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diff report_clonality/naive_downloads.htm @ 52:124b7fd92a3e draft

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author davidvanzessen
date Thu, 25 Feb 2021 13:36:15 +0000
parents 4d2a8f98a502
children 81b3eb11ed2c
line wrap: on
line diff
--- a/report_clonality/naive_downloads.htm	Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_downloads.htm	Thu Feb 25 13:36:15 2021 +0000
@@ -1,197 +1,197 @@
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-<div class=WordSection1>
-
-<p class=MsoNormalCxSpFirst style='text-align:justify'><b><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
-tab</span></u></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Description</span></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%;
-font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a
-name="OLE_LINK14">Allows you to download information on V D and J gene usage,
-the junctions and the amino acid sequence of the sequences that passed the chosen
-filter settings. Note: this file contains only 1 sequences of a replicate
-sequence. </a></span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene
-frequencies</span></b></p>
-
-<p class=MsoNormalCxSpMiddle 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"'>The dataset used to generate the distribution
-of V gene families graph:</span></u><span style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'> Downloads a table with information used to generate
-the distribution of V gene families graph.</span></p>
-
-<p class=MsoNormalCxSpMiddle 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"'>The dataset used to generate  the
-distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'>Downloads a table with information used
-to generate the distribution of D gene families graph.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-dataset used to generate the relative frequency of V gene usage graph:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data used to generate the relative frequency of V gene usage
-graph. In addition information on the chromosomal order of the V genes can be
-found.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-dataset used to generate the relative frequency of D gene usage graph:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data used to generate the relative frequency of D gene usage
-graph. In addition information on the chromosomal order of the D genes can be
-found.<u> </u></span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-dataset used to generate the relative frequency of J gene usage graph: </span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
-the data used to generate the relative frequency of J gene usage graph. In
-addition information on the chromosomal order of the J genes can be found.<u> </u></span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
-color:black'>The dataset used to generate the relative frequency of the D
-reading frame graph</span></u><span lang=EN-GB style='font-size:12.0pt;
-line-height:115%;font-family:"Times New Roman","serif";color:black'>: Downloads
-the data used to generate the relative frequency of the D reading frame. </span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
-color:black'>CDR3 characteristics</span></b></p>
-
-<p class=MsoNormalCxSpMiddle 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"'>The dataset used to generate the CDR3
-length frequency graph:</span></u><span style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'> Downloads a table with information used for the
-length distribution of CDR3 plot. </span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the frequency of the different amino acids in the CDR3 of all
-filtered sequences. This data set is used for the generation of the Amino Acid
-Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
-in included. </span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Heatmaps</span></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VD heatmap for “donor name”:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data set used for the generation of the VD heatmap. For each
-uploaded donor a separate download is generated.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VJ heatmap for “donor name”:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data set used for the generation of the VJ heatmap. For each
-uploaded donor a separate download is generated.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the DJ heatmap for “sample name”:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data set used for the generation of the DJ heatmap. For each
-uploaded donor a separate download is generated.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Circos</span></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VD circus plots for “donor name”:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data set used for the generation of the VD heatmap. For each
-uploaded donor a separate download is generated.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the VJ circus plots for “donor name”:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data set used for the generation of the VJ heatmap. For each
-uploaded donor a separate download is generated.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the DJ circus plots for “sample name”:</span></u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Downloads the data set used for the generation of the DJ heatmap. For each
-uploaded donor a separate download is generated.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-dataset used to calculate clonality score: </span></u><span style='font-size:
-12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
-download information on V D and J gene usage, the junctions and the amino acid
-sequence of the sequences that passed the chosen filter settings. Note: this
-file contains all the replicate sequences form the different input files.</span></p>
-
-<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences
-that are present in more than one replicate:</span></u><span style='font-size:
-12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to
-download a table containing all the sequences that were present in more than
-one replicate. It provides the concidence type, clonaltype, sequence name,
-replicate number, and the nucleotide sequence</span></p>
-
-<p class=MsoNormal>&nbsp;</p>
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+<!--
+ /* Font Definitions */
+ @font-face
+	{font-family:Calibri;
+	panose-1:2 15 5 2 2 2 4 3 2 4;}
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+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><b><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
+tab</span></u></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Description</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a
+name="OLE_LINK14">Allows you to download information on V D and J gene usage,
+the junctions and the amino acid sequence of the sequences that passed the chosen
+filter settings. Note: this file contains only 1 sequences of a replicate
+sequence. </a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene
+frequencies</span></b></p>
+
+<p class=MsoNormalCxSpMiddle 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"'>The dataset used to generate the distribution
+of V gene families graph:</span></u><span style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Downloads a table with information used to generate
+the distribution of V gene families graph.</span></p>
+
+<p class=MsoNormalCxSpMiddle 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"'>The dataset used to generate  the
+distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Downloads a table with information used
+to generate the distribution of D gene families graph.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the relative frequency of V gene usage graph:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data used to generate the relative frequency of V gene usage
+graph. In addition information on the chromosomal order of the V genes can be
+found.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the relative frequency of D gene usage graph:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data used to generate the relative frequency of D gene usage
+graph. In addition information on the chromosomal order of the D genes can be
+found.<u> </u></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the relative frequency of J gene usage graph: </span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
+the data used to generate the relative frequency of J gene usage graph. In
+addition information on the chromosomal order of the J genes can be found.<u> </u></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:black'>The dataset used to generate the relative frequency of the D
+reading frame graph</span></u><span lang=EN-GB style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif";color:black'>: Downloads
+the data used to generate the relative frequency of the D reading frame. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:black'>CDR3 characteristics</span></b></p>
+
+<p class=MsoNormalCxSpMiddle 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"'>The dataset used to generate the CDR3
+length frequency graph:</span></u><span style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Downloads a table with information used for the
+length distribution of CDR3 plot. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the frequency of the different amino acids in the CDR3 of all
+filtered sequences. This data set is used for the generation of the Amino Acid
+Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
+in included. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Heatmaps</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VD heatmap for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VD heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VJ heatmap for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the DJ heatmap for “sample name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the DJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Circos</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VD circus plots for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VD heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VJ circus plots for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the DJ circus plots for “sample name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the DJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to calculate clonality score: </span></u><span style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
+download information on V D and J gene usage, the junctions and the amino acid
+sequence of the sequences that passed the chosen filter settings. Note: this
+file contains all the replicate sequences form the different input files.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences
+that are present in more than one replicate:</span></u><span style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to
+download a table containing all the sequences that were present in more than
+one replicate. It provides the concidence type, clonaltype, sequence name,
+replicate number, and the nucleotide sequence</span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>