Data files and R code for

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

Yunshun Chen, Bhupinder Pal, Jane E. Visvader and Gordon K. Smyth

F1000Research (2017, revised 2018) 6:2055
DOI: 10.12688/f1000research.13196.2

Corrected Preprint

• Corrected Preprint dated 23 October 2018

Data files

The target information of the RRBS data is included in the following tab-delimited text file.

• targets.txt

The compressed Bismark coverage outputs of all six samples described in the paper are available below.

• P6_1.bismark.cov.gz
• P6_4.bismark.cov.gz
• P7_2.bismark.cov.gz
• P7_5.bismark.cov.gz
• P8_3.bismark.cov.gz
• P8_6.bismark.cov.gz

The RNA-seq gene expression data and the list of differentially expressed genes used in the workflow are available below.

• rna.RData
• BvsL-fc3.csv

R code

The following files contain the R commands used in the workflow:

• AnalysisV2.R (Version 2, Published 8 October 2018)
• AnalysisV1.R (Version 1, Published 28 November 2017)

 

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Comments/Questions? Contact Gordon Smyth.
Last modified: 30 July 2019