CAGEr: an R package for CAGE (Cap Analysis of Gene Expression) data analysis and promoterome mining

نویسنده

  • Vanja Haberle
چکیده

4 CAGEr workflow 6 4.1 Specifying input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 4.2 Creating CAGEset object . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 4.3 Reading in the data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 4.4 Correlation between samples . . . . . . . . . . . . . . . . . . . . . . . . . 9 4.5 Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 4.6 Exporting CAGE signal to bedGraph . . . . . . . . . . . . . . . . . . . . 12 4.7 CTSS clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 4.8 Promoter width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 4.9 Creating consensus promoters across samples . . . . . . . . . . . . . . . . 17 4.10 Expression profiling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 4.11 Shifting promoters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

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تاریخ انتشار 2013