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98a86bdf2ad46f243ceef6f6764ac0abfbe23114791e32b555c9a011eb4e37e3 | Text | 1,787 | 38 | # SEDR: Unsupervised Spatial Embedded Deep Representation of Spatial Transcriptomics
## Overview:
__SEDR__ (spatial embedded deep representation) learns a low-dimensional latent representation of gene expression embedded with spatial information for spatial transcriptomics analysis. SEDR meth... |
01c8026070a30f18165056a84c7b5cb5fb9d7dc7bdf6e3f491a47ea66cccab35 | Text | 1,788 | 34 | # Supplemental code for "A fluid-walled microfluidic platform for human neuronal microcircuits and axotomy"
------------------
## Contents
* [Installation](#installation)
* [Files](#files)
* [License and citation](#license-and-citation)
* [Acknowledgements](#acknowledgements)
------------------
## Installation
These ... |
4201f9a1c5db75a0a5678bec9613d550c1481f7c9ad0e45a314cbf5c814693e3 | Text | 1,789 | 38 | # ModulusVascularFlow
Multicase vascular flow PINN based on Nvidia Modulus v20.09 framework
NVIDIA Modulus:https://docs.nvidia.com/deeplearning/modulus/modulus-v2209/index.html#undefined
Codes extention from NVIDIA Modulus can be found in folder ModulusDL
## Examples
#### Multicase PINN for 2D stenosis
stenosis2dsim... |
f1075050499adfb15c0a5ec96ea45f36d99e3b03eef516547fd10184664fe0bc | Text | 1,807 | 55 | # GBM_SV_anaysis
- [Overview](#overview)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [License](#license)
# Overview
`` GBM_SV_anaysis`` Offering code&commands for Hi-C chromatin structure, SVs and neoloop identifications, CUT&tag and RNA-seq analysis, subtype classfic... |
56bc6b077ed3a4d9cb142c62769052e8a3a53ff81597816ce181fe7ab58f0ff4 | Text | 1,818 | 25 | # Autism Hemispheric Specialization 2023
## Purpose
The aim of this study was to estimate hemispheric speiclaization in autism using an individual-level approach and then explore potential relationships between language specialization and behavioral phenotypes including verbal ability, language delay, and autism sympt... |
ad5ef660a373dc2beea9c627576b266edcbcd581a08b50e55dd56e2039a24fa6 | Text | 1,824 | 28 | # Sparse Variable Generalized Linear Model (SVGLM)
The sparse variable generalized linear model framework, termed the `SVGLM`, which is able to track the saccade-induced rapid changes occurring in the spatiotemporal sensitivity of the neurons on a millisecond timescale. The principal idea of the `SVGLM` is that the st... |
9c8d2ca891b95ebcba4ad9a5acd3457cc7322134f43d22437a08707663b0dfa0 | Text | 1,839 | 40 | # freewater-fernet
Note, this is not an original work, but rather a repackaging of the following repository:
[Fernet Freewater Estimation](https://github.com/DiCIPHR-Lab/Fernet)
Used in the following publication. Link:
https://doi.org/10.1093/brain/awad420
Reason for the repackaging instead of branching is that ther... |
72f52ebf1bc89dbd3b8c134356edaa13dd1b306e28fa34cacd894cf2712ca88d | Text | 1,845 | 19 | # TaskFCRemoveMeanActivity
*Code for running simulations and data analysis from*:
Cole MW, Ito T, Schultz D, Mill R, Chen R, Cocuzza C (2019). "Task activations produce spurious but systematic inflation of task functional connectivity estimates". NeuroImage. doi:10.1016/j.neuroimage.2018.12.054
https://doi.org/10.101... |
b5ca13dcb736ea3f73bda00c3dedf468a64501a1629ec42e309ee7d8417e9e9f | Text | 1,888 | 24 | # OXT-Wolf
Code associated with the paper titled "Oxytocin induces the formation of distinctive cortical representations and cognitions biased towards familiar mice." by
David Wolf, Renée Hartig, Yi Zhuo, Max F. Scheller, Mirko Articus, Marcel Moor, Valery Grinevich, Christiane Linster, Eleonora Russo, Wolfgang Weber-... |
15512a60baf0fd3770d280e0fda65b6628b85ab0a6473e727f7358254a1746e1 | Text | 1,892 | 60 | FreeWater and FW corrected DTI metrics pipeline
===============================================
Run the FreeWater pipeline, including FW-corrected DTI metrics estimation
If you use this pipeline, please cite:
```
Kurtzer GM, Sochat V, Bauer MW (2017)
Singularity: Scientific containers for mobility of compute.
