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d3b7b21f786321cd77e77355a4075fc88959724460b067ac69f45ee0aaf4c334 | Text | 4,238 | 124 | ## crossmapy
crossmapy implements several causal inference algorithms based on dynamical causality (DC) framework, including Granger causality (GC),
Transfer entropy(TE), Convergent Cross Mapping(CCM), Partial Cross Mapping(PCM), Cross-Mapping Cardinality(CMC) and Cross-Mapping Entropy(CME).
### Install
```bash
pip ... |
2e52cecc1457a8b79ae7a54be65cbad34b6466fb0eddf1187a6cf58bd181279a | Text | 4,241 | 67 | # spaCI: deciphering spatial cellular communications through adaptive graph model
[](https://zenodo.org/badge/latestdoi/524767107)
Cell-cell communications are vital for biological signaling and play important roles in complex diseases. Recent
advances in single-cell spat... |
ea1026bedf6e7c92dcbc41a57a8d22865882249a81832883c348f79a2a46c63d | Text | 4,247 | 152 | # General :
Our work proposes a graph-based semi-supervised fake news detection method.
First, this repo is a python implementation of the paper
*Semi-Supervised Learning and Graph Neural Networks for Fake News Detection* by Adrien Benamira, Benjamin Devillers,Etienne Lesot,
Ayush K., Manal Saadi and Fragkiskos D. ... |
dd05fe9f7d96f3bb195e3a57eff4ef0ada2802b9ec37c0d420c9c64974675c3d | Text | 4,323 | 52 | # ASRT Process Dissocation Procedures (PDP) Task created with jsPsych
<i>Created by the MEMO Team of Lyon Neuroscience Research Center (CRNL) (PI: Dezso Nemeth)</i>
<img src="static/logo_memo.png" height="100">
<h2>Citation</h2>
If you use the script, please include this citation in your manuscript:
Vékony, T. (202... |
66dbd3031c02721e76aa25d521dd66c8f0efff21df1e86a0683884112f71e3cd | Text | 4,330 | 102 | .. image:: https://travis-ci.org/losonczylab/sima.svg?branch=master
:target: https://travis-ci.org/losonczylab/sima/
.. image:: https://ci.appveyor.com/api/projects/status/q3bgxcoget1xef33/branch/master?svg=true
:target: https://ci.appveyor.com/project/nbdanielson/sima
.. image:: https://coveralls.io/repos/loso... |
3c9e894a7a6dde2a936abb602ff26a667c768cf9cace04978c884dc861cbd6fc | Text | 4,333 | 55 | This file contains instructions for obtaining and running this microbial community taxa-function robustness estimation pipeline. This pipeline takes as input a table of microbial read counts or abundances and produces an estimation of the community's taxa-function robustness. Additionally, various gene distribution fea... |
ddd61f7d0e7590f08973259e3f64014e4a32e8cdb3f6770b81b58741585fb960 | Text | 4,345 | 82 | ## <b>Detecting Photoshopped Faces by Scripting Photoshop</b> <br>[[Project Page]](http://peterwang512.github.io/FALdetector) [[Paper]](https://arxiv.org/abs/1906.05856)
[Sheng-Yu Wang<sup>1</sup>](https://peterwang512.github.io/),
[Oliver Wang<sup>2</sup>](http://www.oliverwang.info/),
[Andrew Owens<sup>1</sup>](http... |
213fe2c9d975a8a3cfbcb5083496d093c455913962b577a624b6431c326ad507 | Text | 4,394 | 77 | # Photonics-FDTD-DRL
Optimization and inverse design of nanoscale laser cavities using Deep Reinforcement Learning. Here is link to our paper: https://www.degruyter.com/document/doi/10.1515/nanoph-2022-0692/html
## Abstrat:<br/>
Photonics inverse design relies on human experts to search for a design topology
that sati... |
71875e85b110d1271a8ca811bf79e479310038406fa2a622fc1aea930f231c2b | Text | 4,397 | 110 | # blinder_script
A simple script for blinded analysis. Assumes structure where data to be analyzed has already been
split into separate files, each of which is subject to varying experimental treatment. The script
copies the files to a new location, replacing the original filenames with a randomly-assigned
number, savi... |
7087e796c4c9bf6819671628ed378624f7d09cd2243c82147140f03c81b6c674 | Text | 4,435 | 109 |
Decoding of the speech envelope using the VLAAI deep neural network.
=============================================================================
[](https://www.python.org/downloads/)
[![Tensorflow version 3.6+](https://img.shields.io/badg... |
d6ae8808bd59934a42fc822948ce12bf006c2c0f00f18a2e528ff5b958833af9 | Text | 4,453 | 132 | # 1. Introduction <img src="biocreative-logo.jpeg" align="right" height = 150/>
Official library to compute results for the BioCreative Task 1 competition. It is intended to be used by BioCreative participants to test their systems before submitting them. It will be used as well by the competition organizers to compu... |
caeb236ef56abbb2703936a1b35fd406d33cb6de94297b54be44a3d966bc8b44 | Text | 4,471 | 100 | # DeepSelectNet
DeepSelectNet is an improved 1D ResNet based model to classify Oxford Nanopore raw electrical signals as target or non-target for Read-Until sequence enrichment or depletion. DeepSelectNet provides enhanced model performances.
