Mercurial > repos > davidvanzessen > argalaxy_tools

annotate report_clonality/naive_cdr3_char.htm @ 56:7ae6b6b5d890 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
author rhpvorderman
date Tue, 14 Dec 2021 12:45:47 +0000
parents 81b3eb11ed2c
children 4c6df851e262
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
54
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
1 <html>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
2
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
3 <head>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
6 <style>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
7 <!--
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
8 /* Font Definitions */
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
9 @font-face
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
10 {font-family:Calibri;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
11 panose-1:2 15 5 2 2 2 4 3 2 4;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
12 /* Style Definitions */
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
13 p.MsoNormal, li.MsoNormal, div.MsoNormal
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
14 {margin-top:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
15 margin-right:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
16 margin-bottom:10.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
17 margin-left:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
18 line-height:115%;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
19 font-size:11.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
20 font-family:"Calibri","sans-serif";}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
21 .MsoChpDefault
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
22 {font-family:"Calibri","sans-serif";}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
23 .MsoPapDefault
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
24 {margin-bottom:10.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
25 line-height:115%;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
26 @page WordSection1
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
27 {size:8.5in 11.0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
28 margin:1.0in 1.0in 1.0in 1.0in;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
29 div.WordSection1
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
30 {page:WordSection1;}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
31 p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
32 {mso-style-priority:1;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
33 mso-style-unhide:no;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
34 mso-style-qformat:yes;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
35 margin:0in;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
36 margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
37 mso-pagination:widow-orphan;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
38 font-size:11.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
39 font-family:"Calibri","sans-serif";
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
40 mso-fareast-font-family:"Times New Roman";
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
41 mso-fareast-theme-font:minor-fareast;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
42 mso-bidi-font-family:"Times New Roman";}
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
43 -->
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
44 </style>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
45
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
46 </head>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
47
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
48 <body lang=EN-US>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
49
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
50 <div class=WordSection1>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
51
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
52 <p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
53 text-align:justify;line-height:normal'><b><u><span style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
54 font-family:"Times New Roman","serif"'>CDR3 characteristics tab</span></u></b></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
55
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
56 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
57 text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
58 font-family:"Times New Roman","serif"'>This tab gives information on the
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
59 different characteristics of the CDR3.</span></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
60
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
61 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
62 text-align:justify;line-height:normal'><b><span lang=EN-GB style='font-size:
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
63 12.0pt;font-family:"Times New Roman","serif"'>Graphs</span></b></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
64
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
65 <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
66 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
67 font-family:"Times New Roman","serif"'>length distribution of CDR3</span></u></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
68
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
69 <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
70 text-align:justify;line-height:normal'><span style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
71 font-family:"Times New Roman","serif"'>Graph visualizing for each donor the
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
72 distribution of the CDR3 length in amino acids between all sequences.</span></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
73
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
74 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
75 text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
76 font-family:"Times New Roman","serif"'>Amino acid composition of CDR3</span></u></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
77
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
78 <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
79 text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
80 font-family:"Times New Roman","serif"'>Bar graph visualizing for each donor how
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
81 frequent each amino acid is used in the CDR3 of all sequences. The red colour
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
82 in the background indicate positively charged amino acids, and the blue colour
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
83 in the background indicate negatively charged amino acids. The amino acids are
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
84 ordered from hydrophilic (left) to hydrophobic (right). </span></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
85
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
86 <p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
87 text-align:justify;line-height:normal'><b><span lang=EN-GB style='font-size:
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
88 12.0pt;font-family:"Times New Roman","serif"'>Table</span></b></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
89
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
90 <p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
91 text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
92 font-family:"Times New Roman","serif"'>Table showing for each donor the median
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
93 CDR3 length.</span></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
94
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
95 <p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
96
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
97 </div>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
98
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
99 </body>
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
100
81b3eb11ed2c "planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents: 52
diff changeset
101 </html>