Your first cache | Comparison to base R save() and load() | Cache names | Creating but not loading caches | Loading multiple caches | Timing cache creating | Complicated code | Custom serialization backends

Generating caches in parallel using batchtools | Lock files

Introduction | GenomicDistributionsData | Downloading files | Distance distribution plots | Partition plots | Add custom partitions | Chromosome plots | Signal in regions - open chromatin signal specificity | Neighbor distance | Width distribution | GC content | Dinucleotide frequencies

Introduction to GenomicDistributions | Philosophy of modular calc and plot functions | Installing GenomicDistributions | Loading genomic range data | GenomicDistributions plot types | Chromosome distribution plots | Feature distance distribution plots | Partition distribution plots | Percentage partition distribution plots | Expected partition distribution plots | Cumulative partition distribution plots | Signal in regions plots | Neighboring regions distance plots | GC content plots | Dinucleotide frequency plots | Width distribution plots | Custom reference and features | Custom reference | Get chromosome sizes | Transcription start sites (TSS) | Gene models | Custom features (partitions) | Conclusion

The COCOA Bioconductor package | Basic workflow | Quantify inter-sample epigenetic variation | Annotate variation with region sets | Permutation test | COCOA for DNA methylation data | Our data | Supervised COCOA | Quantify relationship between chosen sample phenotype and epigenetic data | Score region sets | Estimating statistical significance | Permutations | Fit gamma distribution to null distributions and get p-values | Unsupervised COCOA | Quantify relationship between latent factors and epigenetic data | Further understanding the results (visualization) | Specificity of variation to the regions of interest | The raw data | Feature contribution scores of individual regions | COCOA for chromatin accessibility data (ATAC-seq) | Supervised COCOA | Unsupervised COCOA | Additional details | Method details | Region set database | Aggregating info from individual features | Making a "meta-region" profile | Q and A | Related references

The MIRA Bioconductor package | Required inputs | DNA methylation data | Region sets | Analysis workflow | The input | Expand your regions | Aggregating methylation across regions | Calculating the MIRA score | Interpreting the results | Bonus: Loading region sets with LOLA

Biological Question | Input: | Package workflow | Initial Run-through | Choosing Appropriate Region Sizes | Full MIRA Analysis | Interpreting the Results | General Interpretation Tips and Caveats | Other Tips for Using MIRA