### Abstract
> Nanopore sequencing allows selective sequencing, the ability... |
f250b7c57166ed16bf8ede5ec990716475b4fe8c04a103bdce4a89a3d62e6ee0 | Text | 4,485 | 51 | # AttentionCrossTranslation
## Unsupervised cross-domain translation via deep learning and adversarial attention neural networks and application to music-inspired protein designs
Markus J. Buehler, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
E-mail: mbuehler@MIT.EDU
**Summ... |
416ce80788125dee45d6e0a82850f220dcb233367ff80138a06d40b19fe029be | Text | 4,529 | 77 | # Co-evolution-TRNP1-and-GI
This repository contains data files and scripts to reproduce the analyses and results presented in our paper.
## Protein
All relevant scripts listed below can be found within the `protein/scripts` folder.
### Protein-coding sequence collection
1) `collect_coding_seqs2/run_ccs2_function.... |
f64c9d6b19570034402d74618962c6b0b5c87dd9f2aa912be70718ee4a4e0203 | Text | 4,547 | 70 | # Accelerator for Calcium Trace Extraction from Video (ACTEV)
<img width="300" height="230" alt="ACTEV_LOGO" src="https://github.com/user-attachments/assets/1c34e519-8dfb-40cb-b2c4-3ad81583fd1e" />
## 1. FPGA and Embedded Software
The ACTEV was built on top of the [Ultra96 Platform](https://www.96boards.org/product/... |
14c7615cdb527b7ec85b0a4fa8f6fff8f78228b45989714dec215a71030b5b05 | Text | 4,635 | 56 | # CiliaCoordination
Motile cilia may display remarkable traveling waves of rapidly succeeding ciliary beats across the tissue, much like Mexican waves in a soccer stadium. Those waves are called [metachronal waves](https://en.wikipedia.org/wiki/Metachronal_rhythm).
Ciliacoordination is a collection of functions to qu... |
ab6e29094ae4e38d48ee8a3e630df90ee97ccc027664d15e4356123c4f91b116 | Text | 4,643 | 138 | # Meta_Schz
Code and data for 'Metastability as a neuromechanistic marker for schizophrenia pathology'
The folder structure here just reflects what the code expects.
### Data:
**Cobre** data is openly available from http://fcon_1000.projects.nitrc.org/indi/retro/cobre.html
**Human Connectome Project - Early Psychos... |
6b447a745d0626e3fa7107b0d3ae8734ffbecbea265379427edbe7b6a5141ab0 | Text | 4,697 | 104 | <img src="docs/figs/logo_rc.png" width=400, padding=100>
## Resolution-Adaptive Coarse-to-fine Clusters OptimizatiON
### v 0.5.1
[](https://github.com/shlienlab/raccoon/releases/tag/v0.5.1)
[![PyPI](https://img.shields.io/pypi/v/rac... |
28ed59f5ee99545aaae61114bc480d7d0f7f370a16e98745a68e4ad19dae5131 | Text | 4,745 | 92 | # NAS-FCOS: Fast Neural Architecture Search for Object Detection
This project hosts the train and inference code with pretrained model for implementing the NAS-FCOS algorithm for object detection, as presented in our paper:
NAS-FCOS: Fast Neural Architecture Search for Object Detection;
Ning Wang, Yang Gao, H... |
4655c840389b367d96306ab0c68364e6976af0b4db634c0487c9432c17809ecd | Text | 4,745 | 75 | <div align="center">
# Documentation for smFISH analysis in neurons
</div>
This pipeline is part of the publication [Mendonsa, S. et al. Massively parallel identification of mRNA localization elements in primary cortical neurons. Nat Neurosci 1–12 (2023)](https://www.nature.com/articles/s41593-022-01243-x)
### Pi... |
51848a26577a8a1afe7539e48eccf73dd0c5b91709cb72955d103a7dd5042a63 | Text | 4,748 | 87 | # Linear and Nonlinear Signals
This repo contains the code to reproduce the results of the manuscript "The Effects of Nonlinear Signal on Expression-Based Prediction Performance".
In short, we compare linear and nonlinear models in multiple prediction tasks, and find that their predictive ability is roughly equivalent.... |
cd04321db2ac803e21424842e3864c724f4ccb0c4f8cfe38720f4d4a8db7d8ed | Text | 4,749 | 46 | # RL_model_action_sequences
Model-free reinforcment learning alogrithm with an actor-critic paradigm as an overarching architecture developed to learn sequences of two actions.
