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28f8992c63f1999348a5e7aaa168cfe2360def4472a8f917af5f055e3d7bb91c | Text | 4,559 | 119 | # Disease-driven domain generalization for neuroimaging-based assessment of Alzheimer's disease
This work is published in _Human Brain Mapping_ (https://doi.org/10.1002/hbm.26707).
## Introduction
This repository contains the implementation of a deep learning framework that uses disease-informed prior knowledge to t... |
d0542c850307184a047de3ccf23c8b28813476e94cf62176aed4156ce4478e01 | Text | 4,561 | 85 | ## Reconstructing the cascade of language processing in the brain using the internal computations of transformer language models
This repository accompanies the manuscript "Reconstructing the cascade of language processing in... |
08f0ea80145a3f0a64310621fbd65775405a24f986fa00183b0906fa0e46b562 | Text | 4,601 | 55 | NOTE: MiniscopeAnalysis is not being developed anymore. This version is only compatible with the v3 miniscope DAQ software.
Please keep submiting requests concerning issues or pull requests.
I am currently working on a new analysis pipeline called PIMPN:
https://github.com/etterguillaume/PIMPN
PIMPN performs similar an... |
df8aa047558df7d6b244253c12d6e389b01fc163c5fbf9e387f181d0e6a2248f | Text | 4,622 | 109 | # Blush Regularization Training Code Samples
This repository contains key parts of the code for the training procedure of Blush regularization.
In particular, it contains the data augmentation function and the loss function that where used in the paper.
To train a model, one needs to prepare the training dataset and ... |
29fbd796e39247e5f12157a8f9c105fc9af5426f8ae8c09e1d2cb9fdca2110aa | Text | 4,641 | 51 | # DAE architecture exploration
Pipeline for the exploration of denoising autoencoder (DAE) architectures performed in the paper 'Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders.' If you use this analysis, please cite our paper.
[doi.org/10.1093/bioadv/vbae066](h... |
cfc8af69221574545d0f9d269a25896ba71bf71df8642ea02ea9e70395028596 | Text | 4,642 | 51 | # Lapse-Causes
This is the code for the publication {Title}.
The EEG preprocessing was previously done with the scripts from this [other respository](https://github.com/snipeso/Theta-SD-vs-WM).
The Lateralized Attention Task (LAT) task code can be found [here](https://github.com/snipeso/LAT).
## The Code
### Analyses... |
dc2b50efaefa51f0135bbfd9082dc13db818cdf55b4b64b7e63672c016fe6886 | Text | 4,687 | 58 | # STT
## Introduction
We present a spatial transition tensor (STT) method that utilizes mRNA splicing and spatial transcriptomes through a multiscale dynamical model to characterize multi-stability in space. By learning a four-dimensional transition tensor and spatial-constrained random walk, STT reconstructs cell-sta... |
7b0f6d28e37c9a2fa8d356c955bae6b731a48f6ca50b12a94e5d8d425545ff87 | Text | 4,728 | 88 | # Simulations and other relevant materials for Ozminkowski and Solis-Lemus (2022)
Manuscript:
```
@article{Ozminkowski2022,
author = {Ozminkowski, S. and Sol'{i}s-Lemus, C.},
year = {2022},
title = {{Identifying microbial drivers in biological phenotypes with a Bayesian Network Regression model}},
journal = {In prepar... |
1b507ef30f94210d977f91b43cddbcf6d8e64f55c1ddf1018023177a54c7bce9 | Text | 4,754 | 111 | # csMR
We introduce the **C**ell-**S**tratified **M**endelian **R**andomization (**csMR**) framework to find cell-stratified causality of complex traits/diseases by integrating GWAS and single-cell eQTL data.
## **Workflow**
<p align="center">
<img src="illustration/csMR_workflow.jpg" width="550"/>
</p>
## **In... |
db04177d55a63e1d3f772bd64b7bf4947a80a57ac6e0c1cc63b3c0835c450b8f | Text | 4,763 | 90 | # Real-Time Outage Management in Active Distribution Networks Using Reinforcement Learning over Graphs
## Contents
- [Overview](#overview)
- [Reinforcement Learning Training](#repo-contents)
- [Testing](#system-requirements)
- [Demo](#demo)
# Overview
Self-healing "smart grids" are characterized by fast-acting, in... |
173df967409be6cd04e80bcb92a664a2dc33e443a3a4df70443e3500015aa08b | Text | 4,767 | 44 | # Single-cell recordings from three cortical parietal areas during an instructed-delay reaching task
## Summary
We publish six electrophysiological datasets obtained from three regions (V6A, PEc, PE) within the superior parietal lobule (SPL) of two Macaca fascicularis monkeys (MonkeyS and MonkeyF). The datasets were co... |
ed466b94278af1087f1ba05667f679404ea9488b9be6df3bcbfb9677699910ae | Text | 4,785 | 120 | # Single-cell assisted deconvolutional network
[
VANTAGE is a graphical user interface written in Python that enables users to simultaneosly view VIDEO and TIME-SERIES data.
