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Chromosome

Summary Table

NAME CITATION YEAR
ChromoMap Anand L, Rodriguez Lopez CM. (2022) ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes BMC Bioinformatics, 23 (1) 33. doi:10.1186/s12859-021-04556-z. PMID 35016614 2022
karyoploteR Gel B, Serra E. (2017) karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data Bioinformatics, 33 (19) 3088-3090. doi:10.1093/bioinformatics/btx346. PMID 28575171 2017

ChromoMap

  • NAME : ChromoMap
  • SHORT NAME : chromoMap
  • FULL NAME : chromoMap
  • DESCRIPTION : an R package for interactive visualization of multi-omics data and annotation of chromosomes
  • URL : https://lakshay-anand.github.io/chromoMap/index.html
  • TITLE : ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes
  • DOI : 10.1186/s12859-021-04556-z
  • 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.
  • COPYRIGHT : https://creativecommons.org/licenses/by/4.0
  • CITATION : Anand L, Rodriguez Lopez CM. (2022) ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes BMC Bioinformatics, 23 (1) 33. doi:10.1186/s12859-021-04556-z. PMID 35016614
  • JOURNAL_INFO : BMC bioinformatics ; BMC Bioinformatics ; 2022 ; 23 ; 1 ; 33
  • PUBMED_LINK : 35016614

karyoploteR

  • NAME : karyoploteR
  • SHORT NAME : karyoploteR
  • FULL NAME : karyoploteR
  • DESCRIPTION : karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.
  • URL : https://bernatgel.github.io/karyoploter_tutorial/
  • TITLE : karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
  • DOI : 10.1093/bioinformatics/btx346
  • ABSTRACT : MOTIVATION: Data visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species. RESULTS: We have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation. AVAILABILITY AND IMPLEMENTATION: karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR) and at the examples and tutorial page at https://bernatgel.github.io/karyoploter_tutorial. CONTACT: bgel@igtp.cat.
  • CITATION : Gel B, Serra E. (2017) karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data Bioinformatics, 33 (19) 3088-3090. doi:10.1093/bioinformatics/btx346. PMID 28575171
  • JOURNAL_INFO : Bioinformatics (Oxford, England) ; Bioinformatics ; 2017 ; 33 ; 19 ; 3088-3090
  • PUBMED_LINK : 28575171