The code present in this repository contains the model described in Favila, N., Gurney, K. and Overton, G. P. (2022). The role of NK1 receptor... |
64509751e79ae0e590b3bdb8b66bd74999a72ca46fe191da8c567494687dcbad | Text | 4,798 | 88 | # AttnSleep
### AttnSleep: An Attention-based Deep Learning Approach for Sleep Stage Classification with Single-Channel EEG
#### *by: Emadeldeen Eldele, Zhenghua Chen, Chengyu Liu, Min Wu, Chee-Keong Kwoh, Xiaoli Li, and Cuntai Guan*
This work has been accepted for publication in [IEEE Transactions on Neural Systems ... |
102c24e825f4832b90bd670f1f2650cb9ebe69df8a1b0e80c3df37a97a4c4131 | Text | 4,825 | 85 | # Enva-XR - Environment Aware Augmented Reality
- Web-based framework for environment-aware rendering and interaction in augmented reality based on [WebXR](https://www.w3.org/TR/webxr/) using [three.js](https://threejs.org/)
- The framework handles geometry occlusions, matches the lighting of the environment, casts s... |
d75f5b1c4df6e54e37b38331651722e96b6a7b635c8d427a8ed4ff176d6682ad | Text | 4,845 | 96 | # HERBS
A Python-based GUI for Histological E-data Registration in Brain Space
HERBS is an open source, extensible, intuitive and interactive software platform for image visualisation and image registration. Where the image registration is the process of identifying a spatial transformation that maps images to a temp... |
a0d7f355d66ddecd3137ad2b36be66051b2188584dd05d07e16d2f4ab0d1a0b1 | Text | 4,897 | 114 | # DeepSleepNet #
A deep learning model for automatic sleep stage scoring based on raw, single-channel EEG.
**We have published a more efficient deep learning model, named TinySleepNet, which is much smaller and can achieve a better scoring performance.**
***TinySleepNet: An Efficient Deep Learning Model for Slee... |
5f6308b88d9c5f35e6745c12796dda5da5cb8ad5657739f63922929d85f82d44 | Text | 4,899 | 100 | # OmiEmbed
***Please also have a look at our brand new omics-to-omics DL freamwork 👀:***
[OmiTrans](https://github.com/zhangxiaoyu11/OmiTrans)
[](https://zenodo.org/badge/latestdoi/334077812)
[`` : to connect, DNA appearing as dots under imaging, as if to trace out a constellation
-... |
953fe8e039f6cf89ca8b3aa9bd9d681bb4430efde576f6264994cb0e5e01aa3f | Text | 4,978 | 53 | This repository provides source codes of our drug repurposing study for COVID-19 which titled as "Molecular-evaluated and explainable drug repurposing for COVID-19 using ensemble knowledge graph embedding".
Here we describe the step by step procedure for using the source codes.
**Step-1: Learning the DRKG knowledge gr... |
f1e98419b3601fb10b14cb607233c275047ad09f7a6194d0f9597930adc74746 | Text | 4,992 | 53 | # FedSepsis
**[FedSepsis: A Federated Multi-Modal Deep Learning-Based Internet of Medical Things Application for Early Detection of Sepsis from Electronic Health Records Using Raspberry Pi and Jetson Nano Devices](https://doi.org/10.3390/s23020970)**, Mahbub Ul Alam, Rahim Rahmani. Sensors 23, no. 2: 970, https://doi.... |
4145708627804f92609d9326c947d5838703217e9b8829a85be458dd4b449095 | Text | 5,014 | 131 | An R package for inferring the subclonal architecture of tumors
## Installation instructions:
Both the 'sciClone' package and it's 'bmm' dependency can be installed by doing the following:
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
Bioc... |
cb28e308c25f68e1839698a1e518cc5ed007b479d4c6c192fd90adb35542e4bc | Text | 5,056 | 99 | # deception-detection-review-2022
# Deception Detection with Machine Learning: a literature review and statistical analisys
## Literature review
### Introduction
The files present in this repository are part of the Literature Review Project and aim to disclose the data collected along the process, and work as a memory ... |
02f5337bb8e1169a0cd7f2a9544d304f4eb6d5537a8bdd9743ece466733786ea | Text | 5,112 | 149 |
## TransPath
## Transformer-based Unsupervised Contrastive Learning for Histopathological Image Classification (*Medical Image Analysis*)
The new better and stronger pre-trained transformers models [(**CTransPath**)](https://www.sciencedirect.com/science/article/abs/pii/S1361841522002043) has been released.