For more information please see the [journal article](https://besjournals.onlinelibrary.wiley.com/... |
bef09b83e3e8e74f065d5f105795bd86745975be07407aaa087ba6c3ad1ffba4 | Text | 4,791 | 96 | # PNAbind
PNAbind is a python package and collection of scripts built for computing protein surface meshes, assigning chemical, electrostatic, geometric and MSA features to those meshes, and building/training graph neural network models of protein-nucleic acid binding.
## Overview
The o... |
ce9cc9160f878740a3d4d2b0ec20ee9abe5a2c4b64010f6860a236ea5af9eb1b | Text | 4,807 | 115 | # SpatialPrompt : Spatially aware scalable and accurate tool for spot deconvolution and clustering in spatial transcriptomics
Article url: https://doi.org/10.1038/s42003-024-06349-5 \
SpatialPromptDB database url: https://swainasish.github.io/SpatialPrompt/
### Graphical overview
. This repository contains the source code and links to some datasets used in our paper.
## Abstract
Sequence-based protein–protein interaction (PP... |
6242f9c970696f18167e5d61905db86c7f93e182d8fc5a3c11674bf6596ea19f | Text | 4,824 | 58 | # Neurite_Analyzer
**Citing Neurite Analyzer paper**
Please be so kind to cite our work.
Alexis J. Haas, Sylvain Prigent, Stéphanie Dutertre, Yves Le Dréan, Yann Le Page. Neurite analyzer: An original Fiji plugin for quantification of neuritogenesis in two-dimensional images. Journal of Neuroscience Methods, Volume ... |
23c5f7afcecd51047f57b9a5b528a2d1b642d7059c51a8e5589063f15de062fe | Text | 4,849 | 75 | ## MeshNet: Mesh Neural Network for 3D Shape Representation
Created by Yutong Feng, Yifan Feng, Haoxuan You, Xibin Zhao, Yue Gao from Tsinghua University.
### Introduction
This work was published in AAAI 2019. We proposed a novel framework (MeshNet) for 3D shape representation, which cou... |
537a594fa475b66c4182b8976f1a9ac6d16fe8adf178e6630aed2215bbff1260 | Text | 4,873 | 131 | # EasyDesign
## Table of contents
- [Introduction](#Introduction)
- [Design online](#design-online)
- [Installation](#Installation)
- [Dependencies](#Dependencies)
- [Setting up a conda environment](#setting-up-a-conda-environment)
- [Install and run](#install-and-run)
- [Getting Started](#getting-started)
- [Da... |
1f4f384526c2a86e16179054909426c4bbb775550cfbbd2506a2cb02167a9134 | Text | 4,889 | 63 | # IQ prediction
# Intelligence, brain size, and brain morphometry: resolving conflicting claims
Brain size is associated with intelligence, but the relationship between brain morphometric measures and intelligence is unclear. Studies have produced conflicting results or no significant relations between intelligence ... |
994072400c6ce878396d7fad7032edb499c1fb1cbd59f1ab8985aaf2f14c5d5f | Text | 4,904 | 100 | # Spiking attractor model of motor cortex explains modulation of neural and behavioral variability by prior target information
This is a Python implementation of E/I clustered neural network together with codes to reproduce the figures presented in the paper.
**Vahid Rostami, Thomas Rost, Felix Schmitt, Sacha van Alba... |
27c50d5e673edb6e06c3e54380d86db1069cf615b54e888ea2362934f32083d4 | Text | 4,918 | 60 | # ProcessVast
Scripts and files to perform routine analyses of alternative splicing, based on [_vast-tools_](https://github.com/vastgroup/vast-tools) output
## Summary
This is a tool to make sense of _vast-tools_ output by providing several standard analyses, including similarily of single samples, numbers of changin... |
eed21c779eb666732a1e4d27771f14c0ed127a167759ae41c3798977df482824 | Text | 4,980 | 109 | parsivar
------------
Python library for Persian text preprocessing.
+ Text Normalizing
+ Half space correction in Persian text
+ Word and sentence tokenizer (splitting words and sentences)
+ Word stemming
+ POS tagger
+ Shallow parser (Chunker)
+ Dependency Parser
+ Spell Checker
##requirements
+ [... |
b13141df663e0f2ab3536b948a587bfdfedab8bfcb27145ba438059070294d8e | Text | 4,991 | 84 | <p align="center">
<img src="https://github.com/Tianwei3989/apolo/blob/main/images/annotation_examples.png" width="98%">
</p>
# APOLO: Artwork Provoked Emotion Evaluation
This project is about the study of [Emotional Stimuli Retrieval in Artworks](https://dl.acm.org/doi/10.1145/3652583.3658102) (ICMR 2024).
