chromoMap

chromoMap visualizes annotated chromosomes and associated multi-omics datasets to enable integrated interpretation of genomic, transcriptomic, and epigenomic features.

Key Features:

• Interactive Visualization: Visualizes chromosomes or specific chromosomal regions with mapped features such as protein-coding genes, transposable elements, non-coding RNAs, and microsatellites, and provides hover-over details for annotated elements within defined windows.
• Integration of Multi-Omics Data: Supports genomics, transcriptomics, and epigenomics datasets and displays gene expression levels, DNA methylation patterns, and chromatin modifications relative to chromosomal coordinates.
• Flexible Data Input: Accepts tab-delimited formats (similar to BED files) or R objects that specify genomic coordinates for annotation.
• Customizable Plots: Generates a range of plots via user-defined parameters and can export results as static images or interactive HTML documents.
• Comparative Visualization: Enables concurrent visualization across strands or between homologous chromosomes for comparison among genotypes, including phased diploid and polyploid genomes.

Scientific Applications:

• Genomic Annotation: Maps chromosomal features with known coordinates to support detailed genome annotation.
• Epigenetic Studies: Visualizes DNA methylation and chromatin modification data to investigate regulatory mechanisms.
• Comparative Genomics: Compares genomic features across genotypes or species to support evolutionary and biodiversity analyses.

Methodology:

Renders chromosomes as continuous windows that display detailed annotations upon interaction, maps features using genomic coordinates from tab-delimited (BED-like) files or R objects, and applies user-defined parameters to generate customizable visualizations.