[Jou... |
164136ac5253032e7c4bc7cccf51d3f561d133490c85a388f3e3ee9c63d479a5 | Text | 5,125 | 62 | # Asterophryinae_phylogenetic_data [](https://zenodo.org/badge/latestdoi/534389101)
Data for Asterophryinae frog phylogenetic data: nuclear and mitochondrial sequence data, site and locality, lifestyle, and frog communities
This repository contains the following data type... |
6d89c14872a2ebf6eaef6dfaad7d8fc44f059259465b5b0cd460bbcca6c0e09c | Text | 5,153 | 46 | ## Linear, planar and spherical tensor-valued diffusion MRI data by free waveform encoding in healthy brain, water, oil and liquid crystals
Filip Szczepankiewicz*, Scott Hoge, Carl-Fredrik Westin
Radiology, Brigham and Women’s Hospital, Boston, MA, US
Harvard Medical School, Boston, MA, US
**\*Corresponding autho... |
28d9ab19bc694d968f553a14978c4a9dda011a5a739095300c679f392adbfb16 | Text | 5,155 | 118 | PICAchooser (the package)
=========================
.. figure:: https://raw.githubusercontent.com/bbfrederick/picachooser/master/images/picalogo.png
:alt: Logo
A set of simple gui tools for scanning through MELODIC probabilistic ICA
runs and quickly making decisions about which components to retain, and
what relat... |
6ed3fffe33ea4dea30e37ff3515edd724999c0c477ac224d8827ba8c064104ca | Text | 5,265 | 101 | # seq_to_seq_and_dock_AMU
## Title
```Neural networks in the design of molecules with affinity to selected protein domains.```
# Workflow
Open ```Order_of_usage.md``` to see detalied description of each folder.
## Training data preparation
<p align="center">
<img src="/scheme/data_preparation.png">
</p>
## Model ... |
5aa5c968ebe38bb6e9d8f474b7a0e9277b3e6c08913fec885c9ae4faa5b309ba | Text | 5,277 | 106 | # FNA
Official implementation of [Fast Neural Network Adaptation via Parameter Remapping and Architecture Search (ICLR 2020)](https://openreview.net/forum?id=rklTmyBKPH) and [FNA++: Fast Network Adaptation via Parameter Remapping and Architecture Search (TPAMI)](https://arxiv.org/abs/2006.12986).
Deep neural networks... |
36b8770320ce63840d5f5979925ce8c1b0f78a9130886cb925415dc58e0a6fe1 | Text | 5,281 | 92 | # Retina Vessel Segmentation from OCT Fundus Reconstruction with IterNet
This software is forked from conscienceli/IterNet and allows segmentation of blood vessels in **OCT reconstruction images** of the human eye retina. Details of the application of the software can be found in the paper:
> Marciniak, T.; Stankiewi... |
59f7907f09d8e6dba3befbc5e898591b0f404f5aa793cba150d0214b30f6f3cb | Text | 5,289 | 83 | ## Accurate Clinical Toxicity Prediction using Multi-task Deep Neural Nets and Contrastive Molecular Explanations
Provided here is the code to:
- create multi-task DNN and single-task DNN models to predict <i> in vivo </i> (RTECS), <i> in vitro </i> (Tox21), and clinical (ClinTox) toxicity given molecular input (Mor... |
91de86b3a2ce9bd9bec6b978d51b56ba645eded6535722e64eb8551c2a16485e | Text | 5,322 | 34 | # ImageJ-macros
Humble and customised macros for things I do using ImageJ/FIJI. Most of them have been written in modules to be remixed, combined and recycled. Feel free to do that yourself as well.
You can put them in the folder /FIJI/plugins/macros/ to be visible from the Macros menu (the _ at the beginning of the fi... |
7ee67bb87ba570780f4d9a510fa91413caf2407ffe3a2e030f19b818e28fd3e1 | Text | 5,328 | 72 | # NRN-EZ
Latest release: v1.1.7 (use Latest Release tag on the right side of this page!)
**SYNOPSIS AND MOTIVATION**
NRN-EZ is a software that allows to distribute synaptic inputs onto digitally reconstructed neurons. With NRN-EZ, users can select the location, strength, and activation time of a population of synapti... |
69a068996b03cada8045530718102eec0aa001f1d6910495940b51b625b7c680 | Text | 5,357 | 94 | # mb-dual-dan
**A dual-pathway dopaminergic code for reward prediction and epistemic surprise in the larval *Drosophila* mushroom body.**
Companion code repository for the paper of the same name (manuscript in `paper/manuscript.md`).
## The claim
Four architectural ingredients — signed-weight RPE, a Bayesian surpri... |
617f26f3e46cb3b78ce928cb1c32ff0da24419816332117af6e872eaf2335874 | Text | 5,378 | 146 | AIEchoDx (Demo version 1.0.0)
=====================================
### News
6 May 2019:
* Upload AIEchoDx_demo and AIEchoDx_demo_notebook
5 Jan 2020:
* Upload AIEchoDx_demo 1.0.0
* Upload 25 examples of patients' echocardiographic videos in ```AIEchoDx/AIEchoDx_demo/video_examples/```
### Introduction
AIEchoDx, whi... |
7cfb5e6c096cfaf4910492b3b917ff98d81b7d7191a123e934fcb8204cc4a407 | Text | 5,417 | 166 | #Organoid dataset
This is a small dataset based on multi-channel 3D time lapse movies of
mouse organoid growth. With a supplemental dataset consisting of
mouse embryonic stem cells.