... |
585f3511439b14fc11f3eb982214f7d799248dd3c16c918d6a0ef29eee88d16f | Text | 5,005 | 85 | # DAT2-CWL
[](https://zenodo.org/badge/latestdoi/183195872)
This repository contains the Common Workflow Language (CWL) definitions of the workflows introduced in the book [#NGS_DAT 2nd edition (A tutorial book in Japanese, 次世代シークエンサー DRY 解析教本 改訂第 2 版)](https://www.amazon... |
66a74e620014db1f4b3f82a3248f3a3004946e83913bf9f5cee51e0a2ae74410 | Text | 5,014 | 138 | # EpiTrace
Computing cell age with bulk and single-cell ATAC-seq data
EpiTrace takes an approximation approach to infer single cell age from single cell ATAC data. It infers single cell age by measuring the total opened reference genomic loci. On these loci, heterogeneity of chromatin accessibility decreases as t... |
4d195da2c8ece63d4981d3a15c135e5814f738b0452961a2bb8d1177f57354f5 | Text | 5,036 | 117 | # Re-facing cGAN
Current repo contains the code for anonymous re-facing of 3D T1w MRI scans using a 3D conditional generative adversarial network.
---
## Additional materials
Models' weights can be downloaded using the [link](https://drive.switch.ch/index.php/s/IW5WdeQg6uUhgcR).
## Requirements
The code was compil... |
3b9f1fe9a581c2cec62b12dd921ba5455454b1745de54365b3b4c71513d8aaf6 | Text | 5,052 | 96 | openff-arsenic
==============================
[//]: # (Badges)
[](https://codecov.io/gh/openforcefield/openff-arsenic/branch/master)
[
- [Required files](#Required-files)
- [Instructions](#Instructions)
- [Troubleshooting](#Troubleshooting)
- [Bugs](#Submit-issues-or-bugs)
## About
R-Code to evaluate Drosophila Time Series data.
DTSevaluation is an evaluation R-code to analyze, visua... |
a5041fbf33718ad7ae594c1b29c34fbd8b99e20e10dc7e2e54b6ca3b40d937c3 | Text | 5,138 | 93 | # DeepGlycanSite: A Highly Accurate Carbohydrate-binding Site Prediction Algorithm
Official implementation of **DeepGlycanSite**, a state-of-the-art method for carbohydrate-binding site prediction.
This repository contains all code, instructions, and model weights necessary to run the method or to retrain a model.
If... |
2832205721bb97853ade48994e0ccd750a9bff81c063ffa6c946d53e4068eeea | Text | 5,144 | 128 |
[](https://zenodo.org/doi/10.5281/zenodo.11130555)
[](https://arxiv.org/abs/2304.07599)
## Table of contents
* [General info](#general-info)
* [Methods-pipeline](#methods-pipeline)
* [Contents](#contents)
* ... |
8d6048fcc13b9d0047707b8486bdc24ae436a5d3d7a3ca5945f6bf44430e4501 | Text | 5,145 | 114 | # csMR
We introduce the **C**ell-**S**tratified **M**endelian **R**andomization (**csMR**) framework to find cell-stratified causality of complex traits/diseases by integrating GWAS and single-cell eQTL data.
## **Workflow**
<p align="center">
<img src="illustration/csMR_workflow.jpg" width="550"/>
</p>
## **In... |
427a89d844952b41928a3f813658aa764596a3b2d5829f3498ad86425e23a34c | Text | 5,155 | 58 |
[](http://robot.obolibrary.org/)
<a href="http://dashboard.obofoundry.org/dashboard/ogms/dashboard.html"><img src="https://im... |
175f276090e4490b581c28d6955a0e49d1f24e5831407900ea68fa423c36d9ab | Text | 5,191 | 72 | # SharpWaveRipple
Cite as:
Blake Laham & Einara Zahn. (2023). einaraz/SharpWaveRipple: V0.0.2 (v0.0.2). Zenodo. https://doi.org/10.5281/zenodo.7592606
[](https://zenodo.org/badge/latestdoi/459619241)
# Overview
The provided script is used to detect sharp wave-ripple (S... |
51ed2b7af20a3eaaa190415e6ca509ef7c60cd3bf90c3df6014107fb679e98d9 | Text | 5,191 | 152 | ## Source codes of the manuscript: GPT-based normative models of brain sMRI correlate with dimensional psychopathology
### Please cite:
Sergio Leonardo Mendes, Walter Hugo Lopez Pinaya, Pedro Mario Pan, Ary Gadelha, Sintia Belangero, Andrea Parolin Jackowski, Luis Augusto Rohde, Euripedes Constantino Miguel, João Rica... |
7781e7d76bfefb462ce3e7b01f1d0fa109187bbfcc9fb417b97f71963f6edff3 | Text | 5,243 | 121 | # **sincFold**
This is the repository for sincFold, a new RNA secondary folding prediction tool based on deep learning.