PLoS O... |
f545158a0857ed690fba2f3582fc5972d5b462f1b0a9fd59c2aaa02ce56468cc | Text | 1,902 | 43 | # Interpretable Video-Based Tracking and Quantification of Parkinsonism Clinical Motor States
Authors: Daniel Deng, Jill L. Ostrem, Vy Nguyen, Daniel D. Cummins, Julia Sun, Anupam Pathak, Simon Little, Reza Abbasi-Asl
Manuscript: https://doi.org/10.1038/s41531-024-00742-x
## Installation
In the root directory, inst... |
3d530bf576415f4f15d9d1a8a3a54a0827bf9228dbcaea4776365505ca55eeee | Text | 1,911 | 34 | # PatWay-Net: A machine learning framework for interpretable predictions in patient pathways
# Setup
1. Install Miniconda (https://docs.conda.io/en/latest/miniconda.html)
2. After setting up miniconda you can make use of the `conda` command in your command line (e.g. CMD or Bash)
3. To install required packa... |
aab76f03ba07cb526fb59025f99ed8a25cfe73d4e43e67979841b3204ba933d0 | Text | 1,914 | 46 | # Tracking the neurodevelopmental trajectory of beta band oscillations with OPM-MEG
Lukas Rier and Nathalie Rhodes et al. eLife 2024 (https://doi.org/10.7554/eLife.94561.1)
All data can be found on zenodo:
[](https://doi.org/10.5281/zenodo.11126593)
... |
badffb63cb7f06403d2960d2a3409cf92c5d6a6dcdc05e32ecf0c548d3619c35 | Text | 1,927 | 12 | # PHOENIX
PHOENIX is a tool to infer **biologically explainable** differential equations describing genome-wide regulatory dynamics
**Background:** Models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into impor... |
a92599d503902af130ced18d8f722b57574e5d988f8b8ab337a771b1aeaf38b9 | Text | 1,934 | 29 |
# SpatialSPM
The **SpatialSPM** is a tool designed for the analysis and comparison of gene expression patterns in spatial transcriptomic (ST) data. It adeptly handles the complexity of comparing spatial gene e... |
aa401441ea14a67bc76bdf350fd8a72d15a3e9c7761837ba6b2cd5beb625a7c4 | Text | 1,961 | 53 | # pyrolysis-prediction
Sample code to generate data and extract information on pyolysis
## Required packages
You will need to install RDKit, pubchempy and jcamp using pip.
## Script to remove test flavor compounds from the training data (pyrolysis prediction)
Usage: ```python ./preprocess_reaction_data.py -i TRAIN... |
ad86cca83d4e96e84c03d4fc8f8838402b5217c4b893570dca4c4f6d03bc1818 | Text | 1,961 | 27 | # NEMO
NEMO (NEuron MOrphological analysis tool) is a new freeware for semi automated quantitative and dynamic analysis of neuron morphometry.
NEMO was co-developed at the [Italian National Council of Research Institute of Clinical Physiology (IFC-CNR)] (https://www.ifc.cnr.it/index.php/it/) and the [Research Center "... |
91ec62fdf290363d7707da3990ff23f49687bc902902f0d3ec3d4a598e2d07cd | Text | 1,965 | 65 | # GATSol
GATSol, an enhanced predictor of protein solubility through the synergy of 3D structure graph and large language modeling
## 0.Conda environmennt create
If you want to run this model in a standalone mode on your own linux system, git-clone ProtSol with the following code:
```shell
git clone https://github.... |
fc55cf75856b7f5df762ca4fb3915290dbd805a703a506305dd38b4f0625949a | Text | 1,977 | 18 | # Individualized-closed-loop-sensory-stimulation-reveals-alpha-phase-dependence
This repository accompanies the manuscript "Individualized closed-loop sensory stimulation reveals alpha phase-dependence of sound-driven brain activity in human electroencephalogram (EEG) recordings" (in preparation). In this study, indi... |
f431eb700d2a1ed57466d88c0e3d695344fe121b48c736d8bbd33ec942d3c60f | Text | 1,978 | 38 | This repository contains all code that was used to produce the results of the following publication:
Population-level coding of avoidance learning in medial prefrontal cortex
Ehret B., Boehringer R., Amadei E. A., Cervera M. R., Henning C., Galgali A., Mante V., Grewe, B. F.
Nature Neuroscience 2024
The data asso... |
e76b9c625fea4f50ed6762d91c2da3dad504392cbbd05609e080737aa6c4cd5d | Text | 1,980 | 25 | # ZS-DeconvNet
This repository includes the raw data download link, the python and matlab codes, as well as Fiji plugin for the paper "**Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy**".
For a quick start, check the [brief tutorial](https://tristazeng.github.io/Z... |
151581f1b862b44c9ab0a3019f80fd52079dbaf3badc8723b772722a1aaf7c03 | Text | 1,989 | 7 | Spatiotemporal brain hierarchies of auditory memory recognition and predictive coding
Matlab leading script for the paper entitled: "Spatiotemporal brain hierarchies of auditory memory recognition and predictive coding", Nature Communications (2024). L. Bonetti, G. Fernández Rubio, F. Carlomagno, M.J. Dietz, D. Pantaz... |
db15e66b7e537712279207adc8cce2b581a7b706cece932c908311b0300d40e7 | Text | 1,999 | 37 | # episdet-transformer
This repository includes an implementation of a Transformer Neural Network for any-order epistasis detection.
This implementation has been devised to make use of network interpretation strategies (e.g., attention scores) to identify epistatic interactions and target various AI accelerators (e.g.,... |
005e949b108db16c7f4cfd43d2f7ad336c86c1690711f2ae34a842d15ff4cfe2 | Text | 2,011 | 68 | # DEAttentionDTA
DEAttentionDTA is a deep learning which based on dynamic word embeddings and a self-attention mechanism, for predicting protein-target binding affinity.