## binned-images
This contains the full length movies used for pulbication. They are at
half of the original resolution and converted... |
af8615bae43d0ae5871485cfa1023ce572301cd2e6e625e512f6511cece2244a | Text | 5,419 | 58 | PsPM-DA1 dataset
=================
Repository Version: 2022.05.12
This dataset contains skin conductance responses (SCR), electrocardyogram (ECG), respiration, electromygram (EMG), pupil size (PSR), and gaze coordinates measurements for 97 healthy individuals (49 females and 48 males aged 24.7 +/- 3.9) participa... |
3c209203d6dafdeae67ee08c5cdc01a23ccc3304b341ebc7c40f11933ea253d1 | Text | 5,424 | 85 | [](http://joss.theoj.org/papers/2ee6a3a3b1a4d8df1633f601bf2b0ffe)
[](https://circleci.com/gh/SebastianoF/bruker2nifti)
[</em> [[Paper]](https://pubs.acs.org/doi/10.1021/jacs.2c11420) [[arXiv]](https://arxiv.org/abs/2210.14188) [[PDF]](https://arxiv.org/pdf/2210.... |
9ee86247a7c64a394b947164d929ea5b8eacd4a59551b4b9e7bcf29ccac0ced7 | Text | 5,519 | 54 | # spectrome-stability
`Spectrome` is a combination of the words "spectrum" and "connectome".
<!-- This package is the collection of codes that constructed the analysis for the preprint ["Spectral graph theory of brain oscillations - revisited and improved"](https://www.biorxiv.org/content/10.1101/2021.09.28.462078v1)... |
ddefca679fd04cc1ffe3bbfc5768dd6bbd99bdb55a5c16f1daa467feb8da2db0 | Text | 5,527 | 111 | # OHBA Software Library: Dynamics Toolbox
[](https://pypi.org/project/osl-dynamics/)
[](https://osl-dynamics.readthedocs.io)
[
**FENeRF: Face Editing in Radiance Fields**<br>
Jingxiang Sun, Xuan Wang, Yong Zhang, Xiaoyu Li, Qi Zhang, Yebin Liu and Jue Wang
<br>
https://mrtornado24.github.io/FENeRF/<br>
Abstract: *Previous po... |
afcc7b300e8c55e256dd0cc1c835a3ee95cacbab466349c0d4e8a462392ed885 | Text | 5,565 | 102 | # Deep-Manager
This repository contains the code referred to the paper available at https://www.nature.com/articles/s42003-023-04585-9
This is a guide to set up your envirnoment and use the Deep Manager Toolbox
Requirements
- python >=3.8
- libraries inside requirements.txt
In order to properly install the required ... |
b6ecf675ec5d62eade4a85fae6ee7662a112abb0d55c6e8574ec9832e46dbefe | Text | 5,568 | 117 | WGCNA Script for: Monocyte, Neutrophil and Whole Blood Transcriptome
Dynamics Following Ischemic Stroke
================
07/28/2022
-----
**Monocyte, Neutrophil and Whole Blood Transcriptome Dynamics Following
Ischemic Stroke**
Paulina Carmona-Mora, Bodie Knepp, Glen C Jickling, Xinhua Zhan, Marisa
Hakoup... |
dcad719bcaaafd2314604717d53513c2e46e5829798a25442b50b26dc0fb0ecb | Text | 5,574 | 92 | # Code for "Bayesian inference in ring attractor networks"
This repo contains the code for simulations and figures in
Anna Kutschireiter, Melanie A Basnak, Rachel I Wilson, and Jan Drugowitsch (2023). Bayesian inference in ring attractor networks. Proceedings of the National Academy of Sciences.
## Code structure a... |
3e173ebc6f1d0e1e363fff2be22d46ea4c9e5459aa6354ca77a29ff7ae74286a | Text | 5,606 | 151 | ---
title: 'DDMR: Deep Deformation Map Registration of CT/MRIs'
colorFrom: indigo
colorTo: indigo
sdk: docker
app_port: 7860
emoji: 🧠
pinned: false
license: mit
app_file: demo/app.py
---
<div align="center">
<img src="https://user-images.githubusercontent.com/30429725/204778476-4d24c659-9287-48b8-b616-92016ffcf4f... |
7cde2b65e52822e01371a162ef34effbaec94a2f9d29c74e497e355518cca5bd | Text | 5,621 | 118 | # <p align=center>`SciCite`</p>
[](https://paperswithcode.com/sota/citation-intent-classification-acl-arc?p=structural-scaffolds-for-citation-intent) [
# New maintained VAME repository
This version of VAME is deprecated and no longer maintained, and is made available here as legacy co... |
2c91d42041735d71f58cf3dcd2399af86261e2759ba23f7373e5ebe20a544174 | Text | 5,693 | 135 | # EfficientNet Keras (and TensorFlow Keras)
[](https://badge.fury.io/py/efficientnet) [](https://pepy.tech/project/efficientnet/month)
This repository contains a Keras (and TensorFlow Keras) reimplementat... |
cefa961be7940f2e8821aa6717bf412d08cbe7b7847817f470ccfb35571dde74 | Text | 5,743 | 111 | # PETPVC
[](https://github.com/UCL/PETPVC/actions/workflows/build-test.yml)[](https://dev.azure.com/petp... |
887009c893297ac99ced127fdf7b3d98afedb821d68081a085438bb01e68cbc3 | Text | 5,751 | 149 | # ACTIONet
**A multiresolution framework for characterizing single-cell state landscapes.**
Most single-cell workflows begin by partitioning cells into discrete clusters.