[Check out the paper!](https://academic.oup.com/bib/article/25/4/bbae271/7690295)
<p align="center">
<img src="abstract.png" alt="abstract">
</p>
SincFold is a fast and accurate RNA secondary stru... |
6be02a075c6a914c01381e4442fc8d9358782c65987ea60f7e9bbbc7d411bd2c | Text | 5,260 | 128 | ARGNet
======
A deep neural network for robust identification and annotation of antibiotic resistance genes.
The input can be long amino acid sequences(full length/contigs), long nucleotide sequences,
short amino acid reads (30-50aa), short nucleotide reads (100-150nt) in fasta format.
If your input is short reads yo... |
a65a44fb50cd3f57d780b091fb77874904522e9f8db7b36506ec10e9e3ec658b | Text | 5,315 | 139 | # KPGT
## About
This repository contains the code and resources of the following paper:
A Knowledge-Guided Pre-training Framework for Improving Molecular Representation Learning
## Overview of the framework
KPGT is a novel self-supervised learning framework for the representation learning of molecular graphs, consist... |
225412532cf1a37dec25bf9923b7d0707bbc53edb3619456a6b150049752d39e | Text | 5,341 | 126 | 
[](https://pypi.org/project/zephir/)
[](htt... |
254b8922ac01fe4218b8533ed13adeb7a8b630f974150f9d437240fcc1088d11 | Text | 5,377 | 64 | # SENNet
This repository contains the software implementation of the Spectral Editing Neural Network (SENNet) model, which can distinguish signals of small and macromolecules based on the linewidth at half-height of spectral peaks, and generate the spectra of small and macromolecules simultaneous from blood 1H NOESY-p... |
f0a13bea1240b135de86c8a95983687f01ebad06ae760806b922eecf9d242592 | Text | 5,384 | 60 | # PENSA - Protein Ensemble Analysis
[](https://doi.org/10.5281/zenodo.4362136)
[](http://pensa.rea... |
8e8fa58c75278959e150f1edb7a74679a75ee064345fb5dee53430145ee2f1eb | Text | 5,390 | 119 | # astroCAST
astroCAST is a Python package designed for analyzing calcium fluorescence events in astrocytes. It provides various functionalities to process and explore calcium imaging data, identify events, and perform spatiotemporal analysis.
## Features
- Fast data preparation
- Efficient event detection algorithm
... |
873853f501df5fc5e4d7a1d66b66c7496c7dcb704a189a9dcb4b1138ca7b6706 | Text | 5,401 | 89 |
# FinderSpiker
## Calcium Imaging Signal Processing Toolbox
### Experiment Profile:
* For synthetic dyes or genetically encoded indicators of calcium (neuronal) activity
* Calcium Transients Offline Detector
* Automatic mode and Visual Inspection Mode.
* Multiple conditions ... |
e06f54d24f3bcded38572b1c4e0212f05648013321072e2b8cddabb2956af6a5 | Text | 5,409 | 108 | # Not seeing the forest for the trees: Combination of path integration and landmark cues in human virtual navigation
Jonas Scherer, Martin M. Müller, Patrick Unterbrink, Sina Meier, Martin Egelhaaf, Olivier J. N. Bertrand, Norbert Boeddeker
## readme
This repository accompanies our publication in [frontiers in Behavi... |
487013b499bd252d22d81e21522710292fa6bc224a13ace2569ca5c5da8f4ddb | Text | 5,438 | 53 |
# Non-small Cell Lung Cancer - Parenchymal Attention
Welcome to [ParenchymalAttention](/ParenchymalAttention/). This project is designed to evaluate the level of attention a neural network places on features present in a region of interest for LDCT images. For any inquires regarding data or issues regarding running th... |
8abe77f92134d8b9c639a71bc0c4b5071ca17fa5e3b16e7e59df5023baed6cb0 | Text | 5,460 | 69 | 
