an intrinsic reward for robotics
Paper: [Signal Novelty Detection as an Intrinsic Reward for Robotics](https://doi.org/10.3390/s23083985)
## AutoEncoder Architecture
AutoEncoder is one of the deep neural network methods used to detect anomalies in the signals received from the sensors on... |
e2b87022af5caa11fb8b674155432c7fe79aa17b253fc492ec054f1b8b9f0cd9 | Text | 1,173 | 16 | # Code used to analyze human inferior temporal gyrus data with tau (AT8), neuron (HUD), and nuclei (DAPI) staining
For the manuscript: "Spatial characterization of tangle-bearing neurons and ghost tangles in the human inferior temporal gyrus with three-dimensional imaging" by Zwang et al, Brain Communications 2023
To... |
417cd29bea67a0b0f5673a3c45502c8494c38169fd624a8cca26ab1608a54fcc | Text | 1,198 | 33 | # Near-lifespan longitudinal tracking of microvascular morphology, topology, and flow
Walek, K.W., Stefan, S., Lee, JH. et al. Near-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice. Nat Commun 14, 2982 (2023). https://doi.org/10.1038/s41467-023-38609-z
## Releases
[
This repository contains the source code for our
[2014 paper](https://doi.org/10.1186/2047-217X-3-3)
## Data files
The hdf5/ folder contains the current data files.
## Paper
Material relevant to the paper is in paper/ fold... |
7d46836273f6ab43d77ac1956de1f4db8cb4b077962ed7684bdb483a8651c755 | Text | 1,277 | 52 | Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex (Wei et al, 2021)
## Instructions
* 1) Create a virtual environment
```
$ conda create -n bmtk-ateam python=2.7
$ conda activate bmtk-ateam
$ conda install pandas numpy matplotlib scikit-... |
364deaa84b11a44c45642bc5e88fa25f3e456af7905f992cd65d1e9296469ce5 | Text | 1,292 | 42 | # drosophila_wing_cpg
Minimal code to produce figures in the manuscript "Gap junctions desynchronize a neural circuit to stabilize insect flight".
## Install packages
To create an environment with the packages necessary to run this code use
```bash
conda env create -f drosophila_mini.yml
```
To activate the conda e... |
ef6a24baf5d898123f46b3e5a9f9dc2856e8885eb1f6d4ed9ccecf435357229d | Text | 1,341 | 22 | # CM-graph
[](https://cm-graph.readthedocs.io/en/latest/?badge=latest)
The Python Toolbox for multichannel EEG-EMG connectivity analysis. This package is an extention of mne-tool with the focus on the application of the newest grap... |
096164a167e387f4281a7623d5c71e12643f8e01b811e6eb04ef22142f63b234 | Text | 1,397 | 18 | # Parametrization of Power Spectrum
This code decomposes a Power Spectrum signal into its periodic and aperiodic components. <br>
<br>
This code has an associated article (Gonzalez-Burgos et al. 2023). It generates Figure 1 D-H <br><br>
2. pyyaml
It may be useful to create a conda environment, then activate and thu... |
610c64d2e82fedf422078a5b294b4add0ae8bdb14d5eff16dc309b28c30f17ab | Text | 1,480 | 23 | Data is recorded from one monkey (monkey G) while performing a fixation task. Spiking activity is recorded from the visual area V4 with a 16-channel linear array.
