Man pages for ArnaudDroitLab/RJMCMCNucleosomes
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
| mergeAllRDSFiles | Merge nucleosome information |
| mergeAllRDSFilesFromDirectory | Merge nucleosome information from all RDS files present in a... |
| mergeRDSFiles | Merge nucleosome information from selected RDS files. |
| plotNucleosomes | Generate a graph of nucleosome positions with read coverage |
| postMerge | A internal post treatment function to merge closely... |
| postTreatment | A post-treatment function to merge closely positioned... |
| print.rjmcmcNucleosomes | Formated output of predicted nucleosomes |
| print.rjmcmcNucleosomesBeforeAndAfterPostTreatment | Formated output of predicted nucleosomes |
| print.rjmcmcNucleosomesMerge | Formated output of predicted nucleosomes |
| reads_demo_01 | Forward reads and reverse reads in 'GRanges' format (for demo... |
| reads_demo_02 | Forward reads and reverse reads in 'GRanges' format (for demo... |
| rjmcmc | Nucleosome positioning mapping on a segment |
| rjmcmcCHR | Nucleosome positioning mapping on a large segment, up to a... |
| rjmcmcNucleo | Interface for the RJMCMC nucleosome mapping method in C++ |
| RJMCMCNucleosomes-package | RJMCMCNucleosomes: Bayesian hierarchical model for... |
| RJMCMC_result | Nucleosomes obtained by running RJMCMC function using reads... |
| runCHR | Run 'rjmcmc' on multiples segments and merge results. |
| segmentation | Split a 'GRanges' containing reads in a list of smaller... |
| syntheticNucleosomeReads | Simulated dataset of reads generated by 'nucleoSim' package... |
| validateDirectoryParameters | Parameters validation for the 'mergeAllRDSFilesFromDirectory'... |
| validatePlotNucleosomesParameters | Parameters validation for the 'plotNucleosomes' function |
| validatePrepMergeParameters | Parameters validation for the 'postMerge' function |
| validateRDSFilesParameters | Parameters validation for the 'mergeRDSFiles' function |
| validateRJMCMCParameters | Parameters validation for the 'rjmcmc' function |
| validateSegmentationParameters | Parameters validation for the 'segmentation' function |