# A collaborative rat functional MRI multi-center study.
A Rat fMRI multi-center study
### Executive summary
In this international collaborative project, we seek to gather the rodent imaging community toward performing a rat fMRI multi-center comparison, within the same template as ... |
266ed9ddc022f8023a4c3438fa30712e224e6b7d4b9f6eb9d9bb9e191c97ed61 | Text | 5,492 | 90 | <div align=center><img src="./Figures/applogo.png" alt="applogo" style="width:90%;height:90%;">
</div>
[](https://www.gnu.org/licenses/gpl-3.0) [ in [PyTorch](https://pytorch.org). IpdSAM is a latent [diffusion model](https://en.wikipedia.org/wiki/Diffusion_model) for generating Cα conformations of [intrinsically disordered proteins](... |
7866bbcf84903997bcb7a7a76af65728cbbb1d645169062eb5780327e466d570 | Text | 5,655 | 127 | # toxoplasma3D
toxoplasma3D is a Python-based analysis pipeline for quantifying ZsGreen+ cell volume from whole-brain 3D light-sheet microscopy (mesoSPIM) stacks, including preprocessing, 3D cell detection/segmentation with artifact filtering, and voxelized outputs for visualization. It also registers brains to the Al... |
65d3407bf5865acb10d4a24c616c90fcf6d615a508826702d3d4cd67127edb5e | Text | 5,704 | 120 | # MotorNet
This repository contains **MotorNet**, a python package that allows training recurrent neural networks to control for
biomechanically realistic effectors. This toolbox is designed to meet several goals:
- No hard dependencies beyond typically available python packages. This should make it easier to run thi... |
d535d2e2ec19f7c21e4413500be91308d1a75ec2e8a605ed820f7e0c25dde103 | Text | 5,746 | 111 | # OMTscoring: A Fully Automated and Explainable Algorithm for the Prediction of Malignant Transformation in Oral Epithelial Dysplasia
This repository provides the inference code for the models used for predicting slide-level malignancy transformation in OED. Link to npj Precision Oncology paper [here](https://www.natu... |
dba6ec1b60dda38b6cd5afb2e0b7e3257ef93cd7eb9bf01c3a08ee2d3ea74a5c | Text | 5,751 | 91 | # GeoLDM: Geometric Latent Diffusion Models for 3D Molecule Generation
[](https://github.com/MinkaiXu/GeoLDM/blob/main/LICENSE)
[](https://arxiv.org/abs/2305.01140)
<!-- [[Code]... |
bdc3b224f561c9c954911bebfede413a417aa185cdc967ae21ce5d1d36a11430 | Text | 5,813 | 148 |
## Table of Contents
- [User Guide](#user_guide)
- [Installation](#installation)
- [Preprocessing](#preprocessing)
- [Usage](#usage)
- [About ANNA16](#about)
- [Cite ANNA16](#citation)
# User Guide <a name="user_guide"></a>
**Oct 2026 Update:**
[The Colab notebook for ANNA16](https://colab.research.goog... |
d22dd022cbffc27264e218b4be9fd9bc1a5515531303685bdcc7afdff8181ed4 | Text | 5,863 | 52 | # Spectrome Repository
[Xihe Xie](https://github.com/axiezai), [Megan J. Stanley](https://github.com/megstanley), & [Pablo F. Damasceno](https://github.com/pfdamasceno)
[](https://zenodo.org/badge/latestdoi/217634383)
[](https:... |
64b62a5c1e703552ca9eca7cdf7ad1b8fa6cb1cd597acb2461c29e6f0e3f0a46 | Text | 5,917 | 55 | [](https://github.com/safugl/embanded/actions/workflows/python-app.yml)
# embanded
Expectation-Maximization algorithm for estimating regularized regression model with banded prior structure. Please see [1] as well as [2... |
9e6d706b38215c6979ef398ba72181b0f9099b8150f317c4c221877456c2dc2e | Text | 5,935 | 80 | <div align="center">
<a href="https://docs.langchain.com/oss/python/langchain/overview">
<picture>
<source media="(prefers-color-scheme: dark)" srcset=".github/images/logo-dark.svg">
<source media="(prefers-color-scheme: light)" srcset=".github/images/logo-light.svg">
<img alt="LangChain Logo" s... |
f5aaf22f095842e6c7bf62e6cb3dc03d559a8e388ab43450eea6fc10005c1664 | Text | 5,952 | 94 | # Treepedia
Developed by the MIT [Senseable City Lab](https://senseable.mit.edu/), *Treepedia* aims to raise a proactive awareness of urban vegetation improvement, using computer vision techniques applied to Google Street View images. Our focus is on street trees: Treepedia doesn't map parks, as GSV doesn't venture int... |
6e3cd3dc7a60001efb42952d75cae1d04c4f306ccfede6598fe6c5705cd56de9 | Text | 5,964 | 68 | [](http://robot.obolibrary.org/)
<a href="http://dashboard.obofoundry.org/dashboard/iao/dashboard.html"><img src="https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fob... |
2893aa79437f00d3ff41cbfebc41146dccc90d636de9b1601a4b866dfad8ed3e | Text | 5,978 | 65 | # Neuronal avalanches in temporal lobe epilepsy as a diagnostic tool: a noninvasive investigation of intrinsic resting state dynamics
---
This repository contains the code and supporting documents associated with the following manuscript:
Marie-Constance Corsi, Emahnuel Trois Lopez, Pierpaolo Sorrentino, Alberto Dan... |
e666e42c084696cfda804ecfccb13c40533dbe2f2443f9e47e87e173816682e3 | Text | 5,983 | 62 | # PENSA - Python Ensemble Analysis
[](https://doi.org/10.5281/zenodo.4362136)
[](http://pensa.read... |
5b24b961294bc22052fdb9c896134411e67fae0c255547427ae58e5f7723b6a3 | Text | 5,984 | 78 | # MALARIS
## Info
This is the code and data for our PLOS ONE paper : An automated system for Plasmodium falciparum detection and parasitemia estimation: evaluation on thin blood smear images
The script uses OpenCV for image processing and a pre-trained TensorFlow model for classification.
