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MetaMutationalSigs: comparison of mutational signature refitting results made easy
Abstract Motivation The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each...
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Published in: | Bioinformatics 2022-04, Vol.38 (8), p.2344-2347 |
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container_title | Bioinformatics |
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creator | Pandey, Palash Arora, Sanjeevani Rosen, Gail L |
description | Abstract
Motivation
The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types.
Results
Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages.
Availability and implementation
MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs. |
doi_str_mv | 10.1093/bioinformatics/btac091 |
format | article |
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Motivation
The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types.
Results
Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages.
Availability and implementation
MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btac091</identifier><identifier>PMID: 35157026</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Note ; Humans ; Mutation ; Neoplasms - genetics ; Software</subject><ispartof>Bioinformatics, 2022-04, Vol.38 (8), p.2344-2347</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><cites>FETCH-LOGICAL-c403t-6fa369675cbf3897247e37f7b48e8628d75ed48f9df2c7c060d9e5f8c4bd63213</cites><orcidid>0000-0003-1763-5750</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/PMC9004636/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9004636/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35157026$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Marschall, Tobias</contributor><creatorcontrib>Pandey, Palash</creatorcontrib><creatorcontrib>Arora, Sanjeevani</creatorcontrib><creatorcontrib>Rosen, Gail L</creatorcontrib><title>MetaMutationalSigs: comparison of mutational signature refitting results made easy</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types.
Results
Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages.
Availability and implementation
MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs.</description><subject>Applications Note</subject><subject>Humans</subject><subject>Mutation</subject><subject>Neoplasms - genetics</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><recordid>eNqNkVtLxDAQhYMo3v-C9NGXatKkSeODIOINdhG8PIc0TWqkTdYkFfbfG9l10TefZmDOfHOGA8AJgmcIcnzeWm-d8WGUyap43iapIEdbYB8RCssK1nw795iykjQQ74GDGN8hrBEhZBfs4RrVDFZ0HzzNdZLzKWWMd3J4tn28KJQfFzLY6F3hTTFupkW0vZNpCroI2tiUrOtzF6chxWKUnS60jMsjsGPkEPXxuh6C19ubl-v7cvZ493B9NSsVgTiV1EhMOWW1ag1uOKsI05gZ1pJGN7RqOlbrjjSGd6ZSTEEKO65r0yjSdhRXCB-CyxV3MbWj7pR2KchBLIIdZVgKL634O3H2TfT-U3AICcU0A07XgOA_Jh2TGG1Uehik036Kosousj_Cv6V0JVXBx5if35xBUHwHIv4GItaB5MWT3yY3az8JZAFaCfy0-C_0C_mGobE</recordid><startdate>20220412</startdate><enddate>20220412</enddate><creator>Pandey, Palash</creator><creator>Arora, Sanjeevani</creator><creator>Rosen, Gail L</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/0000-0003-1763-5750</orcidid></search><sort><creationdate>20220412</creationdate><title>MetaMutationalSigs: comparison of mutational signature refitting results made easy</title><author>Pandey, Palash ; Arora, Sanjeevani ; Rosen, Gail L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c403t-6fa369675cbf3897247e37f7b48e8628d75ed48f9df2c7c060d9e5f8c4bd63213</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Applications Note</topic><topic>Humans</topic><topic>Mutation</topic><topic>Neoplasms - genetics</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pandey, Palash</creatorcontrib><creatorcontrib>Arora, Sanjeevani</creatorcontrib><creatorcontrib>Rosen, Gail L</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>Pandey, Palash</au><au>Arora, Sanjeevani</au><au>Rosen, Gail L</au><au>Marschall, Tobias</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MetaMutationalSigs: comparison of mutational signature refitting results made easy</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2022-04-12</date><risdate>2022</risdate><volume>38</volume><issue>8</issue><spage>2344</spage><epage>2347</epage><pages>2344-2347</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types.
Results
Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages.
Availability and implementation
MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>35157026</pmid><doi>10.1093/bioinformatics/btac091</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0003-1763-5750</orcidid><oa>free_for_read</oa></addata></record> |
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language | eng |
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source | PubMed (Medline); Oxford Journals Open Access Collection |
subjects | Applications Note Humans Mutation Neoplasms - genetics Software |
title | MetaMutationalSigs: comparison of mutational signature refitting results made easy |
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