Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/naive_gene_freq.htm @ 54:81b3eb11ed2c draft
"planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
| author | rhpvorderman |
|---|---|
| date | Tue, 16 Nov 2021 15:42:32 +0000 |
| parents | 124b7fd92a3e |
| children | 4c6df851e262 |
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--- a/report_clonality/naive_gene_freq.htm Thu Feb 25 13:39:50 2021 +0000 +++ b/report_clonality/naive_gene_freq.htm Tue Nov 16 15:42:32 2021 +0000 @@ -1,220 +1,220 @@ -<html xmlns:v="urn:schemas-microsoft-com:vml" -xmlns:o="urn:schemas-microsoft-com:office:office" -xmlns:w="urn:schemas-microsoft-com:office:word" -xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" -xmlns="http://www.w3.org/TR/REC-html40"> - -<head> -<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> -<meta name=ProgId content=Word.Document> -<meta name=Generator content="Microsoft Word 14"> -<meta name=Originator content="Microsoft Word 14"> -<link rel=File-List href="Gene%20frequencies%20tab_files/filelist.xml"> -<link rel=themeData href="Gene%20frequencies%20tab_files/themedata.thmx"> -<style> -<!-- - /* Font Definitions */ - @font-face - {font-family:Calibri; - panose-1:2 15 5 2 2 2 4 3 2 4; - mso-font-charset:0; - mso-generic-font-family:swiss; - mso-font-pitch:variable; - mso-font-signature:-536870145 1073786111 1 0 415 0;} - /* Style Definitions */ - p.MsoNormal, li.MsoNormal, div.MsoNormal - {mso-style-unhide:no; 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-font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>This tab gives -information on the frequency of V, D and J gene usage. <o:p></o:p></span></p> - -<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: -justify;line-height:normal'><o:p> </o:p></p> - -<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: -EN-GB'>Graphs</span></b></p> - -<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: -justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Distribution of -V gene families<o:p></o:p></span></u></p> - -<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK121"></a><a -name="OLE_LINK123"></a><a name="OLE_LINK122"></a><span style='mso-bookmark: -OLE_LINK121'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; -mso-ansi-language:EN-GB'>Bar graph showing the frequency of V gene family usage -in all uploaded donors. </span></span><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'><o:p></o:p></span></p> - -<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> - -<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: -justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative -frequency of V gene usage<o:p></o:p></span></u></p> - -<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK124"></a><a -name="OLE_LINK126"></a><a name="OLE_LINK125"></a><span style='mso-bookmark: -OLE_LINK124'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; -mso-ansi-language:EN-GB'>Bar graph showing the frequency of V genes in all -uploaded donors. The order of the V genes on the x-axis can be altered by -altering the “<span style='color:black;background:white'>Order of V(D)J genes -in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span -lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; -color:black;background:white;mso-ansi-language:EN-GB'><o:p></o:p></span></p> - -<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> - -<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: -justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative -frequency of D gene usage<o:p></o:p></span></u></p> - -<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: -EN-GB'>Bar graph showing the frequency of D genes in all uploaded donors. The -order of the D genes on the x-axis can be altered by altering the “<span -style='color:black;background:white'>Order of V(D)J genes in graphs” filter on -the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> - -<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> - -<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: -justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative -frequency of J gene usage<o:p></o:p></span></u></p> - -<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: -EN-GB'>Bar graph showing the frequency of J genes in all uploaded donors. The -order of the J genes on the x-axis can be altered by altering the “<span -style='color:black;background:white'>Order of V(D)J genes in graphs” filter on -the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> - -<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> - -<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: -justify;line-height:normal'><u><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>D -reading frame<o:p></o:p></span></u></p> - -<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: -EN-GB'>Bar graph visualizing the frequency by which each D reading frame is -used in each donor.</span></p> - -</div> - -</body> - -</html> +<html xmlns:v="urn:schemas-microsoft-com:vml" +xmlns:o="urn:schemas-microsoft-com:office:office" +xmlns:w="urn:schemas-microsoft-com:office:word" +xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" +xmlns="http://www.w3.org/TR/REC-html40"> + +<head> +<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta name=ProgId content=Word.Document> +<meta name=Generator content="Microsoft Word 14"> +<meta name=Originator content="Microsoft Word 14"> +<link rel=File-List href="Gene%20frequencies%20tab_files/filelist.xml"> +<link rel=themeData href="Gene%20frequencies%20tab_files/themedata.thmx"> +<style> +<!-- + /* Font Definitions */ + @font-face + {font-family:Calibri; + panose-1:2 15 5 2 2 2 4 3 2 4; + mso-font-charset:0; + mso-generic-font-family:swiss; + mso-font-pitch:variable; + mso-font-signature:-536870145 1073786111 1 0 415 0;} + /* Style Definitions */ + p.MsoNormal, li.MsoNormal, div.MsoNormal + {mso-style-unhide:no; + mso-style-qformat:yes; + mso-style-parent:""; + margin-top:0in; + margin-right:0in; + margin-bottom:10.0pt; + margin-left:0in; + line-height:115%; + mso-pagination:widow-orphan; + font-size:11.0pt; + font-family:"Calibri","sans-serif"; + mso-fareast-font-family:"Times New Roman"; + mso-fareast-theme-font:minor-fareast; + mso-bidi-font-family:"Times New Roman";} +p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing + {mso-style-priority:1; 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+ line-height:115%; + mso-pagination:widow-orphan; + font-size:10.0pt; + font-family:"Calibri","sans-serif";} +</style> +<![endif]--><!--[if gte mso 9]><xml> + <o:shapedefaults v:ext="edit" spidmax="1026"/> +</xml><![endif]--><!--[if gte mso 9]><xml> + <o:shapelayout v:ext="edit"> + <o:idmap v:ext="edit" data="1"/> + </o:shapelayout></xml><![endif]--> +</head> + +<body lang=EN-US style='tab-interval:.5in'> + +<div class=WordSection1> + +<p class=MsoNoSpacing style='text-align:justify'><b><u><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Gene frequencies tab</span></u></b></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>This tab gives +information on the frequency of V, D and J gene usage. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><o:p> </o:p></p> + +<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Graphs</span></b></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Distribution of +V gene families<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK121"></a><a +name="OLE_LINK123"></a><a name="OLE_LINK122"></a><span style='mso-bookmark: +OLE_LINK121'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; +mso-ansi-language:EN-GB'>Bar graph showing the frequency of V gene family usage +in all uploaded donors. </span></span><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'><o:p></o:p></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative +frequency of V gene usage<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK124"></a><a +name="OLE_LINK126"></a><a name="OLE_LINK125"></a><span style='mso-bookmark: +OLE_LINK124'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; +mso-ansi-language:EN-GB'>Bar graph showing the frequency of V genes in all +uploaded donors. The order of the V genes on the x-axis can be altered by +altering the “<span style='color:black;background:white'>Order of V(D)J genes +in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span +lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; +color:black;background:white;mso-ansi-language:EN-GB'><o:p></o:p></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative +frequency of D gene usage<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Bar graph showing the frequency of D genes in all uploaded donors. The +order of the D genes on the x-axis can be altered by altering the “<span +style='color:black;background:white'>Order of V(D)J genes in graphs” filter on +the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative +frequency of J gene usage<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Bar graph showing the frequency of J genes in all uploaded donors. The +order of the J genes on the x-axis can be altered by altering the “<span +style='color:black;background:white'>Order of V(D)J genes in graphs” filter on +the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>D +reading frame<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Bar graph visualizing the frequency by which each D reading frame is +used in each donor.</span></p> + +</div> + +</body> + +</html>