The raw data can be found at [PDBbind](http://pdbbind.org.cn/) including three datasets: version 2020,core2016 and core2014.
Data preprocessing can ... |
0f4296dd78d5a644862c00599f7d669339116af6bc9678ef4882d83778f68e11 | Text | 2,016 | 60 | --------------------------------------------------------------------------------
README : BAMTOOLS
--------------------------------------------------------------------------------
BamTools provides both a programmer's API and an end-user's toolkit for handling
BAM files.
I. Learn More
II. License
III. Acknowledg... |
1337f823439a940a5e630f2ee4ecb521658af508902f1a4a2e6eef029a15e65c | Text | 2,017 | 52 | README
================
This is the code used for data processing and statistical analyses in
Flaherty R, Sui YV, Masurkar AV, Betensky RA, Rusinek H, Lazar M. Diffusion imaging markers of accelerated aging of the lower cingulum in subjective cognitive decline. Frontiers in Neurology. 2024;15. doi: 10.3389/fneur.2024.... |
32855318915435e5173141f9bc1b196e41190f9354ee7cc76488a4878bfe620a | Text | 2,025 | 24 | # Preprocessing and encoding analysis pipelines for the encoding of natural speech at the subcortical and cortical level
This repository contains the data pipelines described in *Data preprocessing* and *TRF modeling* in our paper entitled *Auditory encoding of natural speech at subcortical and cortical levels is not ... |
476c5baa726d4fc2a7cd8783c9988abab4c3397d1adb7e105ea4e164a86594fa | Text | 2,034 | 81 | # OneShotHippocampus
This repository contains the code for the publication
A Hippocampus Model for Online One-Shot Storage of Pattern Sequences
https://arxiv.org/abs/1905.12937
# Create the environment
Conda:
<code>conda env create -f environment.yml
</code>
Pip:
<code>
pip install -r requirements.txt </code... |
e27c265e5ec5712bdfa004c6db9c89b38bd43a8d3bc9fea8566bcfd01ccb22f4 | Text | 2,034 | 38 | # Non-Linear Correction Readme
## Download Example Data (if needed)
If you want to try with the demo data provided in the sub-folder here . Alternatively you can create your own image with a single channel and increase the laser power incrementally.
Requirements
## Works with MATLAB v9.11 and above, you may also need…... |
5907bfe96241673a26d644c7df79cb70aa51391be3b895cd1b0009f35387af1c | Text | 2,051 | 22 | # Tool-Localization-
Real-time Tool Localization for Laparoscopic Surgery Using Convolutional Neural Network
This repository contains the Python implementation of the algorithm for tool segmentation presented on "Real-time Tool Localization for Laparoscopic Surgery Using Convolutional Neural Network".
# Overview
Par... |
e9753b0adf0874d74cc8ecc11b6985b4b1428c490ba8147d368c35ec82c7b696 | Text | 2,057 | 16 | # Partial Discharge Localization
This repository maintains codes and logs for [Partial discharge localization in power transformer tanks using machine learning methods](https://www.nature.com/articles/s41598-024-62527-9) paper [^1].
> refer to [Lee, S.W. et al. 2014, *Neuron*](https://doi.org/10.1016/j.neuron.2013.11.028):
Computations underlying arbitration between MB and MF learning
#### Minor modific... |
749ba82e0f7f6528d3611c5b74870b6fe2ee98243bf84ecc3a3d8b507291a3c0 | Text | 2,117 | 46 | # Getting Started with Create React App
This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
## Available Scripts
In the project directory, you can run:
### `npm start`
Runs the app in the development mode.\
Open [http://localhost:3000](http://localhost:3000) to view... |
edfcd6506a2f7e3136e0ba054afd0f1d7e5ae147942b7fdb2adb2be59db01ca0 | Text | 2,131 | 50 | ## Swc importer and exporter for Imaris 10.0.1
Based on the original implementation by Sarun Gulyanon (2018). Re-implemented from scratch for **Imaris 10.0.1** and **Python 3.7** and updated some things like generation and saving individual filaments separately and exports more consistent with the .swc specifications.... |
b2d6cb70a694d2b8c0d7fcd4966839acbc4680486eb309678d64e97daba16b8e | Text | 2,132 | 17 | # DGCPPISP
A PPI site prediction model based on dynamic graph convolutional network and two-stage transfer learning
## Abstract
We propose a PPI site prediction model (DGCPPISP) based on a dynamic graph convolutional neural network and a two-stage transfer learning strategy.First, we introduce the transfer learning... |
53b40c5d1be4f10a61b3a337c15dee8234ad67b389255b0260e1163a80876bbc | Text | 2,141 | 51 | # SPA-REM2
## Description
Our application Structural assessment of Proteins using Ancestral sequence reconstruction (SPA) is designed to examine the evolutionary history of a protein.