That is a useful simplification, but it is a simplification: cell identity is
often continuous, cells sit between states, and the resolution at whi... |
9739f12beefb4124e8cf164765539981d619aa618735c18546a75cb5f06e39f8 | Text | 5,766 | 126 | [](https://zenodo.org/badge/latestdoi/510674217)
# Linescan-analysis
Code for the post-processing of line-scan measurements of vessels and astrocyte endfoot diameter oscillations and simulations presented in:
* <i>Sleep cycle-dependent vascular dynamics and the predicted... |
133a84dcc7e987452f85fac4805c18dd3f3f2c528942d9ec0c5bf7fe01261cf3 | Text | 5,767 | 100 | 
# 3D Segmentation of Mitochondrial Structures
A Deep Learning package for accurate segmentation of mitochondria and granules captured using cryo-electron tomography. This repository contains code for our papers
- **[CryoET Reveals Organelle... |
a55fa05702c4ca2405514966fdf126dd5cc9991cbaf48bcfdc2c7c7800cc0929 | Text | 5,786 | 116 | # SAFT : Semi Automatic Fluorescent Trace analysis
v. 0.5 2022-08-22
SAFT was written in Python 3 for macOS. In principle it is cross-platform, in practice it was never launched on Windows or Linux. If you happen to get it working on either of these platforms, please let us know. SAFT runs normally on M1 Macs.
This... |
042abcc1fe11aabb56b571c4be80221d6e2a36b37eeebf0e2298612d9cda8f12 | Text | 5,796 | 76 | ## RISC
### Overview
Integrated analysis of single cell RNA-sequencing (scRNA-seq) data from multiple batches or studies is often necessary in order to learn functional changes in cellular states upon experimental perturbations or cell type relationships in a developmental lineage. Here we introduce a new algorithm (... |
5f2d32717e5e7cee21c5fb0992d79b4818a0cc65485d7f0371abc83e79da058e | Text | 5,799 | 140 | # RapheGIF
<div style="text-align: center;">
<img
src="https://img.shields.io/badge/python-2.7-important.svg"
alt="Python 2.7"/>
<img
src="https://img.shields.io/badge/os-macOS%20|%20linux-informational.svg"
alt="macOS or Linux"/>
<a href="LICENSE.txt">
<img
src="https://img.shields.io/badge/license-MIT-green.svg"
alt... |
b60954e7066fb23852181d09717162e5ee8ff663f4b6456be74a54387134f0c5 | Text | 5,853 | 93 | [](http://navis.readthedocs.io/en/latest/?badge=latest) [](https://github.com/schlegelp/navis/actions/workflows/test-package.yml) [ published in ACSAC 2020.
We propose a blind detection approach called NoiseScope for discovering GAN images among real images. NoiseScope r... |
bdbc6aba38ba90a476e1a7077495b4d8a6b72e5cd739cbcd036bd1ebe861c173 | Text | 6,016 | 89 | # REMBRANDTS
### REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability
REMBRANDTS is a package for analysis of RNA-seq data across multiple samples in order to obtain unbiased estimates of differential mRNA stability. It uses DESeq to obtain estimates of differential pre-mRNA and mature mRNA abunda... |
8e61e714526602c461b05f74408442970ddc96c435d59b5ab278e1082c900f2f | Text | 6,020 | 83 | # Online supplement for published manuscript
[Emergent behaviour and neural dynamics in artificial agents tracking odour plumes (Nature Machine Intelligence. 2023 Jan)](https://www.nature.com/articles/s42256-022-00599-w)
Authors: Satpreet H. Singh, Floris van Breugel, Rajesh P. N. Rao, Bingni Wen Brunton
Contact: satsi... |
147f82584dd70776e4eb7efb0ac1fecb9da32109c462d0098192283714ef2434 | Text | 6,045 | 63 | # Genetic architecture of Alzheimer's disease
Snakemake workflow for investigating the genetic architecture of Alzheimer's disease across multiple genome-wide association studies.
## Workflow
Rules for defining the workflow are in `workflow/Snakefile` and the individule script files used by specific rules are avali... |
dcfe8ab9a48a577439d2f3332e6432acd6649e6fdc683d5119ffbd823ba04907 | Text | 6,047 | 77 | # GliaMorph Introduction
GliaMorph Toolkit to process and analyse Müller glia morphology (implemented as Fiji Macros to allow modular application).
