MS-DArT-seq: A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.

This repository contains the analytical code necessary to reproduce the results described in the paper: "A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing."

The datasets necessary to reproduce the results can be find in figshare: https://doi.org/10.6084/m9.figshare.10305431

List of softwares, and their versions, used to generate the results described in the paper:

• R : 3.5.1
• trimmomatic : 0.36
• bowtie2 : 2.3.5
• samtools : 1.8
• bedtools : 2.27.1
• subread : 1.6.2
• fastqc : 0.11.4

List of R packages, and their versions, used to generate the results described in the paper:

• alluvial: 0.1.2
• berryFunctions: 1.18.2
• corrplot: 0.84
• data.table: 1.12.2
• docopt: 0.6.1
• doMC: 1.3.5
• dplyr: 0.8.3
• foreach: 1.4.4
• gdata: 2.18.0
• ggfortify: 0.4.6
• ggplot2: 3.2.1
• ggsci: 2.9
• ggthemes: 4.2.0
• googleVis: 0.6.3
• gridExtra: 2.3
• gridGraphics: 0.4.1
• Matching: 4.9.6
• plyr: 1.8.4
• RColorBrewer: 1.1.2
• reshape2: 1.4.3
• sjstats: 0.17.6
• splitstackshape: 1.4.8
• stringr: 1.4.0
• tidyr: 1.0.0
• tidyverse: 1.2.1
• VennDiagram: 1.6.20
• AnnotationForge: 1.24.0
• biomaRt: 2.38.0
• clusterProfiler: 3.10.1
• DESeq2: 1.22.2
• edgeR: 3.24.3
• GenomicRanges: 1.34.0
• ggbio: 1.30.0
• Gviz: 1.26.5
• rtracklayer: 1.42.2