## Initial setup by the user.
Place the SLAC json in the data folder `mammalian_REM2_codons.SA.FilterOutliers.fasta.SLAC.json`
Plac... |
1510f426ccfa3e2f66c60b41d6fddbb7daf0ce76dd435a3a64c934787f314e9a | Text | 2,148 | 40 | # Vulcan
[](https://travis-ci.com/Aifred-Health/Vulcan)
[](https://vulcanai.readthedocs.io/en/latest/?badge=latest)
Vulcan is Aifred Health's framework f... |
c69e8fdbce1f16bd0b3e6d26ecec669a80f37306b9517a6af9f96555fb967c18 | Text | 2,150 | 24 | # Single-MITOchondrion (SMITO) Data Analysis Scripts
## Overview
This repository contains code for SMITO data analysis.
For SMITO computational pipeline, see [smito-pipeline](https://github.com/kimpenn/smito-pipeline).
## Author
Youtao Lu (<luyoutao@sas.upenn.edu>)
## Copyright
```
Copyright (c) 2021-2023, Youtao Lu,... |
c73f7fcdce1d3f79a822f06f79e3c6c6c7c8ee0929e36c2b988c1931e11ffa95 | Text | 2,151 | 72 | # MIGRATION WARNING
pyComBat has been merged into [InMoose](https://github.com/epigenelabs/inmoose), and is no
longer maintained as a standalone package.
This repository remains up for reference, but will no longer be updated.
# pyComBat
pyComBat [1] is a Python 3 implementation of ComBat [2], one of the most widely... |
74bb2aa091bb36a8f010da10f0ae4008d79877ac810f052d9a1d170c7b03798c | Text | 2,177 | 25 | # NKK
Neural network kinetics - NNK
Vacancy diffusion barrier dataset for NNK model: https://doi.org/10.5281/zenodo.17069342
This data repository contains the data for training the neural network model in the following paper.
Xing, B., Rupert, T. J., Pan, X., & Cao, P. (2024). Neural network kinetics for exploring ... |
0ce95d3a43ecb3713a00188d8196d69fdc1cde0aebde615198521fa6631b2e03 | Text | 2,191 | 28 | # Single-cell classification based on label-free high-resolution optical data of cell adhesion kinetics
This is the supplementary repository for our paper titled "Single-cell classification based on label-free high-resolution optical data of cell adhesion kinetics". This was originally forked from the [DL-4-TSC](https... |
b33fe677e41cf3f321d3ad5f3220bfc5a2bff1bf53c468911cd48141c5923a17 | Text | 2,193 | 41 |
# The Open-Source Electrophysiological Toolbox
## INTRODUCTION
OSET is a collection of electrophysiological data and open source codes for biological signal generation, modeling, processing, and filtering, originally released in June 2006. The toolbox is distributed under the BSD License ... |
9b154e469b89dd06725e15d31e49a9a4fc2d2ec903dff02dea69a2db86630bae | Text | 2,221 | 23 | # Interdependence-of-cellular-and-network-properties-in-respiratory-rhythm-generation
Instructions for running simulation code.
1. Copy spk.cc file to new directory and create subdirectory labeled "data"
2. Compile code using g++ compiler (ver. 9.3.0) using the command:
```
g++ -std=c++0x -O2 spk.cc -o spk
... |
22df83d84f98b1816544c6dddbd07244abefa00094d8fe28855d8077561525c0 | Text | 2,237 | 40 | # ComMat
Community-based Deep Learning and Antibody H3 Loop Modeling
## Installation
Create a conda environment with this command. It will automatically create an
environment named `h3_loop`. You could also optionally provide the name of
the environment.
```bash
conda env create -f environment.yml [-n <name>]
```
If... |
bc28f66a3340631b424eff2e64c2d804349555e54a0445152127c479120d864c | Text | 2,242 | 40 | # Panoramic Dental X-Ray Image Semantic Segmentation with TransUnet
The unofficial implementation of [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://arxiv.org/abs/2102.04306) on Pytorch
*Output of my implementation. (A) Original X-Ray Image; (... |
0fabb60a79f4b700434371f5af955fa1d8160dbb2bf2bf66d6d4ad1940032abe | Text | 2,243 | 21 | # Hu_scRNA_COVID Project
[](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularit... |
9a751a65451fb814e17bcda7b281cc5385324681efff5a1ab58cdfdccaf7fe6d | Text | 2,257 | 64 | ---
license: agpl-3.0
language:
- en
metrics:
- mae
- mse
- accuracy
tags:
- biology
- plant
- vitis
- downey mildew
- Plasmopara viticola
- OIV 452-1
base_model: microsoft/swin-tiny-patch4-window7-224
---
# OIV Leaf Disc Phenotyping
Companion repository for the article
"Phenotyping grapevine resistance to downy mild... |
d81cfa943cde1e7120c1b2b2cb27e89b10caf2b1163ee8d279073770cff16100 | Text | 2,266 | 23 | Neurocarta is a MATLAB toolbox for the construction and analysis of neural networks based on neural projections data from the Allen Brain Atlas.
## About
This toolbox can be used to compile neural projections data from the Allen Mouse Connectivity Atlas (AMBCA), and construct and analyze neural networks based on th... |
80caad9f6bdcaccf3aaba4e459bcffa32dcd1e9f263f6ac5a3333293497aa949 | Text | 2,272 | 42 | # Image Warping Code
### There are two main functions (python) for warping an image to the shape of curved screen.
### 0. Prerequisite
- As only a part of display pixels can be projected onto a screen, it is crucial to know which are the usable pixels.
