CAGEr: an R package for CAGE (Cap Analysis of Gene Expression) data analysis and promoterome mining
نویسنده
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
منابع مشابه
CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses
Cap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high resolution and functional significance, published CAGE data are still underused in promoter analysis due to the absence of tools that enable its efficient manipulation and int...
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