Data set includes 5 recording sessions 2013_06_05, 2013_06_15, 2013_06_16, 2013_06_18, 2013_06_20. Each session contains two folders:
1) FixationTask: rec... |
107cf68d1832fa5dbefb00f2cdc37d117387bc3dc933fee68f251cf343961072 | Text | 1,518 | 32 | # Adapted LDRB method for ventricular fibers
This is a MATLAB implementation of the Laplace–Dirichlet Rule-Based (LDRB) algorithm for generating ventricular fibers. The original algorithm [[1](#1)] was adapted to eliminate a discontinuity of fibers in the free walls and to yield a fiber rotation that is directly propo... |
12d03504fbe2b9775c89466c45dec2be2cd01717d1e0072572b665aab7ee1feb | Text | 1,530 | 34 | <p align="center">
<img src="https://raw.githubusercontent.com/jbrea/FoodCachingExperiments.jl/master/fig1.png" />
</p>
## Simulate Food Caching Experiments in Julia and Python
The code in this repository defines a domain specific language to describe food
caching experiments. This repository is a submodule of [Foo... |
7f5e04656cf1b9e4c7c2e905314e10e77421b5a4b980b392574cd2200a8e2b2e | Text | 1,602 | 23 | [](https://paperswithcode.com/sota/classification-on-corbel?p=investigation-of-deep-learning-models-on)
# CORBEL
Implementation and dataset of publication [Investigation of ... |
a0de346356b7c33b7c19ecde483afad2da3292ae0366a9e0d5f77191b08fa056 | Text | 1,627 | 30 | # The effect of weight loss following 18 months of lifestyle intervention on brain age assessed with resting-state functional connectivity
Python implementation of the analysis from Levakov et al. 2023 paper, "The effect of weight loss following 18 months
of lifestyle intervention on brain age assessed with restin... |
9e4ee6f7c29b34207c271673dee38c77134f4e0c189d7318ca505fb10851f615 | Text | 1,659 | 32 | # Welcome to Mousebytes!
This platform is based on ASP.NET WEB API framework in which Angular 18.0 was used in the client side, and .NET 8.0 was used in the server side. Angular is a Typescript framework consisting of HTML templates, TypeScript components, modules, and services. The client
communicates with the serv... |
0b7d348aa8ebbbce269d7434f51d63de3a4e269ad8a73800bf0e511b622cfca4 | Text | 1,675 | 27 | # circRNA_neuro
In this repository you will find source code and data sets related to our manuscript:
## Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein
Michelle Watts (1,2), Marika Oksanen (1,2,3), Sanna Lejerkrans (1,2), Francesca Mastro... |
02eeb11c0b0c612e5bbcc376bf4130d035de42ee67b58c9cb5911b98e88f3594 | Text | 1,687 | 34 | Signal Hunter is an open-source and free software developed using
MATLAB 2014 (Mathworks, Natick, USA) for electrophysiological signal
analysis. Research groups lack software that allows assisted processing and
automatic tools to analyze electroencephalography (EEG) and
electromyography (EMG) recordings. Theref... |
124a1ebcf3f41ba2760da17f11fbedccffa152e5eb005b0ee29dd94185bbe790 | Text | 1,690 | 43 | # Learning Cortical Hierarchies with Temporal Hebbian Updates
This repository is the official implementation of the
Frontiers Computational Neuroscience submission 2023
"Learning Cortical Hierarchies with Temporal Hebbian Updates".
## Install Python packages
All the needed Python libraries can be installed with conda ... |
7bfa09c37bb898cf62bbf999de4ca7e9b09fcbccd5346a1189f2261817d022c6 | Text | 1,722 | 45 | # PAH-biomarker
Analysis pipeline for the PAH biomarker study by Sonnweber T et al.
## Summary
A complete R pipeline for search of novel, clinically applicable signatures of pulmonary artherial hypertension mortality risk.
<br>
<p align = "center">
<img src = "https://user-images.githubusercontent.com/80723424/2... |
26fac4737105a9f1642c331f224fb91061614bc13adf85d05dd5c39e6a055e88 | Text | 1,732 | 26 | exceRpt small-RNAseq pipeline
====================
Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets.
AUTHOR/SUPPORT:
Rob Kitchen, r [dot] r [dot] kitchen [@] gmail
CONTENTS:
exceRpt_smallRNA -- This choreographs the processing, filtering, and alignment of a single smallRN... |
30a9eebca0a3d00ff8270bfbe8966776befa5055d7109f78c74255b9c32424d7 | Text | 1,753 | 54 | .. image:: neuromaps_logo.png
The ``neuromaps`` toolbox is designed to help researchers make easy,
statistically-rigorous comparisons between brain maps (or brain annotations).
The accompanying paper is published in `Nature Methods <https://www.nature.com/articles/s41592-022-01625-w>`_.