- For this, we need to get 3 or more points (x, y coordinates)... |
5edb64094af1bc4d1e939fd2688f1b9b2373dbbde31e756713df088d3de6beaa | Text | 2,314 | 31 | # MRIgeneralizedBloch.jl
| **Documentation** | **Generalized Bloch Paper** | **In Vivo Imaging Paper** | **Build Status** |
|:------------------------- |:------------------------------|:----------------------------- |:------------------------------------- |
| [![][docs-img]][docs-ur... |
dcd3535b5c86d417d25622f18e70adf5a537e202e2a2cb4661930c6e90417680 | Text | 2,314 | 19 | ## About
The repository contains code for the following tasks included in [A prognostic neural epigenetic signature in high-grade glioma](https://www.nature.com/articles/s41591-024-02969-w) [1]:
|Task | Description | Source |
|:--------------------- |:------------------- |:-------------------:|
| A... |
348298f164cc96dab7280b8aa8e26190c4f02f28c38b9bb9bbe0a09f393d0fb6 | Text | 2,329 | 39 | Code for "Computational reconstruction of mental representations using human behaviour" (Caplette & Turk-Browne, 2024, Nature Communications) (preprint: https://psyarxiv.com/7fdvw)
This python code should work on all platforms, however it has only been tested on macOS 11, 12 and 13.
Various Python libraries are requi... |
d79ec4969d428d5fb292c7865f8896a9112230333931737c112a987f9b1448b2 | Text | 2,336 | 39 | Code for "Computational reconstruction of mental representations using human behaviour" (Caplette & Turk-Browne, forthcoming, Nature Communications) (preprint: https://psyarxiv.com/7fdvw)
This python code should work on all platforms, however it has only been tested on macOS 11, 12 and 13.
Various Python libraries ar... |
f53dce8abc51dbd202213eb7e68fdfda08a5de7913874e91a3ab750e94aec563 | Text | 2,344 | 49 | > [!WARNING]
> The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
> Future development will take place at: https://github.com/openbraininstitute/atlas-enhancement
# Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel colum... |
4520ac31c4060067478f5c845318f39c4bd860b08c649a35a763810fae6973a5 | Text | 2,348 | 86 |
<div align="center">
<p align="center">
<img src="./artwork/poet_header.png" alt="plot" width="400">
</p>
[📚Documentation]() |
[💡DEMOS]() |
[🛠️ Installation]() |
[🌎 Home Page]() |
[🚨 News]() |
[🪲 Reporting Issues](https://github.com/peach-lucien/poet)
## Description
This repo is the implementation accompanying the above mentioned paper. The directory structure is as follows:
-Data contains a subdirectory (brainTumo... |
e9b316b9c4b3f6a6bac7e47f5a53810ff70ab7b387bf17297cf5bc706b7ada4a | Text | 2,362 | 57 |
## Integrating fNIRS and Machine Learning: Shedding Light on Parkinson's Disease Detection
---
About the project
---
This project presents a methodology for the analysis of fNIRS signals with Machine learning for assisting in the diagnosis of Parkinson's disease(PD).
The following steps are performed with this code:
... |
38236c0e905ed2f88618be7019ad238a1fb8f573a51cf70a0b10c0cd3e7c86d2 | Text | 2,364 | 42 | # Brain inter-regional molecular connectivity analysis in AD
This is the official repository of the paper ["*Alzheimer’s disease rewires gene coexpression networks coupling different brain regions*"](https://www.biorxiv.org/content/10.1101/2022.05.22.492888v1) by Sanga Mitra (+), Kailash B P (+), Srivatsan C R, Naga V... |
cc75585c5cde22a9971110727ceed05e0723e3e683ad8dccdddc5c3a2c0416f7 | Text | 2,389 | 61 | # RiboDiffusion
Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models
[](https://github.com/ml4bio/RiboDiffusion/blob/main/LICENSE)
[](https://arxiv.org/... |
ecddffe6b4bfff263328af9f8d4e431177888c21cb0f3ec0450aabbf9c882ad5 | Text | 2,405 | 56 | <!--- [](https://travis-ci.org/choderalab/perses/branches) --->
[](https://github.com/choderalab/perses/actions?query=branch%3Amaster)
[
This repository contains the experiments done in the work [An Empirical Evaluation of Generic Convolutional and Recurrent Networks for Sequence Modeling](https://arxiv.org/abs/1803.01271) by Shaojie Bai, J. Zico Kolter and Vladlen Koltun.
We sp... |
ea65c7554730a1a508af4e02089c07cada4f555cc2f5bbbeada3b255e1b60ecc | Text | 2,424 | 44 | mrQA : automatic protocol compliance checks on MR datasets
=============================================================
.. image:: https://img.shields.io/pypi/v/mrQA.svg
:target: https://pypi.python.org/pypi/mrQA
.. image:: https://app.codacy.com/project/badge/Grade/8cd263e1eaa0480d8fac50eba0094401
:... |
4e54300305d775e853ca73358fb3ff17dc0a9d47fd23aecdb8a533e53ec60605 | Text | 2,426 | 50 | # LVPP sigma-profile database
This is the LVPP sigma-profile database for COSMO-based models. It currently contains information for more than **1700 molecules**.
