Package: regioneR 1.45.0

Introduction | Quick Start | Permutation tests | How does a permutation test work? | How to perform a permutation test with r BiocStyle::Biocpkg("regioneR") | A note on the number of permutations | Randomization Functions | randomizeRegions | circularRandomizeRegions | resampleRegions | Evaluation Functions | numOverlaps | meanDistance | meanInRegion | Custom Functions | Custom Evaluation | Custom Randomization | A note on reproducibility | Local Z-score | Region Sets | Genomes and Masks | Genomes | Masks | How to retrieve a genome and mask | Filtering Chromosomes | Region Set Helper Functions | Functions operating on a single RS | Functions operating on two RS | Other Functions: functions not returning a GRanges object | Usage Examples | Example 1: CpG Islands and Gene Promoters. A basic example. | Question: Are Cpg islands and promoters associated? | Brief Problem Description: | Datasets: | Step-by-step analysis: | References: | Example 2: Analysis of ChIP-seq peaks. Advanced usage and local Z-score. | Question: In the cell line Hepg2 (Human hepatocellular carcinoma ), is Rad21 (Cohesin) associated with CTCF? And with gene promoters? Are these associations different? | Benchmarks and Performance | Technical Considerations | Memoisation | Session Info