Introduction | Current Features | Processing speed | Reference-free processing | Sample data | Amplicon-based methylation NGS data | Capture-based methylation NGS data | Long-read native NGS data (adaptive sampling) | Manually creating sample BAM files | Typical workflow | Requirements | Short-read sequencing | Long-read sequencing | Reading the data | Specific considerations for long-read sequencing data: | Optional calling of cytosine methylation | Making cytosine reports | Making VEF reports for a set of genomic regions | Linearized MHL reports | Exploring DNA methylation patterns | Exploring sequence variants in epialleles | Plotting the distribution of per-read beta values | Other information | Citing the epialleleR package | The data underlying epialleleR manuscript | Our experimental studies that use the package | Session Info | References

Introduction | Session Info

Introduction | Current Features | Major improvements | v1.16 [BioC 3.21] | Reading data | Using data from NCBI GEO | Using Bismark cytosine report files | Simulating data | AMR identification | AMR annotation and enrichment analysis | Other information | Citing the ramr package | The data underlying ramr manuscript | Session Info

Probability density function: | Cumulative distribution function: | Log-likelihood function: | Score function vector: | Observed information matrix:

Probability density function: | Cumulative distribution function: | Log-likelihood function: | Score function vector: | Observed information matrix:

Introduction | Parameter Estimation | Distribution selection | Weighted sample | References