.. image:: https://zenodo.org... |
424ea2fc595842b1b5f9da8ebee319d41ce1ff818adec6ba56587561f3d72d39 | Text | 1,782 | 32 | # 2023_cVA_Taisz_Galili
Public data and code for connectomic analyses in Taisz, Galili et al. (2023)
To analyse connectomic data we relied on the `natverse` toolbox from our group: [Bates et al. (2020)](https://doi.org/10.7554/eLife.53350).
https://natverse.org/
Datasets:
1. FAFB – [Zheng et al. (2018)](https://doi.o... |
746f12b31f55237220a92508f985c1a10e0f075499ac0de7f8ed19565ba22cd4 | Text | 1,791 | 44 | # DV-axis projection
This repository contains a small package designed to assess the relation between
an observation's position along the dorsal-ventral axis in the spinal cord
and the value of a feature of interest (FOI), as presented in the manuscript
_"Decoding the development of the human spinal cord by multi-omic... |
fc0acbafd667c995c2ff8998c56a6e0d376b57fe23cf7484e376c8a12faf68d4 | Text | 1,792 | 63 | # MASQ
*MASQ* is a framework able to run inference of ML models
directly on DBMSs. *MASQ* not only averts expensive data movements for those predictive
scenarios where data resides on a database,
but it also naturally exploits all the “Enterprise-grade” features such
as governance, security and auditability which mak... |
6345ff520aaa55f640eb60777616093d8701756cd0fecabe62b5d8eaacf4eddf | Text | 1,805 | 25 |
# Multilayer-Network-Centrality
This repository contains scripts to calculate centrality of genes in a multi-tissue network.
<object data="https://github.com/tarunkumariitm/Multilayer-Network-Centrality/blob/main/MultiCens.pdf" type="application/pdf" width="700px" height="700px">
<embed src="https://github.com/t... |
cf9d6a03c214108fc66d8ced973f9c5bf190bc1cd71d6aa2c754c189e4aeae3b | Text | 1,829 | 32 | # 2023_cVA_Taisz_Galili 
Public data and code for connectomic analyses in Taisz, Galili et al. (2023)
To analyse connectomic data we relied on the `natverse` toolbox from our group: [Bates et al. (2020)](https://doi.org/10.7554/eLife.53350).
https://natverse.org/
Datasets... |
26cdf20ce034107c28325fc9321051a3aaef781179d44ed6c825138fb8144e38 | Text | 1,835 | 51 | # BRIEF-IBS
LAST UPDATED: [Arvid Lundervold](https://www.uib.no/en/persons/Arvid.Lundervold), 2023-05-31
Code and [data](./data/questionnaire_BRIEF_and_more_66x18.csv) accompanying the paper: A.J. Lundervold, ..., A. Lundervold. "Assessment of self-reported executive function in irritable bowel syndrome using a machi... |
6202bb92a868026a9ca6af9ef70868ff8796cbc82382a28da17ab5bda72a3331 | Text | 1,866 | 11 | # Driving-Semantics-SNN
The implementation of the paper "Understanding human common driving semantics for autonomous vehicles". The abstract is "Autonomous vehicles will share the road with human-driven vehicles during the transition to full autonomy transport networks. The challenge of co-existence requires autonomous... |
92b6cd22dbcda39d90c3792e37d6f4eac7a6de6f20652b9fbc6701a4196e9d7b | Text | 1,874 | 33 | Peptide Dashboard
=====
We present three deep learning sequence-based prediction models for peptide properties including hemolysis, solubility, and resistance to nonspecific interactions that achieve com... |
b04e7727286b11c8bad98451a3ac9144f7d2d729164e1ef5114ebe7043108d45 | Text | 1,879 | 37 | # Scaffold hopping by holistic molecular descriptors in drug design
## Preliminary steps
In order to download and run the code, ensure you have the following software on your machine: <div>
* Anaconda (for Python 3.7): www.anaconda.com <div>
* Git: https://www.atlassian.com/git/tutorials/install-git.
## Getting the ... |
19d172e18729e876fffa492ccb293df7aa53f545598a3fe5c974502079fccd3a | Text | 1,899 | 47 | #############
Contrasting action and posture coding with hierarchical deep neural network models of proprioception, eLife 2023
#############
Authors: Kai J Sandbrink, Pranav Mamidanna, Claudio Michaelis, Matthias Bethge, Mackenzie W Mathis and Alexander Mathis
Affiliation: Brain Mind Institute, School of Life Scien... |
9508f2da970a6035979bd21cb9082d240c2c955b36bcf6695ef0fca43655b6c4 | Text | 1,900 | 72 | cylouvain: Cython Louvain
=========================
cylouvain is a Python module that provides a fast implementation
of the classic Louvain algorithm for node clustering in graph.