Currently, in this repository we only provide the COSMO apparent surface charges computed either with
[GAMESS](http://www.msg.ameslab.gov/gamess/) or [MOPAC... |
69112c9a265b6e4748324c361d221f11e2814e0c4fc97982011e48dfe7bbcbc1 | Text | 2,455 | 39 | # SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations
## Setup:
```bash
$pip install -r requirements.txt
```
## Download processed datasets from Zenodo
```bash
$pip install zenodo-get
$zenodo_get 10.5281/zenodo.10076432
```
## Cross-validation of SAFER-C2 model... |
406884c97d9de71db6865156679be9304d40075dd9697706f6caf1e4fc793e55 | Text | 2,467 | 31 | ## Repository containing scripts, notebooks and preprocessed datasets for:
============================================================================
# Patch-seq of endocrine cell exocytosis links physiologic dysfunction in diabetes to single-cell transcriptomic phenotypes
## by Camunas-Soler J, Dai X, et al., http... |
d55734f1731d67a376ed70a562c1b7539c63c7f48c7ff01fde06be58c13ae38a | Text | 2,470 | 57 | # Learning Bayes-optimal dendritic opinion pooling
This repository contains data and analysis scripts to reproduce the figures as well as source code and simulation scripts to perform the experiments described in [1].
<div style="text-align:center"><img src="intro.png" alt="intro" width=100%/></div>
<sub>__Dendritic... |
f694862017bf0f030c7ac5096c9ca6d650dd6d429ca980db9a2e6bc34df494e7 | Text | 2,476 | 66 | # BiœmuS: Biomimetic Emulation of Single compartment neurons
## Overview
BiœmuS is a biomimetic real-time Spiking Neural Network (SNN) emulating single compartment Hodgkin & Huxley neurons running on SoC FPGA (AMD Zynq UltraScale+ MPSoC).
_Maintainers_: Timothée Lévi (timothee.levi@u-bordeaux.fr), Jérémy Cheslet (je... |
06f82533cfed1062b786c87c8f51cc894ae484e8b6e0f95a55ceeb896131abe9 | Text | 2,489 | 23 |
# Romanian, Russian, and English Proficiency Language Tests: The GAT and SHIPLEY
The Grammatical Assessment Test (GAT) was constructed following a similar methodology as in Linebarger et al., 1983, originally developed to assess comprehension failures in agrammatic aphasics (Linebarger et al., 1983).
A new set of se... |
708cf5c540929f7f856488fbc381abc80f6c80aebb56a82599eeba897bdd7d7d | Text | 2,506 | 14 | # frailty-depression
Association between physical frailty and incident depression
Cox proportional hazard models were used to estimate the association between frailty status and depression incidence with follow-up time as the time-dependent variable. Individuals classified as non-frail were used as the reference grou... |
fa6b18cf0a5c82bdfa1ab7119ff516a01f0ae302734ffb603829b21dc2315e51 | Text | 2,516 | 48 | # LIBD Sex Differences in Schizophrenia
**Abstract**<br>
Schizophrenia is a complex neuropsychiatric disorder with sexually dimorphic features, including
differential symptomatology, drug responsiveness, and male incidence rate. Prior large-scale
transcriptome analyses for sex differences in schizophrenia have focus... |
661e11101fc619f6751f1366ca4080584d824980d5e0aba8a73db3849bda013e | Text | 2,537 | 91 | # Retina-chatbands
A CNN-based detection of retina ChAT-bands.
Further details can be found in: Muellner & Roska 2023, https://doi.org/10.1101/2023.03.22.533751
Please cite our manuscript if you use this code.
## Installation
Frist, clone or download this repository.
Create a python environment (Optional, but rec... |
e1fa2d0d24e0e9c7a225c01925abfb14cb1dcb7cf3e76c96f4cbe26163df0b5f | Text | 2,549 | 46 | # SNN4Agents: A Framework for Developing Energy-Efficient Embodied Spiking Neural Networks for Autonomous Agents
SNN4Agents is a framework for enabling efficient embodied SNN deployments for autonomous agents. It consists of a set of optimization techniques for designing energy-efficient embodied SNNs targeting auton... |
63abe55c2b551b056fd40fb805ce212d73b844f9a68426e6d7df741b64f1ca9b | Text | 2,573 | 75 | # Information Bottleneck-Based Hebbian Learning Rule Naturally Ties Working Memory and Synaptic Updates
A biologically plausible implementation of the HSIC objective.
