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| 142 | <div·class="frontmatter"> | 142 | <div·class="frontmatter"> |
| 143 | <div·class="title"><h1>Obtaining·and·Utilizing·TxDb·Objects</h1></div> | 143 | <div·class="title"><h1>Obtaining·and·Utilizing·TxDb·Objects</h1></div> |
| 144 | <div·class="author"><h2>list(name·=·“Marc·Carlson”) | 144 | <div·class="author"><h2>list(name·=·“Marc·Carlson”) |
| 145 | list(name·=·“Patrick·Aboyoun”) | 145 | list(name·=·“Patrick·Aboyoun”) |
| 146 | list(name·=·“Herv<U+00E9>·Pag<U+00E8>s”) | 146 | list(name·=·“Herv<U+00E9>·Pag<U+00E8>s”) |
| 147 | list(name·=·“Seth·Falcon”) | 147 | list(name·=·“Seth·Falcon”) |
| 148 | list(name·=·“Martin·Morgan”)</h2></div> | 148 | list(name·=·“Martin·Morgan”)</h2></div> |
| 149 | <div·class="date"><h3> | 149 | <div·class="date"><h3>Wednesday,·December·10,·2025</h3></div> |
| 150 | </div> | 150 | </div> |
| 151 | <div·class="body"> | 151 | <div·class="body"> |
| 152 | <h1·id="introduction">Introduction</h1> | 152 | <h1·id="introduction">Introduction</h1> |
| 153 | <p>The·<code>GenomicFeatures</code>·package·implements·the·<code>TxDb</code>·container·for | 153 | <p>The·<code>GenomicFeatures</code>·package·implements·the·<code>TxDb</code>·container·for |
| 154 | storing·transcript·metadata·for·a·given·organism.·A·<code>TxDb</code>·object | 154 | storing·transcript·metadata·for·a·given·organism.·A·<code>TxDb</code>·object |
| 155 | stores·the·genomic·positions·of·the·5’·and·3’·untranslated·regions | 155 | stores·the·genomic·positions·of·the·5’·and·3’·untranslated·regions |
| 156 | (UTRs),·protein·coding·sequences·(CDSs),·and·exons·for·a·set·of·mRNA | 156 | (UTRs),·protein·coding·sequences·(CDSs),·and·exons·for·a·set·of·mRNA |
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| 563 | ##·Matrix·products:·default | 563 | ##·Matrix·products:·default |
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| 565 | ##·LAPACK:·/usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3.12.0 | 565 | ##·LAPACK:·/usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3.12.0 |
| 566 | ##· | 566 | ##· |
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| 1 | *\x8**\x8**\x8**\x8**\x8**\x8*·O\x8Ob\x8bt\x8ta\x8ai\x8in\x8ni\x8in\x8ng\x8g·a\x8an\x8nd\x8d·U\x8Ut\x8ti\x8il\x8li\x8iz\x8zi\x8in\x8ng\x8g·T\x8Tx\x8xD\x8Db\x8b·O\x8Ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·*\x8**\x8**\x8**\x8**\x8**\x8* | 1 | *\x8**\x8**\x8**\x8**\x8**\x8*·O\x8Ob\x8bt\x8ta\x8ai\x8in\x8ni\x8in\x8ng\x8g·a\x8an\x8nd\x8d·U\x8Ut\x8ti\x8il\x8li\x8iz\x8zi\x8in\x8ng\x8g·T\x8Tx\x8xD\x8Db\x8b·O\x8Ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·*\x8**\x8**\x8**\x8**\x8**\x8* |
| 2 | *\x8**\x8**\x8**\x8**\x8*·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“M\x8Ma\x8ar\x8rc\x8c·C\x8Ca\x8ar\x8rl\x8ls\x8so\x8on\x8n?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“P\x8Pa\x8at\x8tr\x8ri\x8ic\x8ck\x8k·A\x8Ab\x8bo\x8oy\x8yo\x8ou\x8un\x8n?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8= | 2 | *\x8**\x8**\x8**\x8**\x8*·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“M\x8Ma\x8ar\x8rc\x8c·C\x8Ca\x8ar\x8rl\x8ls\x8so\x8on\x8n?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“P\x8Pa\x8at\x8tr\x8ri\x8ic\x8ck\x8k·A\x8Ab\x8bo\x8oy\x8yo\x8ou\x8un\x8n?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8= |
