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| Bam_Handler | A class to manage BAM files. |
| get_demo_bam_files | Get BAM filenames for demo |
| get_demo_design | Get a demo design object |
| get_demo_metagene | Get a demo metagene object |
| get_demo_regions | Get regions filenames for demo |
| get_promoters_txdb | Extract Entrez genes promoters from TxDb object. |
| metagene | A class to manage metagene analysis. |
| permutation_test | Perform a permutation test on 2 matrices |
| plot_metagene | Produce a metagene plot |
| promoters_hg18 | Promoters regions of hg18 Entrez genes. |
| promoters_hg19 | Promoters regions of hg19 Entrez genes. |
| promoters_mm10 | Promoters regions of mm10 Entrez genes. |
| promoters_mm9 | Promoters regions of mm9 Entrez genes. |