by [Aniss Acherar, Ph.D](http... |
ded508502ed0ab192dfe1a3d67743bf3b066eb17c16ed47dc93d4e81cd2eba2a | Text | 5,987 | 131 | ## Shortcut Learning in Medical AI Hinders Generalization: Method for Estimating AI Model Generalization without External Data
Link to publication: [Shortcut learning in medical AI hinders generalization](https://www.nature.com/articles/s41746-024-01118-4)
### Overview
### Abstract
... |
b7e626753ddc6662fee4cb8ce2b7d5c6b6d4a70196d95e883ac1a6d295fd45d7 | Text | 5,991 | 126 | Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
Building samtools
=================
The typical simple case of building Samtools using the HTSlib bundled within
t... |
da16aad754fbbe698bf9b642195eb01e2b1fc718080722c5701e240ea5c82cc4 | Text | 5,999 | 169 | README
================
2024-06-12
# Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq
Peer-reviewed manuscript:
[](https://doi.org/10.1186/s12964-024-01686-8)
Pre-print: ... |
2633b6a568ca17d4f1c7caeeb9cd8eed5d17d55c707944b953e49204dce499d9 | Text | 6,023 | 62 | # CCNL_DecodingEP
This repository contains code and data created in support of my project "Decoding Early Psychoses: Unraveling Stable Microstructural Features Associated with Psychopathology Across Independent Cohorts". All code was written in Python.
## Prerequisites
Before you begin, ensure you have met the follow... |
718d76e477410788a465d8d335148a97af5fecec6c30d538055ebb61be6576ae | Text | 6,068 | 149 | # napari-k2-WaveBreaker
[](https://github.com/SamKVs/napari-k2-WaveBreaker/raw/main/LICENSE)
[](https://pypi.org/project/napari-k2-WaveBreaker)
[](https://bitbucket.org/koopa31/napari_svetlana/src/main/LICENSE)
[](https://pypi.org/project/napari_svetlana)
[![Python Version](https://img.shields.io/... |
838a1008e0de153d41b337ef52126d77cf82108024340fd4852a0c1475d650d4 | Text | 6,124 | 106 | <p align="center">
<img src="logo/logo.png">
</p>
[](https://github.com/geronimp/enrichM/actions/workflows/publish.yml)
EnrichM is a set of comparative genomics tools for large sets of metagenome assembled genomes (MAGs). T... |
9b830877353495fb0172bf3c3ed5cfcf4b49bcbaaf9161f066de52a8b13e44fc | Text | 6,144 | 100 | # metamats.burden.treatment
This code provides functions and scripts to model metastatic development with integration of neoadjuvant treatment. Specifically, it allows to:
1. Model and simulate (pre-surgical) primary tumor growth and pre- and post-surgical metastatic development. To do so, you define
1. A primary tu... |
dd3d9fcce6de1bd84d97e2c27ea267115aca547b49abf2ba9f3bd1b629747bdd | Text | 6,158 | 195 | # OptofMRI5HT [Hamada et al., bioRxiv, 2022, accepted in principle]
This is the code repository for the project about optogenetic fMRI stimulating dorsal raphe serotonin neurons [Hamada et al., 2022].
Findings of the works
1. Functional map of serotonergic activation by optogenetics, including reward-related network
2... |
550ca307f3bd464eb6f98f65e33cab5d3e3e77e010ca5740f692d1242f7227f8 | Text | 6,179 | 101 | # TrG2P: A transfer learning based approach to improve genomic prediction
TrG2P is a novel strategy to improve genomic prediction (GP) performance based on transfer learning. TrG2P aims to get knowledge from the source task's learning system to improve the target GP task. Two main functions were designed in this app... |
1d3d16d0f595717433afa2ba21eeaa7f24f768b62f0a98830985b26b63d69fac | Text | 6,198 | 89 | # ColocQuiaL
This repository contains the code needed to generate dependency files and run ColocQuiaL. Given GWAS signals of your choosing, this pipeline will run COLOC on your signals and all eQTL or sQTL summary statistics that you have available to you. For example, this pipeline will work with the single-tissue eQ... |
77d33efab300c1017c220a43b43001222a56e5af4044c6681b7d10c86dfb2a58 | Text | 6,229 | 126 | # AGILE
This is the official codebase for **AGILE Platform: A Deep Learning-Powered Approach to Accelerate LNP Development for mRNA Delivery**.
🥳 **Updates**: AGILE has been accepted to [Nature Communications](https://www.nature.com/articles/s41467-024-50619-z)!
