Introduction | Installation | Why pyramidal images? | Usage | EBImage | magick images | OME.TIFF (Bio-Formats) images | Use cases | Visualizing H&E images | Interactive Shiny Applications | Session info

Introduction | Installation | HDF5DataFrame Methods | Coercion | Session info

Introduction | Simulation | Unintegrated data | anglemania | extract the anglemania genes from the SCE object | select_genes | MNN integration | HVGs | 500 HVGs | 2000 HVGs | anglemania genes | Plot | UMAP embeddings | Overlap | Seurat | Integration | Showcase underlying functions | Normal anglemania workflow | factorise | get_list_stats | sessionInfo

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

Introduction | Smoothing single-cell gene expression data with netSmooth() function | Optimizing the smoothing parameter alpha | Getting robust clusters from data | Deciding for the best dimension reduction method for visualization and clustering | Frequently asked questions | How can I make smoothing faster ? | What happens if all the genes are not in my network ?

Introduction | Obtaining network data from stringDB

Introduction | Access the data | Data input | Extraction and visualization of genomic data | Extraction of data over genomic windows | Visualization of multiple genomic experiments | Annotation of genomic intervals | Annotation by generic features | Annotation of genomic intervals by gene structures | Use cases for genomation package | Visualization of ChiP sequencing data | Combinatorial binding of transcription factors | Using data from AnnotationHub | sessionInfo