This module uses Cython in order to obtain C-like performance with
code mostly writen in Python.
Installation
------------
Install the l... |
a7dafa3168a0a8aec376f61570cd938fa448f2f1c974a3439163578210714b1c | Text | 1,945 | 23 | # yasa_classifiers
This repository contains the notebooks used to generate the pre-trained classifier of [YASA sleep staging module](https://raphaelvallat.com/yasa/build/html/generated/yasa.SleepStaging.html). The main GitHub repository of YASA can be found [here](https://github.com/raphaelvallat/yasa).
For more deta... |
d20ea940800f8b4597de325b2e1f4da5695c8c39b6c611413eb39919058a9e75 | Text | 1,955 | 21 | # PERSIST
**Predictive and robust gene selection for spatial transcriptomics (PERSIST)** is a computational approach to select target genes for FISH studies. PERSIST relies on a reference scRNA-seq dataset, and it uses deep learning to identify genes that are predictive of the genome-wide expression profile or any oth... |
3695e2d0bde8753dc0b4b7eb83be23de81b9ab5709228937fc380d6eee79bd12 | Text | 1,964 | 41 | # Variationally Regularized Graph-based Representation Learning for Electronic Health Records
This repository contains the code for the paper [Variationally Regularized Graph-based Representation Learning for Electronic Health Records](https://arxiv.org/abs/1912.03761).
## Introduction
In this paper, we design a nove... |
5a8ccad9064b1a9d94304535904488566cbf6a833f3fc3528a0b29da8ac9a123 | Text | 1,971 | 42 | [](https://doi.org/10.5281/zenodo.7837349)
# Retrosynthesis prediction using an end-to-end graph neural network for molecular graph editing
Inspired by the arrow-pushing formalism in chemical reaction mechanisms, we present a novel end-to-end architecture f... |
a55dd2bfe50274f227e9ac997b587c8c6a66c1082cf19a71b8c9170689472524 | Text | 2,014 | 25 | # Biosynthetic gene cluster (BiG) convolutional autoencoding representations of proteins (CARP)
This repo contains training and plotting code for the paper [Deep self-supervised learning for biosynthetic gene cluster detection and product classification](https://doi.org/10.1101/2022.07.22.500861). Model weights, data,... |
b9c1672ebcff76ff9903055bf2618f3cae80a06d6387e970f9731d24cb94a7b2 | Text | 2,016 | 35 | ## Overview
Codes for running the network model with spatial connectivity (in 2D or 1D) to study how network structure affects spatiotemporal correlations.
For model details and its neuroscietific implications check:
Zeraati, R., Shi, Y., Steinmetz, N. A., Gieselmann, M. A., Thiele, A., Moore, T., Levina, A. & Enge... |
bdf736775a3241a18ea50f11b167aff9a5e1c41b04d6275f8aacd01310aded68 | Text | 2,033 | 26 | # PT27-WetLab_vs_Simulation
This matlab code is build to generate data sets for wet-lab and isolated contractile element experiments, and analyze the output from both experiments. The main code is the 'wet_lab_sim_run_main_trial.m' file. This code contains all necessery codes for the analysis. Brief details about the ... |
8f9880d229a205cda789e2586387f089d627dcd541ff07c713fad1ca4ad278e0 | Text | 2,060 | 15 | # CKC-EEG-Networks
A compilation of MATLAB scripts for performing network-based corticokinematic coherence (CKC) analysis for EEG data recorded under repetitive hand movement stimulation.
