ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes
Abstract Background The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-ass...
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| Format: | Article |
| Language: | English |
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BMC
2022-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-021-04556-z |
| _version_ | 1798026246123159552 |
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| author | Lakshay Anand Carlos M. Rodriguez Lopez |
| author_facet | Lakshay Anand Carlos M. Rodriguez Lopez |
| author_sort | Lakshay Anand |
| collection | DOAJ |
| description | Abstract Background The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots. Results We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms with a genome assembly. ChromoMap can also integrate multi-omics data (genomics, transcriptomics and epigenomics) in relation to their occurrence across chromosomes. ChromoMap takes tab-delimited files (BED like) or alternatively R objects to specify the genomic co-ordinates of the chromosomes and elements to annotate. Rendered chromosomes are composed of continuous windows of a given range, which, on hover, display detailed information about the elements annotated within that range. By adjusting parameters of a single function, users can generate a variety of plots that can either be saved as static image or as HTML documents. Conclusions ChromoMap’s flexibility allows for concurrent visualization of genomic data in each strand of a given chromosome, or of more than one homologous chromosome; allowing the comparison of multi-omic data between genotypes (e.g. species, varieties, etc.) or between homologous chromosomes of phased diploid/polyploid genomes. chromoMap is an extensive tool that can be potentially used in various bioinformatics analysis pipelines for genomic visualization of multi-omics data. |
| first_indexed | 2024-04-11T18:32:12Z |
| format | Article |
| id | doaj.art-8e724816b8524b56ab7048d72324eb01 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-11T18:32:12Z |
| publishDate | 2022-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-8e724816b8524b56ab7048d72324eb012022-12-22T04:09:24ZengBMCBMC Bioinformatics1471-21052022-01-012311910.1186/s12859-021-04556-zChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomesLakshay Anand0Carlos M. Rodriguez Lopez1Environmental Epigenetics and Genetics Group, Department of Horticulture, University of KentuckyEnvironmental Epigenetics and Genetics Group, Department of Horticulture, University of KentuckyAbstract Background The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots. Results We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms with a genome assembly. ChromoMap can also integrate multi-omics data (genomics, transcriptomics and epigenomics) in relation to their occurrence across chromosomes. ChromoMap takes tab-delimited files (BED like) or alternatively R objects to specify the genomic co-ordinates of the chromosomes and elements to annotate. Rendered chromosomes are composed of continuous windows of a given range, which, on hover, display detailed information about the elements annotated within that range. By adjusting parameters of a single function, users can generate a variety of plots that can either be saved as static image or as HTML documents. Conclusions ChromoMap’s flexibility allows for concurrent visualization of genomic data in each strand of a given chromosome, or of more than one homologous chromosome; allowing the comparison of multi-omic data between genotypes (e.g. species, varieties, etc.) or between homologous chromosomes of phased diploid/polyploid genomes. chromoMap is an extensive tool that can be potentially used in various bioinformatics analysis pipelines for genomic visualization of multi-omics data.https://doi.org/10.1186/s12859-021-04556-zGenome visualizationMulti-omics data visualizationR package |
| spellingShingle | Lakshay Anand Carlos M. Rodriguez Lopez ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes BMC Bioinformatics Genome visualization Multi-omics data visualization R package |
| title | ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes |
| title_full | ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes |
| title_fullStr | ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes |
| title_full_unstemmed | ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes |
| title_short | ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes |
| title_sort | chromomap an r package for interactive visualization of multi omics data and annotation of chromosomes |
| topic | Genome visualization Multi-omics data visualization R package |
| url | https://doi.org/10.1186/s12859-021-04556-z |
| work_keys_str_mv | AT lakshayanand chromomapanrpackageforinteractivevisualizationofmultiomicsdataandannotationofchromosomes AT carlosmrodriguezlopez chromomapanrpackageforinteractivevisualizationofmultiomicsdataandannotationofchromosomes |