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View Code? Open in Web Editor NEWR codes of the figures from the Epigenetics CSMD1 paper
R codes of the figures from the Epigenetics CSMD1 paper
##################################### ## Source Codes of the CSMD1 Paper ## ##################################### 1. Figures This is where you would see the figure when you run the R codes explained below. 2. Rscript This is where the actual R codes are and the directory structure looks like this: 2.0. Library files lib/local.R lib/multiplot.R lib/theme_publish.R 2.1. R scripts for the main figures (Fig1-Fig6) CSMD1.paper.figures.main.R CSMD1.Fig1.R CSMD1.Fig2.R CSMD1.Fig3.R CSMD1.Fig4.R CSMD1.Fig5.R CSMD1.Fig6.R 2.2. R scripts for the supplementary figures Suppl/CSMD1.Suppl.Fig3.CSMD1.DMR2.RoadMap.R Suppl/CSMD1.Suppl.Fig4.canonical.promoter.PT.R Suppl/CSMD1.Suppl.Fig6.putative.promoter.PT.R Suppl/CSMD1.Suppl.Fig8.putative.promoter.RoadMap.R Suppl/CSMD1.Suppl.Fig9.fetal.embryo.pheatmap.R 3. RData This is where the data/files are. However following files were omimitted due to the size limit (>25Mb) 436M PT.CG.dt.meth.region.RData 145M PT.CG.dt.merged.RData 88M hg19ensGene.sqlite 42M rnb.meth.diff.PT.RData 4. Track hub To browse methylation & expression level we presented in the paper, visit the links shown below: http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://www.obgyn.cam.ac.uk/TrackHub/CamObsGynaeHub.txt&org=human&db=hg19&position=chr8:2792000-3040000 or, http://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://www.obgyn.cam.ac.uk/TrackHub/CamObsGynaeHub.txt&org=human&db=hg19&position=chr8:2792000-3040000 Following two URLs are pre-configured track hubs links, which we presented in the supplemental figure 5 and 7: Supplemental Figure S5. The reconstructed transcript of placenta CSMD1 compared with the reference gene annotation https://goo.gl/yjflRX Supplemental Figure S7. Genome annotations that support the putative promoter region in the placenta https://goo.gl/i3xrNN ----- Sungsam Gong <[email protected]; [email protected]> First created 8/Dec/2016 Last modified 9/Jan/2018
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