TL;DR (Too long; didn't read) | Introduction to normR | Toy Examples | enrichR(): Calling Enrichment with an Input Control | Analyzing Results | Exporting Results | diffR(): Calling Differential Enrichment without a Control Experiment | regimeR(): Identify Enrichment Regimes in ChIP-seq Experiments | Advanced Topics | Change Read Counting Strategy with NormRCountConfig-class | Analyzing Predefined Regions | Post-processing of Difference Calls with CNV information

Loading toy data | Counting reads in given ranges with bamCount() | Basic counting | Accounting for fragment length | Counting on each strand separately | Read profiles for each region with bamProfile() | Regions of the same width | Binning counts | Read coverage with bamCoverage() | Advanced bamsignals filtering options | Exclude ambiguous reads with the mapq argument | Filter reads with the filteredFlag argument | Paired End Data | Paired end data handling with the paired.end argument | Filtering fragments with the tlenFilter argument