Please cite our work if you use this codebase for research purposes:
```bibtex
@article{10.3389/fncom.2024.1240348,
author = {Daruwalla, Kyle and Lipas... |
1a8c8595fc4bc6edeec96b65752b81aade0332a617075c8773dc32d7b4fe531a | Text | 2,584 | 41 | # Uncovering spatial representation in large scale recordings using topological data analysis and unsupervised ensemble detection
Code for the analysis conducted in "Uncovering 2-D toroidal representations in grid cell ensemble activity during 1-D behavior" - E. Hermansen, D. A. Klindt. & B. A. Dunn (https://www.biorx... |
06bf05adcc604a17177f04d6dade8f5cc5a8ec58c3e48252baba8f193b7d0fcc | Text | 2,590 | 45 | # Data for the Franke, Willeke, et al. (2022) article: 'State-dependent pupil dilation rapidly shifts visual feature selectivity'
## Summary
Here we provide the complete data for the article Franke, Willeke, et al., 2022 'State-dependent pupil dilation rapidly shifts visual feature selectivity'.
https://www.nature.... |
3abd2ce26bd95c3ddc5417afddd13f400671e987ee9690a0bda1bf00b8b33de7 | Text | 2,604 | 24 | # Few-Shot-Proto-TL
This is a repo for the paper titled Post-Stroke Hand Gesture Recognition via One-Shot Transfer Learning using Prototypical Networks
The research presented in this paper improves the classification accuracy of subject-independent models for hand-gesture recognition post-stroke by using prototypical ... |
1717a50a718f9231c6c0f8e04b66abedbaa135e55a3b9e7cfcf7b9be4fa05da0 | Text | 2,611 | 35 | # stMDA
stMDA (Multi-modal domain adaptation for spatial transcriptomics) is a python tool for spatial transcriptomics analysis.
## Abstract
Spatially resolved transcriptomics (SRT) has emerged as a powerful tool for investigating gene expression in spatial contexts, providing insights into the molecular mechanisms ... |
44eecc6aa419ea5c4260ce3b937ce990e6146cb22ada6d79c16064fa5a7236c0 | Text | 2,613 | 88 | # Retina-chatbands
A CNN-based detection of retina chatbands.
## Installation
Frist, clone or download this repository.
Create a python environment (Optional, but recommended):
```
conda create -n retina-env python=3.6
conda activate retina-env
```
If you are on a machine with a CUDA-compatible GPU, you should f... |
a0df1d29819f09c57aecb2f1e20d3c940f80033e852401b07fef6f87416c5103 | Text | 2,620 | 63 | .. inclusion-marker-do-not-remove
SPANN
=====
paper “SPANN: Annotating
single-cell resolution spatial transcriptome data with scRNA-seq data”
(under peer-review at bib) |image|
File Descriptions and data requirement
======================================
SPANN is a single-cell resolution spatial transcriptome data ... |
e264d7170d298fac88a512808a9088f2d7743a2686f2e4fa4ef3326296328aae | Text | 2,634 | 43 | # EBC Diffusion MRI Preprocessing
Scripted processing of the post-mortem chimpanzee diffusion MRI (dMRI) dataset acquired within the framework of the Evolution of Brain Connectivity (EBC) project.
## Input
- DMRI EBC Dataset in Bruker PV 6.0.1 File structure
- High-Resolution FLASH Dataset in PV File structure
## Out... |
038f0608974abe8f3232340ca58beced0bea7857d5bebf4a8828f54cfe440d8e | Text | 2,641 | 37 | # SPANN
jupyter notebooks for bioinformatics paper "SPANN: Annotating single-cell resolution spatial transcriptome data with scRNA-seq data" (published at briefings in bioinformatics) https://academic.oup.com/bib/article/25/2/bbad533/7590316
. Below provides an illustration of the sampling process.
## Inst... |
9bbdf17fe44c5539123c3f3d0ed344f9d246c726280995fef8da7ba5b1ed716c | Text | 2,673 | 59 | # neurovisfit
[](https://img.shields.io/github/v/release/sacadena/neurovisfit)
[](https://github.com/sacadena/neurovisfit/actions/workf... |
566c8def7d5fe36eae7ff2726d945d5af277ccb55278a312a4593ab56de0f38c | Text | 2,675 | 60 | Please refer to the manuscript for context, data collection methods and statistical analyses.
For questions or to notify the authors of any errors, please contact the corresponding authors at: zegni.triki@gmail.com, and angelo.guadagno@unibe.ch
############################
cichlid_data.csv
######################... |
0a984959113c7c3a691087097b50d2ad00ed28c6012ac4fafc1f5921a2805db1 | Text | 2,679 | 29 | # nNRF_validitystudy
## DESCRIPTION
Establishing a standardised approach for the measurement of neonatal noxious-evoked brain activity in response to an acute somatic nociceptive heel lance stimulus - scripts for figures and analysis.
These are the scripts used in the analysis of data for a study that was pre-registe... |
07d36526f89f7960ff2800c94ec0d726f36e290028560ebcb00c841379f79cc0 | Text | 2,681 | 56 | # BCN 20000 tools for assembling and training
<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/"><img alt="Creative Commons Lizenzvertrag" style="border-width:0" src="https://i.creativecommons.org/l/by-nc/4.0/80x15.png" /></a>
This repository gives access to the tools to train the models presented... |
de9fed9e5b6f3065eb1025bf76c80375bd2e99e8a7b640c231565b1185358a21 | Text | 2,712 | 42 | # Model and Data for Perturbed Balance Control Simulation
The purpose of this simulation experiment was to explore the effects of COM feedback delay duration on balance. These experiments were performed in SCONE (with Hyfydy, version 2.0.6.2448,https://scone.software/).
