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an-explainable-model-of-host-genetic-interactions-linked-to-covid19-severity

This project focused on the mapping of the host-genetics factors determining COVID-19 severity using Machine learning approaches (supervised, unsupervised Machine learning methods, Pathway signaling processes, and Open Targets web-based Platform). Our study utilized the whole-exome sequencing genome dataset of 2000 European descent patients collected from the GEN-COVID Multicenter Study group (https://clinicaltrials.gov/ct2/show/NCT04549831) coordinated by the University of Siena. The whole-exome genome sequencing dataset contained 1.057M genetic variants of the patients. We used the 2000 patients’ original phenotype information to filter only patients with severity and asymptomatic across all classification criteria (841 patients). We introduced an innovative variant screening strategy that applied K-stratified fold splits of the original dataset to randomly draw a unique 5-fold pool of variants using the patients’ original phenotype information (841 unique patients).

android-app-development

This repository contains all the source code examples and the FAQ for our Android App Development Specialization for Coursera

arduino

open-source electronics prototyping platform

article-resources

A repository for the source code, notebooks, data, files, and other assets used in the data science and machine learning articles on LearnDataSci

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bioinformatics

bolognamaster

carnival

CAusal Reasoning for Network Identification with integer VALue programming in R

causal-inference-and-discovery-in-python

Causal Inference and Discovery in Python by Packt Publishing

ceg

chain-event graph for R. This package implements the theory of CEG. Generate and plot CEG objects from manual input or from formatted data.

cegpy-binder

chain-event-graphs

R and Python scripts for my Summer 2021 undegraduate research project on Chain Event Graphs as part of the URSS scheme

covid-19

COVID-19 Italia - Monitoraggio situazione

drug.ontarget

Identifying drug targets by integrating large-scale drug and genetic screens.

e-driver

This repository contents a script to run e-Driver as well as the necessary files to reproduce the results presented in the paper describing the algorithm.

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

full-stack-flask-and-react

Full-Stack Flask and React, published by Packt

fullstack-course1-module1

glmnet_python

graphiql-explorer

Explorer plugin for GraphiQL

hmmer

HMMER: biological sequence analysis using profile HMMs

lb1-2

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

matching_vips_nonvips

Pipeline to match VIPs with similar non-VIPs and estimate introgression enrichments

nedb

The JavaScript Database, for Node.js, nw.js, electron and the browser

pdf_reports

:closed_book: Python library and CSS theme to generate PDF reports from HTML/Pug

peprmint-web

Web-tool for calculating and visualizing hydrophobic protrusions

precog

An ML-based predictor of GPCR/G-protein couplings using only sequence information

react-json-wpbuilder

recipes