The code was developed for the study (2022): "Cortical networks show characteristic recruitment patterns after somatosensory stimula... |
667186eb6027f7c19c4914a679e82444583eed34408de3c382118a51047ed5eb | Text | 2,110 | 23 | # MLP-GNN ensemble
Harnessing Shannon entropy of molecular symbols in deep neural networks to enhance prediction accuracy
------------------------------------------------------------------------------------------------------
This repository holds the codes pertaining to Fig. 3 of the article 'Harnessing Shannon entrop... |
55985f2d0232c2a9bae8af5fd7426fb9d28908a9261ab0d072f3c20c712aa625 | Text | 2,134 | 27 | # 2023_laperle_et_al
R script for:<br/>
*Human iPSC-derived neural progenitor cells secreting GDNF provide protection in rodent models of ALS and retinal degeneration*<br/>
<br/>
Authors:<br/>
  Alexander H. Laperle<sup>1\*</sup>, Alexandra Moser<sup>1\*</sup>, Pablo Avalos<sup>1</sup>, Bin Lu<sup>1</sup>, Am... |
c330a0ffb58ed041c4f5c933c19a38ccb1c66217e93eb77246729678c28dbe19 | Text | 2,149 | 21 | ### Summary:
MicroRNAs (miRNAs) function as a master regulator of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play unique roles during cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexibl... |
2f9e773a36899b38f98ef2c5cacc359bcb9fa163e6f73f5cf56db89baaa2ec56 | Text | 2,150 | 43 |
# An example workflow of dendritic spine image processing
Scripts for dendritic spine data analysis and visualization that demonstrated in the paper "Li, Ben-Zheng, Anna Sumera, Sam A. Booker, and Elizabeth A. McCullagh. "Current Best Practices for Analysis of Dendritic Spine Morphology and Number in Neurodevelopmenta... |
4157cc845c3b35132c36c04652abca5f0a1406a2c3a8c2fc2082401c955a43ad | Text | 2,153 | 34 | # precise-db
PRECISE is an RNA-seq compendium for _Escherichia coli_ from the Systems Biology Research group at UC San Diego.
[](https://zenodo.org/badge/latestdoi/187104662)
## Data
The following data files are available in the `data` folder:
* log_tpm_full.csv: Express... |
cfafa143493f0ec187c219f7fddb177607447486d950b9de0ea607c8159a054f | Text | 2,153 | 38 | [](https://zenodo.org/badge/latestdoi/366038263)
## Overview
Codes for running the network model with spatial connectivity (in 2D or 1D) to study how network structure affects spatiotemporal correlations.
For model details and the implications of these models to study th... |
b40d76974ab1877ca32e27840bb1c06d4aad6b148828f55ca4fefd884ae2c7d8 | Text | 2,167 | 59 | # deepCNNvalid
Code accompanying the publication "Validation of genetic variants from NGS data using Deep Convolutional Neural Networks" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05255-7).
The recommended way to run it is to download and decompress the version archived
at Zenodo (https:/... |
7b36c50788b2b01c66a20529672ee89e61cd8158965862af161c7c9eb26fa419 | Text | 2,221 | 38 | This study describes a high-resolution in-vivo magnetic resonance imaging atlas of the human hypothalamic region.
We employed a minimum deformation averaging (MDA) pipeline to produce a normalized (MNI152b), high-resolution template
from multimodal (T1w and T2w) magnetic resonance imaging (MRI) datasets. 990 subjects... |
4f3a223b39acaa85c6776c4100d39d7789e1cf68363f89f0a59a7b00dd328f29 | Text | 2,285 | 82 | 
# launchcontainers
[](LICENSE)
A Python tool for launching neuroimaging analysis pipelines on HPC clusters
with reproducib... |
7bcbd9aa2b950e075879d326004e528cc5eb9a63b708ca0bede672fabcf15152 | Text | 2,306 | 62 | # The contribution of the basal ganglia and cerebellum to motor learning: a neuro-computational approach
Code for the paper:
Baladron, J., Vitay, J., Fietzek, T. and Hamker, F. H. \
**The contribution of the basal ganglia and cerebellum to motor learning: a neuro-computational approach**\
*PLoS Comput Biol 19(4): e1... |
9d7355549711fe5b2169c7d659c85c137fb0df3abacd09a31c7702643a165304 | Text | 2,363 | 77 | This repo contains code to analyze and generate figures for Joshi et al., 2023 "Dynamic synchronization between hippocampal representations and stepping.".
