README.md

In metamaden/recountmethylationManuscriptSupplement: Supplement for the manuscript "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus"

recountmethylationManuscriptSupplement

This repo contains supplemental methods, data, code, and scripts for the manuscript "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus."

Install as an R package

This repo is designed to work like a typical R packaage. You can install and load the repo from an active R session with:

pkg.name <- "recountmethylationManuscriptSupplement"
repo.path <- file.path("metamaden", pkg.name)

devtools::install_github(repo.path, build_vignettes = TRUE)

library(recountmethylationManuscriptSupplement)

Documentation, including Supplemental Information and vignettes that reproduce the manuscript figures, can be found using:

doc.path <- system.file("docfiles", package = pkg.name)
list.files(doc.path)

Resources of interest

The following resources include data, code, and scripts to reproduce findings in the main manuscript.

• recountmethylation -- Bioconductor package to access, query, and analyze full database compilations and sample metadata. https://bioconductor.org/packages/release/bioc/html/recountmethylation.html

• recountmethylationManuscriptSupplement -- GitHub repo for manuscript supplemental files, scripts, and data. https://github.com/metamaden/recountmethylationManuscriptSupplement

• figshare project -- Supplemental files, metadata, and DOIs for the manuscript https://figshare.com/account/home#/projects/90758

• recount.bio/data -- Location of large supplemental data files. https://recount.bio/data/recountmethylation_manuscript_supplement/

• recount-methylation-server -- Server software for identifying, downloading, and managing IDATs and SOFT files. https://github.com/metamaden/recount-methylation-server

• rmpipipeline -- GitHub repo with resources for processing GEO IDATs and SOFT files. https://github.com/metamaden/rmpipeline

metamaden/recountmethylationManuscriptSupplement documentation built on May 31, 2021, 5:27 a.m.