ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
Abstract Motivation The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here,...
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| Veröffentlicht in: | Bioinformatics 2022-08, Vol.38 (15), p.3844-3846 |
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| container_title | Bioinformatics |
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| creator | Gustavsson, Emil K Zhang, David Reynolds, Regina H Garcia-Ruiz, Sonia Ryten, Mina |
| description | Abstract
Motivation
The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.
Availability and implementation
ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/. |
| doi_str_mv | 10.1093/bioinformatics/btac409 |
| format | Article |
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Motivation
The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.
Availability and implementation
ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btac409</identifier><identifier>PMID: 35751589</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Notes ; Protein Isoforms - genetics ; Sequence Analysis, DNA - methods ; Software</subject><ispartof>Bioinformatics, 2022-08, Vol.38 (15), p.3844-3846</ispartof><rights>The Author(s) 2022. Published by Oxford University Press. 2022</rights><rights>The Author(s) 2022. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c408t-6e9fd744b8d261cc5a298365c3f99319fbf3aeff3cdefc2cdcbb773d8a9922723</citedby><cites>FETCH-LOGICAL-c408t-6e9fd744b8d261cc5a298365c3f99319fbf3aeff3cdefc2cdcbb773d8a9922723</cites><orcidid>0000-0003-0541-7537 ; 0000-0001-9520-6957 ; 0000-0001-6470-7919 ; 0000-0003-4913-5312 ; 0000-0003-2382-8460</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9344834/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9344834/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35751589$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gustavsson, Emil K</creatorcontrib><creatorcontrib>Zhang, David</creatorcontrib><creatorcontrib>Reynolds, Regina H</creatorcontrib><creatorcontrib>Garcia-Ruiz, Sonia</creatorcontrib><creatorcontrib>Ryten, Mina</creatorcontrib><title>ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.
Availability and implementation
ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/.</description><subject>Applications Notes</subject><subject>Protein Isoforms - genetics</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Software</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNkUlLBDEQhYMoLqN_QXL00pqtl3gQRNxAEETPIZ1OeqI9SZukB_TXG5lxu3lKkXr11aMeAIcYHWPE6UlrvXXGh4VMVsWTNknFEN8Au5hVqCCo5Ju5plVdsAbRHbAX4zNCJWaMbYMdWtYlLhu-C-Z9n4J0UQU7plMoHXyAo1Qvstcw42Gaa7i0cZKDfc-rvMuSDlqXdBiDTqsvb-APBNroP41FOEXretj34-AT2QdbRg5RH6zfGXi6uny8uCnu7q9vL87viuy_SUWluelqxtqmIxVWqpSEN7QqFTWcU8xNa6jUxlDVaaOI6lTb1jXtGsk5ITWhM3C24o5Tu9Cd0i5bG8QY7EKGN-GlFX87zs5F75eCU8YayjLgaA0I_nXSMYmFjUoPg3TaT1GQqsGIkTqfdQaqlVQFH2PQ5nsNRuIzJvE3JrGOKQ8e_jb5PfaVSxbglcBP43-hH8Z2qs0</recordid><startdate>20220802</startdate><enddate>20220802</enddate><creator>Gustavsson, Emil K</creator><creator>Zhang, David</creator><creator>Reynolds, Regina H</creator><creator>Garcia-Ruiz, Sonia</creator><creator>Ryten, Mina</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0541-7537</orcidid><orcidid>https://orcid.org/0000-0001-9520-6957</orcidid><orcidid>https://orcid.org/0000-0001-6470-7919</orcidid><orcidid>https://orcid.org/0000-0003-4913-5312</orcidid><orcidid>https://orcid.org/0000-0003-2382-8460</orcidid></search><sort><creationdate>20220802</creationdate><title>ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2</title><author>Gustavsson, Emil K ; Zhang, David ; Reynolds, Regina H ; Garcia-Ruiz, Sonia ; Ryten, Mina</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c408t-6e9fd744b8d261cc5a298365c3f99319fbf3aeff3cdefc2cdcbb773d8a9922723</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Applications Notes</topic><topic>Protein Isoforms - genetics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gustavsson, Emil K</creatorcontrib><creatorcontrib>Zhang, David</creatorcontrib><creatorcontrib>Reynolds, Regina H</creatorcontrib><creatorcontrib>Garcia-Ruiz, Sonia</creatorcontrib><creatorcontrib>Ryten, Mina</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gustavsson, Emil K</au><au>Zhang, David</au><au>Reynolds, Regina H</au><au>Garcia-Ruiz, Sonia</au><au>Ryten, Mina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2022-08-02</date><risdate>2022</risdate><volume>38</volume><issue>15</issue><spage>3844</spage><epage>3846</epage><pages>3844-3846</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.
Availability and implementation
ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>35751589</pmid><doi>10.1093/bioinformatics/btac409</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0003-0541-7537</orcidid><orcidid>https://orcid.org/0000-0001-9520-6957</orcidid><orcidid>https://orcid.org/0000-0001-6470-7919</orcidid><orcidid>https://orcid.org/0000-0003-4913-5312</orcidid><orcidid>https://orcid.org/0000-0003-2382-8460</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics, 2022-08, Vol.38 (15), p.3844-3846 |
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| source | Oxford Journals Open Access Collection; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Applications Notes Protein Isoforms - genetics Sequence Analysis, DNA - methods Software |
| title | ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2 |
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