BioRxiv manuscript - GliaMorph biological application: XXX
BioRxiv manuscript - step-by-step protocol: XXX <br/>
Example Data: **Data Link**: https://zenodo.org/record/5... |
7c4790d3ed62d4a38e0f0af811ca2189ba6a0e7988533ff5692e65b57e885bff | Text | 6,054 | 142 | # BenchNIRS
<img title="BenchNIRS" align="right" width="150" height="150" src="https://hanbnrd.gitlab.io/assets/img/logos/benchnirs.png" alt="BenchNIRS">
*Benchmarking framework for machine learning with fNIRS*
**Quick links**
→ [*Journal article*](https://www.frontiersin.org/articles/10.3389/fnrgo.2023.99496... |
90d9a9824280bb0ee8841aa945885357d3a1c118e38a59a52a08b46790865b5b | Text | 6,137 | 223 | # Ontology Access Kit
Python lib for common ontology operations over a variety of backends.
[](https://badge.fury.io/py/oaklib)
[![badge](https://img.shields.io/badge/launch-binder-579AC... |
6cbc88ece216f214bdf689885835f75a6ffcd3e22465de4d2a81ff08f781d03a | Text | 6,169 | 109 | # Single CEll Variational Aneuploidy aNalysis
<div>
<img src="LogoSCEVAN.png" align="right" width="200">
<img src="SCEVAN_workflow.png" align="center" width="590" height="700">
</div>
Article: [A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data
](https://www.natu... |
c3dfa78ffb792b05797a8c02d9e7a9522f2c4c8764a095fad4dcf163fd340593 | Text | 6,169 | 119 | # FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures
Lisa Mais\*, Peter Hirsch\*, Claire Managan, Ramya Kandarpa, Josef Lorenz Rumberger, Annika Reinke, Lena Maier-Hein, Gudrun Ihrke, Dagmar Kainmueller
\* shared first authors
## General
For more details and th... |
c7a2c8a8e63c9ac86556b0e8111980c5f3152cd9e1fbed02a99d55e029451a4d | Text | 6,346 | 110 | 📣 📣 📣 Update: Check out [**PRIDICT2.0**](https://github.com/uzh-dqbm-cmi/PRIDICT2/) from our updated study [here](https://www.biorxiv.org/content/10.1101/2023.10.09.561414v1). 📣 📣 📣
# PRIDICT: PRIme editing guide RNA preDICTion
For accessing Supplementary Files, click [her... |
51f37a1405f28477760758b9425a74a3dafcd29d17bc96200ac94fd1941a6135 | Text | 6,373 | 71 | # Implementation of Kim & Hummer (KH) Model [1] in LAMMPS
This project uses continuous piecewise Lennard-Jones-like potentials to implement the KH Model A & D in LAMMPS.
Instead of writing a custom pair_style, only standard pair_styles are used.
This method can thus be used quickly and easily on most versions of LAM... |
d79a734101a32aa92eaa36e5f691e3b06f4fb42673e185d50092a32d53703333 | Text | 6,472 | 94 | # Feature importances for scikit-learn machine learning models
By <a href="http://explained.ai/">Terence Parr</a> and <a href="https://www.linkedin.com/in/kerem-turgutlu-12906b65/">Kerem Turgutlu</a>. See [Explained.ai](http://explained.ai) for more stuff.
The scikit-learn Random Forest feature importances strategy i... |
8244155eba8fc514486e8c07818a3c814c1fd00b07d152a5186a3535d949d22a | Text | 6,561 | 130 | % ===============================================================
The dataset in this package provides the real-world noisy images
as described in the following paper:
Jun Xu, Hui Li, Zhetong Liang, David Zhang, and Lei Zhang
Real-world Noisy Image Denoising: A New Benchmark
https://arxiv.org/abs/1804.02603, 20... |
d6f2828f3e31cee58ef10db4aec48445f69380091bbc4e70acfcde66415c96f5 | Text | 6,568 | 118 | # (s)BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks
This repository provides step-by-step instructions on how to process [BLISS](https://www.nature.com/articles/ncomms15058) or sBLISS data.
We assume that the user is using the Linux operating system (modifications to... |
a0322a9d2ed106586612cf67e097692330fb1bf8b7bb289867eb991d0df21306 | Text | 6,575 | 99 | # Algorithmic encoding of protected characteristics in chest X-ray disease detection models
This repository contains the code for the paper
> B. Glocker, C. Jones, M. Bernhardt, S. Winzeck
> [**Algorithmic encoding of... |
28d3a1c6497785d2380e21dbcb4ca696e66a79b5e5601d697d1bd667df12d898 | Text | 6,637 | 81 | # SingleR - Single-cell Recognition
[](https://bioconductor.org/packages/release/bioc/html/SingleR.html "How long has SingleR been in a release of Bioconductor")
[. It was tested on ... |
ffab3f7b9f94bf9b641fd8e68ebdab4cb507bff636eb18c48be68c8767b10e3d | Text | 6,765 | 149 | # :warning: Archiving Note
This repository is no longer being maintained and has been archived for historical purposes.