Data was acquired using Trodes1.8.2 and 30-tet DKR drive versions for five rats, extracted using Trodes export functions, then processed and analyzed in MATLA... |
8771351fe4e19f1e184ecfb7794808fe841dbfcfe97be85e623a0387149d7057 | Text | 2,428 | 49 | # fMRI Deconvolution Toolbox
[](https://GitHub.com/Naereen/StrapDown.js/graphs/commit-activity)
[](https://www.python.org/)
, including using NS equation, RANS euqation with turbulent eddy viscosity, RANS equation w... |
c7735aaa0747836f55c101ab68ae2f9aa8959e16e43577411dcb192beb136bf0 | Text | 2,500 | 31 | # Code for the reproduction of [De Filippo et al., 2022](https://elifesciences.org/articles/85488).
The ***complete*** manuscript (text included) can be reproduced using the Python code present in this repository. Each number present in the text is an f-String that can be traced back to a data structure (see [End2EndPa... |
f65aac0c6d3f7a9b2eab5b361344b39ab2c1e024ab29c19a6dcbf2f36897ed8c | Text | 2,535 | 33 | # TMSsimCNN_Aberra2023
Code associated with Aberra AS, Lopez A, Grill WM, Peterchev AV. (2023). "Rapid estimation of cortical neuron activation thresholds by transcranial magnetic stimulation using convolutional neural networks". Neuroimage
1) Install python dependencies (recommended to install into a virtual environ... |
2a003ac7020c38b443c1248406c95a5a1ae40e1279e8479977ec58ece8be13eb | Text | 2,621 | 32 | [](https://zenodo.org/badge/latestdoi/169761536)
[](https://doi.org/10.12688/wellcomeopenres.15334.1)
# MR-Base case studies
This repository contains the case studies associated wi... |
6e226c9d5e98796c41e99043d7acc8be69355b622a5faace649eb69df8124ecb | Text | 2,642 | 38 | # PERSIST
**Predictive and robust gene selection for spatial transcriptomics (PERSIST)** is a computational approach to select target genes for FISH studies. PERSIST relies on a reference scRNA-seq dataset, and it uses deep learning to identify genes that are predictive of the genome-wide expression profile or any oth... |
2d6fa83b339b22258f376116dad93af84384dce6a6a9d4907df6447d0d2850f0 | Text | 2,693 | 49 | # svmGNT workflow script
R code for pre-processing of Illumina methylation array data, consensus clustering, t-SNE plots, and SVM glioneuronal classification model training. Used in "DNA methylation-based classification of glioneuronal tumours synergises with histology and radiology to refine accurate molecular strati... |
96e3b985162d531a1f32e78c7e875ee94272faa7146573c8bd31588e06726270 | Text | 2,808 | 28 | > Developed by [Yeison Nolberto Cardona Álvarez](https://github.com/yeisonCardona)
[Andrés Marino Álvarez Meza, PhD.](https://github.com/amalvarezme)
César Germán Castellanos Dominguez, PhD.
> _Digital Signal Processing and Control Group_ | _Grupo de Control y Procesamiento Digital de Señales ([GCPDS](https://... |
4c8a29a7c33674c30f140349e69e4d0a628314261e09e160490b14cd76ab5e6a | Text | 2,822 | 39 | # BonsaiLoomStim
The files contained in this repository run in the editor of the visual programming language, Bonsai.
Use these files to generate visual, looming stimuli used in Gonzalez and Fisher et. al.
## Set Up
Download Bonsai from [Open Ephys](https://bonsai-rx.org/docs/articles/installation.html)
Upon openin... |
588e5b40bf251bbdbb056c8d89eb8f7b25df70a742da443bfce7d4d05a551fef | Text | 2,869 | 59 | [](https://pypi.org/project/seg2link/) [](https://github.com/WenChentao/3DeeCellTracker/blob/master/LICENSE)
## Language
- [English](README.md) | [中文](README_zh.md) | [日本語](README_jp.md)
# , BEng
nicolas.sauthier@umontreal.ca
## Project Description
This is a machine learning project. The goal is to classify patients in potential organ do... |
e7ab2c37662ba04bfedd4811c6d23fe800fd25a43fab9f837f34f7a7508e61ac | Text | 3,431 | 61 | [](https://www.repostatus.org/#wip)
[![codecov](https://codecov.io/gh/philshams/opto-analysis/branch/master/graph/badge.svg?token=IDL... |
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