Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/naive_downloads.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_downloads.htm Thu Feb 25 13:39:50 2021 +0000 +++ b/report_clonality/naive_downloads.htm Tue Nov 16 15:42:32 2021 +0000 @@ -1,197 +1,197 @@ -<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;} - /* Style Definitions */ - p.MsoNormal, li.MsoNormal, div.MsoNormal - {margin-top:0in; - margin-right:0in; - margin-bottom:10.0pt; - margin-left:0in; - line-height:115%; - font-size:11.0pt; - font-family:"Calibri","sans-serif";} -.MsoChpDefault - {font-family:"Calibri","sans-serif";} -.MsoPapDefault - {margin-bottom:10.0pt; - line-height:115%;} -@page WordSection1 - {size:8.5in 11.0in; - margin:1.0in 1.0in 1.0in 1.0in;} -div.WordSection1 - {page:WordSection1;} ---> -</style> - -</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> </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;} + /* Style Definitions */ + p.MsoNormal, li.MsoNormal, div.MsoNormal + {margin-top:0in; + margin-right:0in; + margin-bottom:10.0pt; + margin-left:0in; + line-height:115%; + font-size:11.0pt; + font-family:"Calibri","sans-serif";} +.MsoChpDefault + {font-family:"Calibri","sans-serif";} +.MsoPapDefault + {margin-bottom:10.0pt; + line-height:115%;} +@page WordSection1 + {size:8.5in 11.0in; + margin:1.0in 1.0in 1.0in 1.0in;} +div.WordSection1 + {page:WordSection1;} +--> +</style> + +</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> </p> + +</div> + +</body> + +</html>