| 3 | ?\x8“H\x8He\x8er\x8rv\x8v<\x8<U\x8U+\x8+0\x800\x80E\x8E9\x89>\x8>·P\x8Pa\x8ag\x8g<\x8<U\x8U+\x8+0\x800\x80E\x8E8\x88>\x8>s\x8s?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“S\x8Se\x8et\x8th\x8h·F\x8Fa\x8al\x8lc\x8co\x8on\x8n?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“M\x8Ma\x8ar\x8rt\x8ti\x8in\x8n | 3 | ?\x8“H\x8He\x8er\x8rv\x8v<\x8<U\x8U+\x8+0\x800\x80E\x8E9\x89>\x8>·P\x8Pa\x8ag\x8g<\x8<U\x8U+\x8+0\x800\x80E\x8E8\x88>\x8>s\x8s?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“S\x8Se\x8et\x8th\x8h·F\x8Fa\x8al\x8lc\x8co\x8on\x8n?\x8”)\x8)·l\x8li\x8is\x8st\x8t(\x8(n\x8na\x8am\x8me\x8e·=\x8=·?\x8“M\x8Ma\x8ar\x8rt\x8ti\x8in\x8n |
| 4 | M\x8Mo\x8or\x8rg\x8ga\x8an\x8n?\x8”)\x8)·*\x8**\x8**\x8**\x8**\x8* | 4 | M\x8Mo\x8or\x8rg\x8ga\x8an\x8n?\x8”)\x8)·*\x8**\x8**\x8**\x8**\x8* |
| 5 | *\x8**\x8**\x8**\x8*· | 5 | *\x8**\x8**\x8**\x8*·W.We.ed.dn.ne.es.sd.da.ay.y,.,·D.De.ec.ce.em.mb.be.er.r·1.10.0,.,·2.20.02.25.5·*\x8**\x8**\x8**\x8* |
| 6 | *\x8**\x8**\x8**\x8**\x8**\x8*·I\x8In\x8nt\x8tr\x8ro\x8od\x8du\x8uc\x8ct\x8ti\x8io\x8on\x8n·*\x8**\x8**\x8**\x8**\x8**\x8* | 6 | *\x8**\x8**\x8**\x8**\x8**\x8*·I\x8In\x8nt\x8tr\x8ro\x8od\x8du\x8uc\x8ct\x8ti\x8io\x8on\x8n·*\x8**\x8**\x8**\x8**\x8**\x8* |
| 7 | The·GenomicFeatures·package·implements·the·TxDb·container·for·storing | 7 | The·GenomicFeatures·package·implements·the·TxDb·container·for·storing |
| 8 | transcript·metadata·for·a·given·organism.·A·TxDb·object·stores·the·genomic | 8 | transcript·metadata·for·a·given·organism.·A·TxDb·object·stores·the·genomic |
| 9 | positions·of·the·5’·and·3’·untranslated·regions·(UTRs),·protein·coding | 9 | positions·of·the·5’·and·3’·untranslated·regions·(UTRs),·protein·coding |
| 10 | sequences·(CDSs),·and·exons·for·a·set·of·mRNA·transcripts.·The·genomic | 10 | sequences·(CDSs),·and·exons·for·a·set·of·mRNA·transcripts.·The·genomic |
| 11 | positions·are·stored·and·reported·with·respect·to·a·given·genome·assembly.·TxDb | 11 | positions·are·stored·and·reported·with·respect·to·a·given·genome·assembly.·TxDb |
| 12 | objects·have·numerous·accessors·functions·to·allow·such·features·to·be | 12 | objects·have·numerous·accessors·functions·to·allow·such·features·to·be |
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| 2 | title:·"Obtaining·and·Utilizing·TxDb·Objects" | 2 | title:·"Obtaining·and·Utilizing·TxDb·Objects" |
| 3 | author: | 3 | author: |
| 4 | -·name:·Marc·Carlson | 4 | -·name:·Marc·Carlson |
| 5 | -·name:·Patrick·Aboyoun | 5 | -·name:·Patrick·Aboyoun |
| 6 | -·name:·Hervé·Pagès | 6 | -·name:·Hervé·Pagès |
| 7 | -·name:·Seth·Falcon | 7 | -·name:·Seth·Falcon |
| 8 | -·name:·Martin·Morgan | 8 | -·name:·Martin·Morgan |
| 9 | date:·" | 9 | date:·"Wednesday,·December·10,·2025" |
| 10 | package:·GenomicFeatures | 10 | package:·GenomicFeatures |
| 11 | vignette:·| | 11 | vignette:·| |
| 12 | ··%\VignetteIndexEntry{Obtaining·and·Utilizing·TxDb·Objects} | 12 | ··%\VignetteIndexEntry{Obtaining·and·Utilizing·TxDb·Objects} |
| 13 | ··%\VignetteEngine{knitr::rmarkdown} | 13 | ··%\VignetteEngine{knitr::rmarkdown} |
| 14 | ··%\VignetteEncoding{UTF-8} | 14 | ··%\VignetteEncoding{UTF-8} |
| 15 | ··%\VignetteDepends{GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,BSgenome.Hsapiens.UCSC.hg19} | 15 | ··%\VignetteDepends{GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,BSgenome.Hsapiens.UCSC.hg19} |
| 16 | ··%\VignetteKeywords{annotation,·database} | 16 | ··%\VignetteKeywords{annotation,·database} |
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