## Setup
This folder contains the files needed... |
8b3d649a7c56e5621b9ba7750549c249fa224e0e0ad19a486422649ff7fec681 | Text | 2,725 | 31 | # volDNN
This package might help you train volumetric DNN models (think trained on 3D MRI data) in a repeated, nested, k-fold cross-validation scheme using pytorch. It contains code used for this preprint, where we showed 3D CNNs improve classification of chronic stroke patients with severe language deficits by identi... |
5e03211bde35301cbd84cff9cf6bd3d6b81f138181d2002060a68b9b5807c4a5 | Text | 2,743 | 18 | # Convolutional Neural Network based Thalamic Nuclei Segmentation for MPRAGE images
Thalamic nuclei have been implicated in several neurological diseases. Thalamic nuclei parcellation from structural MRI is challenging due to poor intra-thalamic nuclear contrast while methods based on diffusion and functional MRI are a... |
ed856d48a1e4c2cf82511980510dc9603eb009a9816eac40bbbbd5fea65d39c0 | Text | 2,753 | 63 | # ReMIND Data Conversion Scripts
This repository includes scripts designed for the conversion of ReMIND data between NRRD and DICOM formats. The scripts serve two primary purposes:
1. **Conversion from NRRD to DICOM for TCIA:**
- Step 1: Conversion of NRRD images to DICOM images for ultrasound and MR data.
- ... |
7c3abda61a3d952ed10a732fb39007ae3e8776a1c7fda958be9987d9649b724a | Text | 2,789 | 26 | # KineticAssembly_AD
Python code for numerical simulations of self-assemly with optimization by automatic differentiation
## Installation ##
The easiest way to install the simulator is to clone this repo and then build an environment containing all dependencies using the provided `base_requirements.txt` file. In orde... |
fe51783e533ad24386e55f6f55efc0ece3c7d3659bb9adaae46a28e6b3fb300f | Text | 2,798 | 67 | [](https://github.com/cgat-developers/cgat-flow/actions/workflows/cgatflow_python.yml)
CGAT Flow
=========
We have developed a set of [ruffus](http://www.ruffus.org.uk) based pipelines in comparative genomics an... |
26b7708ea22dbe5d46ef75b8da5828df9e2ffbb14f5427da4138ee617088ec62 | Text | 2,827 | 44 | # ldr: Dockerized LD regression
This repository provides a Dockerized version of `ldsc`, a tool for performing LD Score regression. It is intended to facilitate the production of custom binary annotations for SNPs and computing partitioned heritability as described in [Finucane, HK, et al. Partitioning heritability by... |
35be5a97ffee913d647603002660bbd11486d23ce83691ef36f38d3e6171ef69 | Text | 2,847 | 40 | # MRIgeneralizedBloch.jl
| **Documentation** | **Generalized Bloch Paper** | **In Vivo qMT Paper** | **unconstrained T<sub>1</sub> Paper** | **Build Status** |
|:------------------------- |:------------------------------|:----------------------------- |:-------------------------... |
269f40d4cd693fba6692dcc94449b77575a5538294117926834dd47e8f517bc7 | Text | 2,864 | 11 | # TetO-shTPH2_rats
Code and data for the article: Poor Decision Making and Sociability Impairment following Central Serotonin Reduction in Inducible TPH2-Knockdown Rats
Article: Alonso L, Peeva P, Fernández-del Valle Alquicira T, Erdelyi N, Gil Nolskog Á, Bader M, Winter Y, Alenina N, Rivalan M. 2024. Poor Decision M... |
479325482f7caa2d5eab5390b607fd5f6a72cfcf36f645c330661694aef7331b | Text | 2,877 | 55 | # VRF-and-progression-of-WML
This repository contains analysis and simulation scripts for the pre-registered project on the association of vascular risk factors and progression of white matter hyperintensities.
To rerun the analysis with a surrogate dataset, please use `calc_models_on_synthdata.R`:
## synthetic_impu... |
42572ee2d5d6ec900da8113f900b0dafe073a0e619a6efa535230203a22842bf | Text | 2,885 | 49 | # Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning
This repository contains data analysis and sequence design code from [Castillo-Hair et al. *Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning.* Nat. Commun. 2024](https://www.nature.com/articles/s4146... |
9a9281af8e81d8c02f56192ce5dce36df2315fa7878731fcd51522572cf3fdf1 | Text | 2,896 | 51 | # LVPP sigma-profile database
[](https://doi.org/10.5281/zenodo.3613785)
[](https://doi.org/10.1021/acs.jctc.5c01368)
This is the LVPP sigma-profile database for COSMO-based models. It... |
5ca46fccc4f0d01b45d2fb75bf6af66824faf5f36ab252769d3ff3706acfb3ff | Text | 2,916 | 33 | # scim
Code for Universal Single-Cell Matching with Unpaired Feature Sets
Integrates datasets from multiple single cell 'omics technologies in two steps:
* Constructs a technology invariant latent space
* Matches cells across technologies by bipartite matching of latent representations
See demo.ipynb for how to set... |
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