Introduction | Installation | Importing data | modBAM data | Tabular data (Modkit, Megalodon, Nanopolish, f5c) | Modkit | Megalodon | Importing to tabix format | Quick start | Constructing the NanoMethResult object | Basic Plotting | Exporting data | bsseq and DSS | edgeR | Importing Annotations | Dimensionality reduction | Preparing data for dimensionality reduction | Package options | Site filtering | Region annotation colours

Introduction | Case Study: Preprocessing CEL-seq2 data | Getting started | Organising the files required | Data Preprocessing | Fastq reformatting | Aligning reads to a reference genome | Assigning reads to annotated exons | De-multiplexing data and counting genes | Preprocessing data generated by other protocols | Quality Control | Downstream analysis

Introduction | Workflow | Getting started | Fastq reformatting | Aligning reads to a reference genome | Demultiplexing the BAM file | Remove duplicates | Gemerating a fragment file | Peak calling | Assigning reads to features and feature counting | Generating the Single-cell Experiment (SCE) object | A convenience function for running the whole pipeline | Downstream analysis | Session Information

Introduction | Quick start | Downloading benchmark data | Key objects and concepts | Function piping | Mapping or list-apply | List of datasets | List of functions | Benchmark tibble and list-columns | Applying methods | Advanced usage | Multithreading | Function return caching | Constructing functions with parameter range | Summary

Introduction | Benchmark Tibble | Basics | Operations On Benchmark Tibbles | Operations On list-columns | Unnesting with Lists of data.frames | Manipulating Functions | Basics of Functional Programming | Partial Application | Sequence of Partial Applications | Memoisation | Further Reading

Introduction | Functional Programming with purrr | Methods as Function Objects | Function Composition | Mapping Over Lists | Table Manipulation with dplyr | Operations on the Benchmark tibble | Calculating multiple columns of metrics | Plotting with ggplot2 | Basic Plotting | Facetting

Introduction | MDS Plot | Interactions with the plot | Modifications to the plot | MA Plot | Using limma | Using edgeR | Volcano Plot | Saving widgets | Session Info

Session Info

Introduction | MDS Plot | Interactions with the plot | Modifications to the plot | MA Plot | Saving widgets | Session Info

Introduction | Wrapper Guidelines | Practical Examples | Simple Wrapper | Final remarks

Introduction | Timing methods | Summary