Biomarker identification for COVID-19 Severity in BALF cells Single-cell RNA-seq data

Overview

scBALF Covid-19 dataset Analysis

Here is the Github page that has the codes for the bioinformatics pipeline described in the paper COVID-Datathon: Biomarker identification for COVID-19 severity based on BALF scRNA-seq data.

Biomarker Identification By Monocle:

The scBALF_Monocle.md file from the Monocle folder explains how one can extract the list of potential COVID-19 severity biomarkers using Monocle. The R markdown files are also available in the same folder.

GitHub Logo

BALF Cells Classification:

In the second step of our proposed pipeline we run multiple linear and non-linear machine learning classification algorithms to perform cell classification ( One lable vs the rest). Here we explain how one can run these classification algorithms:

GitHub Logo

  1. Lindear Discriminant Aanlysis (LDA):

The LDA.md file from the LDA folder explains how one can run perform cell classification using LDA. The R code files are also available in the same folder.

  1. Quadratic Discriminant Aanlysis (QDA):

The QDA.md file from the QDA folder explains how one can run perform cell classification using QDA. The R code files are also available in the same folder.

  1. Fleaxible Discriminant Aanlysis (FDA):

The FDA.md file from the FDA folder explains how one can run perform cell classification using FDA. The R code files are also available in the same folder.

  1. Support Vector Machine (SVM) with RBF kernerl

The SVM.md file from the SVM folder explains how one can run perform cell classification using SVM. The R code files are also available in the same folder.

  1. Random Forest (RF)

The RF.md file from the RF folder explains how one can run perform cell classification using RF. The R code files are also available in the same folder.

Owner
Nami Niyakan
PhD Candidate @ Texas A&M University
Nami Niyakan
내가 보려고 정리한 <프로그래밍 기초 Ⅰ> / organized for me

Programming-Basics 프로그래밍 기초 Ⅰ 아카이브 Do it! 점프 투 파이썬 주차 강의주제 비고 1주차 Syllabus 2주차 자료형 - 숫자형 3주차 자료형 - 문자열형 4주차 입력과 출력 5주차 제어문 - 조건문 if 6주차 제어문 - 반복문 whil

KIMMINSEO 1 Mar 07, 2022
Pretrained SOTA Deep Learning models, callbacks and more for research and production with PyTorch Lightning and PyTorch

Pretrained SOTA Deep Learning models, callbacks and more for research and production with PyTorch Lightning and PyTorch

Pytorch Lightning 1.4k Jan 01, 2023
Yolo algorithm for detection + centroid tracker to track vehicles

Vehicle Tracking using Centroid tracker Algorithm used : Yolo algorithm for detection + centroid tracker to track vehicles Backend : opencv and python

6 Dec 21, 2022
A 3D sparse LBM solver implemented using Taichi

taichi_LBM3D Background Taichi_LBM3D is a 3D lattice Boltzmann solver with Multi-Relaxation-Time collision scheme and sparse storage structure impleme

Jianhui Yang 121 Jan 06, 2023
Optical Character Recognition + Instance Segmentation for russian and english languages

Распознавание рукописного текста в школьных тетрадях Соревнование, проводимое в рамках олимпиады НТО, разработанное Сбером. Платформа ODS. Результаты

Gerasimov Maxim 21 Dec 19, 2022
Current state of supervised and unsupervised depth completion methods

Awesome Depth Completion Table of Contents About Sparse-to-Dense Depth Completion Current State of Depth Completion Unsupervised VOID Benchmark Superv

224 Dec 28, 2022
​ This is the Pytorch implementation of Progressive Attentional Manifold Alignment.

PAMA This is the Pytorch implementation of Progressive Attentional Manifold Alignment. Requirements python 3.6 pytorch 1.2.0+ PIL, numpy, matplotlib C

98 Nov 15, 2022
This is an open-source toolkit for Heterogeneous Graph Neural Network(OpenHGNN) based on DGL [Deep Graph Library] and PyTorch.

This is an open-source toolkit for Heterogeneous Graph Neural Network(OpenHGNN) based on DGL [Deep Graph Library] and PyTorch.

BUPT GAMMA Lab 519 Jan 02, 2023
Repository for code and dataset for our EMNLP 2021 paper - “So You Think You’re Funny?”: Rating the Humour Quotient in Standup Comedy.

AI-OpenMic Dataset The dataset is available for download via the follwing link. Repository for code and dataset for our EMNLP 2021 paper - “So You Thi

6 Oct 26, 2022
Topic Modelling for Humans

gensim – Topic Modelling in Python Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. Targ

RARE Technologies 13.8k Jan 03, 2023
SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks (Scientific Reports)

SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks Molecular interaction networks are powerful resources for the discovery. While dee

Kexin Huang 49 Oct 15, 2022
Learning Continuous Image Representation with Local Implicit Image Function

LIIF This repository contains the official implementation for LIIF introduced in the following paper: Learning Continuous Image Representation with Lo

Yinbo Chen 1k Dec 25, 2022
Implementation of "JOKR: Joint Keypoint Representation for Unsupervised Cross-Domain Motion Retargeting"

JOKR: Joint Keypoint Representation for Unsupervised Cross-Domain Motion Retargeting Pytorch implementation for the paper "JOKR: Joint Keypoint Repres

45 Dec 25, 2022
Unified learning approach for egocentric hand gesture recognition and fingertip detection

Unified Gesture Recognition and Fingertip Detection A unified convolutional neural network (CNN) algorithm for both hand gesture recognition and finge

Mohammad 227 Dec 25, 2022
Machine Learning Privacy Meter: A tool to quantify the privacy risks of machine learning models with respect to inference attacks, notably membership inference attacks

ML Privacy Meter Machine learning is playing a central role in automated decision making in a wide range of organization and service providers. The da

Data Privacy and Trustworthy Machine Learning Research Lab 357 Jan 06, 2023
FCA: Learning a 3D Full-coverage Vehicle Camouflage for Multi-view Physical Adversarial Attack

FCA: Learning a 3D Full-coverage Vehicle Camouflage for Multi-view Physical Adversarial Attack Case study of the FCA. The code can be find in FCA. Cas

IDRL 21 Dec 15, 2022
Sketch-Based 3D Exploration with Stacked Generative Adversarial Networks

pix2vox [Demonstration video] Sketch-Based 3D Exploration with Stacked Generative Adversarial Networks. Generated samples Single-category generation M

Takumi Moriya 232 Nov 14, 2022
PyTorch implementation of "Simple and Deep Graph Convolutional Networks"

Simple and Deep Graph Convolutional Networks This repository contains a PyTorch implementation of "Simple and Deep Graph Convolutional Networks".(http

chenm 253 Dec 08, 2022
[ACM MM2021] MGH: Metadata Guided Hypergraph Modeling for Unsupervised Person Re-identification

Introduction This project is developed based on FastReID, which is an ongoing ReID project. Projects BUC In projects/BUC, we implement AAAI 2019 paper

WuYiming 7 Apr 13, 2022
这是一个利用facenet和retinaface实现人脸识别的库,可以进行在线的人脸识别。

Facenet+Retinaface:人脸识别模型在Pytorch当中的实现 目录 注意事项 Attention 所需环境 Environment 文件下载 Download 预测步骤 How2predict 参考资料 Reference 注意事项 该库中包含了两个网络,分别是retinaface和

Bubbliiiing 102 Dec 30, 2022