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eczemadrs

Processing and analysis of human Atopic Dermatitis direct RNA-seq data

https://github.com/drchriscole/eczemadrs

Science Score: 41.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Processing and analysis of human Atopic Dermatitis direct RNA-seq data

Basic Info
  • Host: GitHub
  • Owner: drchriscole
  • License: mit
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 1.02 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 12 years ago · Last pushed over 4 years ago
Metadata Files
Readme Citation

README.md

DOI

Eczema DRS Paper Code Repository

Within this repository you will find all the code and data files as used/described in the Cole et al paper (see CITATION).

It has also been adapted for work on a collaboration with Ryan O'Shaughnessy (UCL) on RPTOR gene expression (see CITATION).

The repository has the following structure:

app/ - Shiny app for visualising gene expression bin/ - scripts for processing the source data
data/ - source data
CITATION - information on how to cite this work
README.md - information on the code and data (this file)
LICENCE - information on the licencing of the code
Makefile - code for running scripts via make
Makefile.RPTOR - code for performing RPTOR-specific analysis

Requirements

This code requires you have make and R on your $PATH and have the following R packages installed:

edgeR (tested with 3.14.0)
sqldf (tested with 0.4.10)
gplots (tested with 3.0.1)

For the Shiny App the shiny R library will also be required.

R version 3.3.0 was used during development (but should work with anything newer than 2.15.1).

Quickstart

To run all the scripts and generate all figures and data, type:

make

To run just the analyses and generate data, type:

make analysis

To run generate just the plots, type:

make figures

To delete all outputs, type:

make clean

To run RPTOR-specific analysis as per our 2016 paper (see CITATION):

make -f Makefile.RPTOR

Details

This github repository accompanies two papers and covers the differential gene expression analysis in a cohort of Irish peadiatric eczema cases in comparison to their filaggrin, FLG, genotype.

The simplest way to use the code is via the Quickstart guide above, but each script found under bin/ can run be individually if you know what you're doing. Code has some in-line comments.

Shiny App

A utility webapp has also been developed with RStudio's Shiny framework to perform gene-specific searches of expression profiles between cases and controls or stratified by FLG genotype.

To run the Shiny App do the following:

  1. Clone this repository into a new RStudio project
  2. Open the app\DRSexpr\app.R file
  3. Click the 'Run App' button

Owner

  • Name: Chris Cole
  • Login: drchriscole
  • Kind: user
  • Location: Scotland
  • Company: University of Dundee

Health Informatics, Bioinformatics and all things data.

Citation (CITATION) 

The code and data in this github repository can be cited via this doi: https://doi.org/10.5281/zenodo.3903509


The results of the analysis are part of the following publication:

Cole, Christian, Karin Kroboth, Nicholas J. Schurch, Aileen Sandilands, Alexander Sherstnev, Grainne M. O’Regan, Rosemarie M. Watson, et al. ‘Filaggrin-Stratified Transcriptomic Analysis of Pediatric Skin Identifies Mechanistic Pathways in Patients with Atopic Dermatitis’. Journal of Allergy and Clinical Immunology, 134(1), 82-91 (2014). 
https://doi.org/10.1016/j.jaci.2014.04.021

Please cite both of the above when referencing this work.
Many thanks.

For the analysis performed on the RPTOR gene, please cite the following:

Naeem AS, Tommasi C, Cole C, Brown SJ, Zhu Y, Way B, Willis Owen SAG, Moffat M, Cookson WO, Harper JI, Di WL, Brown SJ, Reinheckel T & O'Shaughnessy RFL. 'A mechanistic target of rapamycin complex 1/2 (mTORC1)/V-Akt murine thymoma viral oncogene homolog 1 (AKT1)/cathepsin H axis controls filaggrin expression and processing in skin, a novel mechanism for skin barrier disruption in patients with atopic dermatitis' Journal of Allergy and Clinical Immunology, 139(4), 1228–1241 (2017).
https://doi.org/10.1016/j.jaci.2016.09.052

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