## Introduction
AGILE (**A**I-**G**uided **I**onizab... |
9a0d49b82d44207b3be35b614933ec93e7dda6b0586efd07f2372d4b542e1697 | Text | 6,275 | 38 | # App_Spike_Train_Analysis_V3
This is an improved version of the MATLAB software for the classification of spontaneous firing patterns based on regularity, grouping of spikes into bursts, and inter- and intra-burst firing frequency.
This version is an update of the previous one, which can be found here: https://github... |
f1d29b205d3a8ef8338a4b4474834e58bd9b90bfc7c422a4acdd9f2d96ff72d8 | Text | 6,338 | 106 | # RIFT phase and visibility
The experiment and analysis code for Spaak, Bouwkamp, & De Lange (2024). [Perceptual foundation and extension to phase tagging for rapid invisible frequency tagging (RIFT)](https://doi.org/10.1162/imag_a_00242). Imaging Neuroscience, 2, 1–14. [https://doi.org/10.1162/imag_a_00242](https://d... |
cba51089beefd4a25461debaa4c574255683a20bb06c911e6ef0c5318e7a9550 | Text | 6,342 | 94 | <p align="center">
<img src="./logo.png" width="50%" title="Allegro" alt="Allegro"/>
</p>
<br/>
[](https://allegro.readthedocs.io/en/latest/?badge=latest)
[](https://... |
4db189a52ee4238aca155f30e1885ad0bc6cdcc5b4ecb5856032a3078df5fa89 | Text | 6,343 | 145 | # Supporting materials — Two omitted controls in data-driven battery degradation analysis
Code, pre-registration documents and result registries supporting the preprint
*Two omitted controls in data-driven battery degradation analysis:
identical-history testing of order effects and entity-level coverage of
prediction ... |
68a5a69de81ec6cbd1d9d3c1d9d3250a6e7c540f345e83c1858df4aac444dd4f | Text | 6,383 | 115 | <!-- PROJECT LOGO -->
[](https://wispermed.org/)
# Download
1. Install the package manager [poetry](https://python-poetry.org/docs/#installation)
2. Clone the repository
```shell
git clone... |
99b875735a6e88f2b18a7d1a87c6997b839786b8e696ea98288a021da3b50a26 | Text | 6,403 | 95 | # Code, derived data and results
For the manuscript *Impact of evaluation protocol on battery state of health estimation accuracy and uncertainty from laboratory cells to electric vehicles*.
The archive holds everything needed to rebuild every number, table and figure of the paper from public raw data: the data-proce... |
c7ddaefce4646ac1f8fd1989a67f169e8f772f4597ec8cc16fa03c0c70e0bfa1 | Text | 6,432 | 59 | # StabilitySelection
This is a package for performing stability selection in MATLAB, using a variety of feature selection/ranking algorithms that come packaged with MATLAB's machine learning toolbox. This comes with a variety of live code tutorials that show how to: 1) run stabSel, 2) properly set up cross-validation a... |
621ec7bacca400abd231b9a9ab005a9a672874242cd4fde5195cc2dfd2307e3b | Text | 6,442 | 73 | ## Dependencies
 
  and R code of the [GDCRNATools Workflow](https://github.com... |
c0f8c7660e49a8dde3ba2ab7a1ffbaaa832684c9d2e59e029852e52bd56ac587 | Text | 6,586 | 235 | # go_enrichment
Transcripts annotation and GO enrichment Fisher tests
## Overview
`go_enrichment` annotates transcript sequences and performs GO enrichment
Fisher tests. The transcript sequences are blasted against the swissprot
protein database and the uniprot information corresponding to the hit is
retrieved from ... |
08bea442f8a50c231391a5eb1b64dd5854f8b4478b44ec07bc978a38b64d62c3 | Text | 6,714 | 60 | # Array Designer #
### Created by Dr. Rob Cooper and Dr. Sabrina Brigadoi ###
#########################################################
If you use any of these tools please cite:
Sabrina Brigadoi, Domenico Salvagnin, Matteo Fischetti, Robert J. Cooper, "Array Designer: automated optimized array design for functional ... |
286decd7a3276f9d17ce889e90dc8c2767a221e1d0d806103f2281cd0e1bfeff | Text | 6,727 | 122 | # Divergent cranial suture fusion at the marsupial-placental boundary
__Authors:__
[Heather E White](mailto:heather.white.17@ucl.ac.uk),
Abigail S Tucker,
Anjali Goswami
__To cite the paper__:
>White HW, Tucker AS, Goswami A. Divergent cranial suture fusion at the marsupial-placental boundary. Journal details need... |
