Git Product home page Git Product logo

covid-19's Introduction

COVID-19: association between expression and AGE/SEX

Script structure

Pipeline: bash run.sh 
download_data.sh: download data from GTEX and Gencode for downstream analysis
Script dependencies include the following R packages:
  • dplyr
  • data.table
  • ggplot2
  • sva
Approach I: Perform SVA to learn about the SVs, and test asscoations with AGE and SEX controlling for the SVs 
extract_protein_coding_lincRNA_genes.sh: Extract genes that are protein coding or lincRNA
generate_tissue_wise_TPM.R: Generate a matrix of genes by samples for each tissue
SVA_compute_SV.R: Infer about surrogate variables (SVs) using SVA
SVA_followedby_LR.R: Perform association tests controlling for SVs

Rscript SVA_followedby_LR.R ENSG00000130234.10 ACE2
Rscript SVA_followedby_LR.R ENSG00000184012.11 TMPRSS2
Approach II: Test asscoations with AGE and SEX controlling for known confounders 
Rscript LR_confounders.R ENSG00000130234.10 ACE2
Rscript LR_confounders.R ENSG00000184012.11 TMPRSS2
	* DTHHRDY  - Death Circumstances
	* SMRIN  - RIN number
	* SMTSISCH - Total Ischemic time
	* SMEXNCRT - Exonic Rate

covid-19's People

Contributors

aomdahl avatar heyuan7676 avatar

Watchers

avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.