There is a new version called [DeepRank-GNN-esm](https://github.com/haddocking/DeepRank-GNN-esm) which incorporates the ESM embeddings as replacement of the PSSM profile as features. This version i... |
1ff3c75f3f5d9b875ab680dd492e16bac70bbc6e5a1a566b384540260e7a15c7 | Text | 6,784 | 98 | # Arduino Temperature Control
## Temperature regulation with an Arduino board.
Measures temperature with a thermocouple and, computes an error signal with respect to a target temperature and update the PWM frequency to mitigate power delivered to a Peltier module through a PID loop.
Along with the Arduino code, there... |
7b8731b764e04cac4575eced62267dbdc1604561cc66e95925331b8bac171ae6 | Text | 6,798 | 203 | # PanExplorer_workflow
# About
This workflow is a snakemake worklow that can be run in the backend of the PanExplorer web application.
**Homepage:** [https://panexplorer.southgreen.fr/](https://panexplorer.southgreen.fr/)
It allows to perform a pan-genome analysis using published and annotated bacteria genomes, usi... |
69524716ba8be5d3badd48212567820c68d0ffbd3175e506a4530f5fda2b7dcd | Text | 6,808 | 127 | # PCWA
A highly parallel and fast event detector based on CWT transform. *PCWA* is a multiscale approache to find events with any shape with a mother wavelet that matches with events shape (details provided in the *Nature Communications* manuscript currently under review). Unlike previous CWT based peak finders, *PCWA*... |
37c7adc62bd31b4d335fc2d66fcd5b05455f0d25b35e6eefe2d3f9db104aa109 | Text | 6,825 | 139 | # Verbal N-back Task (jsPsych)
<p>This repository provides a <b>Verbal N-back task</b>, a continuous performance task commonly used to assess <b>working memory capacity</b>. The task is implemented using the <b>jsPsych</b> library.</p>
* **Original Concept:** Kirchner, W. K. (1954)
* **jsPsych Framework:** de Leeuw, ... |
fe327c29a8597bf513342089a44021bdb73e930f0195a45631ac7cc6ffa15fd1 | Text | 6,832 | 145 | 
## PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting viral sequences
Read more about PACIFIC here:
> [__Acera Mateos P., Balboa R.F., Easteal S., Eyras E., and Patel, H.R.__ PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting R... |
6a7e280fe17e4e22d251e949bda887dcc62d7890c034fb07a4e2d525a5fc3134 | Text | 6,846 | 100 | ## Analysis of Hand Segmentation in the Wild
### Abstract
A large number of works in egocentric vision have concentrated on action and object recognition. Detection and segmentation of hands in first-person videos, however, has less been explored. For many applications in this domain, it is necessary to accurately seg... |
bde6e2166b1c279dd1ffa00469967a2b5f9bcb557d7178aed3252d96f21057f9 | Text | 6,880 | 86 | 
# Welcome to Robin's Viewer (RV)
Robin's Viewer (RV) is a user-friendly EEG viewer with the main purpose of annotating time-series EEG data. It is implemented as an interactive web-application and... |
2ba5b84bf952be48a9e4cb1f87dc96b6fb12cb3154a0a373a46916325d20388e | Text | 6,975 | 158 | # Multispecies_paper_ML
Scripts used for Multispecies paper (Wyatt et al. Unpublished). These scripts allow a bespoke way to do svm machine learning on non-genome guided RNAseq data (Trinity), across multiple species (given one queen and one worker sample per species). This process is not automated, and requires a len... |
31943ca9e9714e11b901f8c015cf56602ca108f7a5f6dd3297bbf1a76b4bf363 | Text | 7,032 | 116 | # Overview
This repository contains code for methods to register serial two-photon tomography (STPT) images
from the Allen Mouse Connectivity Atlas as described in
[Oh et. al., 2014](https://www.ncbi.nlm.nih.gov/pubmed/24695228/) and
[Kuan et. al., 2015](https://www.ncbi.nlm.nih.gov/pubmed/25536338/).
These methods w... |
915cbea08f67d674a7b0a50bc62e913b35d9a23ff5eec8ff0f588b47d71f6f07 | Text | 7,121 | 108 | # zebrafishGC
Python and MATLAB code for Granger causality analysis on empirically observed calcium transients in zebrafish neuronal populations, and on synthetic dynamics generated on toy networks. This set of codes is assciated with the manuscript "Granger causality analysis for calcium transients in neuronal network... |
5d4df534dfa8f71053a62f9d6bc963a1e9f3f0f5a9f3ce5586a09958d8b4d18c | Text | 7,217 | 132 | # PrognosAIs_glioma
This repository contains the code and trained models required for the running of the PrognosAIs model trained for the prediction of the IDH mutation status, 1p/19q co-deletion status, and grade of glioma based on pre-operative MRI scans. The model also automatically segments the tumor.
The model a... |
176add8a12c387524623d473c571f5a57e5be0f750b8ce0ed40e7f8cbf4792e3 | Text | 7,262 | 248 | # Ontology Access Kit (OAK)
Python lib for common ontology operations over a variety of backends.
<img src="docs/logos/oak-logo_black-icon.png" width="20%">
[](https://badge.fury.io/py/oaklib)
![](https://github.com/incatools/ontology-access-kit/workflows/Build/bad... |
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