5b90d79423606c304e356087cdfdfcff7e7d4c26cc3cb8f739fc270d2f50f3af | Text | 6,736 | 123 | # Divergent cranial suture fusion at the marsupial-placental boundary
__Authors:__
[Heather E White](mailto:heather.white.17@ucl.ac.uk),
Abigail S Tucker,
Anjali Goswami
__To cite the paper__:
>White HW, Tucker AS, Goswami A. Divergent cranial suture fusion at the marsupial-placental boundary. Journal details need... |
a7864a3e44f0983051ae618f7be5ceb12b739f7c78b1b703ab9991d5ef4ee526 | Text | 6,739 | 102 | # pyebm - A toolbox for Event Based Models
If you would like to use the algorithms, install the toolbox using pip:
- `pip install pyebm`
The examples to use the toolbox can be found in the jupyter notebook at: [link](https://github.com/88vikram/pyebm/tree/master/notebooks)
The event-based model (EBM) for data-drive... |
f958613166572b2223bfcda23adbfcd73ab0ae538af198cfafe2fc71eb571e5a | Text | 6,758 | 76 | # RAYX
[](https://hz-b.github.io/rayx/latest/)
[](https://hz-b.github.io/rayx/latest/Introduction/03-Getting-Started/)
<table>
<tr>
<td>
<im... |
62ecc817c0cedeb9186b17287d811527d069f6f1dc0aa79c6c14051a6e223654 | Text | 6,831 | 189 | SVTyper
=======
[](https://raw.githubusercontent.com/hall-lab/svtyper/master/LICENSE)
[](https://travis-ci.org/hall-lab/svtyper)
Bayesian genotyper for structural variants
## Ov... |
dde804b207f435307dae0dbdace9ed1e3bcd42364dc6590edfbc2f467d001b26 | Text | 6,839 | 127 | # Scoval pipeline
Command line and supplements for the project
## Introduction
We developed Scoval, a Single-cell sequencing COVerage and ALlele-based approach, to combine read-depth and phased LOH metrics, and identify neuronal CNVs that were supported by both orthogonal measurements.
## Required third party tools ... |
1f9c06061e75851a90c6328b9a51cc006f8f6cf003c27b1008886d864baaad23 | Text | 6,906 | 36 | Title
Resting-state fMRI data of Mexican children with a Reading Learning Disorder
Abstract:
Resting-state fMRI data of children with a reading learning disorder (RLD) from Mexico with an age range between 7 and 11 years (n = 25, 7 females). Every participant was assessed using the cognitive test “Escala Neurológi... |
fb3b7d8a295efeeddc9dbcd4ee61f2ffc26fa45cc622461bbba387bf32d65b10 | Text | 6,956 | 114 | # fetal_brain_multiomics
[Mannens, C.C.A., Hu, L., Lönnerberg, P. et al. Chromatin accessibility during human first-trimester neurodevelopment. Nature (2024). https://doi.org/10.1038/s41586-024-07234-1](https://www.nature.com/articles/s41586-024-07234-1)
## Download the loom files
[Pool_peaks.loom](https://www.drop... |
224fe1444bc31eda1c157a769bf36cb52d5ea0118d27460822f93a4b4385b404 | Text | 6,999 | 115 | # [A ConvNet for the 2020s](https://arxiv.org/abs/2201.03545)
Official PyTorch implementation of **ConvNeXt**, from the following paper:
[A ConvNet for the 2020s](https://arxiv.org/abs/2201.03545). CVPR 2022.\
[Zhuang Liu](https://liuzhuang13.github.io), [Hanzi Mao](https://hanzimao.me/), [Chao-Yuan Wu](https://chaoy... |
f5f54bd9e06de4e46acbcd3bbd9360f8fbe43c2da662d45a36547cfbd6e232f4 | Text | 7,079 | 249 | # cayo_brain_transcriptome_sex
#### Repository for the sex-biased brain transcriptome project from Cayo Santiago macaques (bulk-tissue RNA-seq)
This repository contains scripts used in the analysis of sex effects in bulk-tissue RNA-seq data for the Cayo Santiago rhesus macaque population.
Note that we ran most step... |
35f48f28e326540d213aa43a17c56309bc384ef52cb09e2d1ef1ee942bc8798d | Text | 7,132 | 131 |
The source code of paper 'Whole Brain Alignment of Spatial Transcriptomics between Humans and Mice with BrainAlign'
# BrainAlign
[](https://opensource.org/licenses/MIT-2.0)
`BrainAlign` is a Python package containing tools for independence testing u... |
c10c2056d97f85f76780e727534ac7ba73496433900d04f20deeaed3a765217e | Text | 7,204 | 138 | <p align="center">
<img src="https://github.com/divelab/AIRS/blob/main/AIRS_logo.png" width="225" class="center" alt="logo"/>
<br/>
</p>
[license-image]:https://img.shields.io/badge/license-GPL3.0-green.svg
[license-url]:https://github.com/divelab/AIRS/blob/main/LICENSE
[contributing-image]:https://img.shields.io/... |
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