ChromoMap is a fast and easy-to-use tool for visualizing genomic elements and related data (such as multi-omics data) in relation to their chromosome-by-chromosome occurrence for any genome assembly. 

ChromoMap provides customizable displays that allow for the comparison of data individually connected with each strand of a specific chromosome, as well as homologous chromosomes of any size. Individual viewing of multi-omics data in all homologous chromosomes of phased diploid/polyploid genomes is also possible with ChromoMap.

Example plot generated using chromLinks: Normalized expression of the top 50 highly expressed orthologous genes in mouse (Mus musculus) and rat (Rattus norvegicus) during pluripotent cell determination (NCBI Gene Expression Omnibus id: GSE42081) [16]. Orthologous gene pairs are connected with colored links. Each orthologous pair is indicated by a different link color. 
Image Source: ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes

chromoMap is built by using two languages, R and JavaScript. The features of chromoMap include visualizing options for point and segment annotations, group annotations, labeling, and hyperlinking genomic features.

The package ChromoMap  and its documentation are available under the GPL-3 Open Source license from:  https://CRAN.R-project.org/package=chromoMap

Story Source: Anand, L., Rodriguez Lopez, C.M. ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes. BMC Bioinformatics 23, 33 (2022). https://doi.org/10.1186/s12859-021-04556-z

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