Overview | Installation | Example data used in this vignette | Available motif sets | Binding sites: getTFbindsites() | GC frequency tables: getGCfreq() | Genome-wide GC distribution: getGenomeGC() | Using the annotations with methylTFR | Reading the real data from AnnotationHub | Cleaning up | Session info

Overview | Installation | Example data used in this vignette | Available motif sets | Binding sites: getTFbindsites() | GC frequency tables: getGCfreq() | Genome-wide GC distribution: getGenomeGC() | Using the annotations with methylTFR | Reading the real data from AnnotationHub | Cleaning up | Session info

Introduction | Installation | Getting Started | Read a Sample File | Annotation Resources | Input Data | Compute Deviation Score for a Single Sample and Single Motif | Run methylTFR on multiple samples and motifs | Run methylTFR directly on an RnBeads object | Session Information

Introduction | The example dataset | Accessing the two assays | 1. Dimensionality reduction | 2. Differential TF activity | Ranking motifs by variability | Testing between two groups | Choosing an effect-size threshold | Visualising the differential motifs | 3. Comparing the two compartments | 4. Motif footprints | Observed and expected profiles | Bias-corrected footprint | References | Session Information

Introduction | Installation | Data | Comprehensive Human Methylome Reference Atlas | Illumina Infinium MethylationEPIC v1.0 B5 Manifest Probes (hg38) | Example Workflow For Whole Genome Bisulfate Sequencing Data | Expanding Reference Atlas | Constructing tissue specific CpG signature matrix | Constructing tissue specific DMPs | Example Workflow For RNA Sequencing Data | sessionInfo