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seohyonkim committed Feb 18, 2025
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305 changes: 282 additions & 23 deletions pr-preview/pr-325/_sources/air_repertoire/ir_profiling.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3223,25 +3223,289 @@
"id": "e7b77012",
"metadata": {},
"source": [
"## Quiz\n",
"## Quiz"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "35d2d491",
"metadata": {
"tags": [
"remove_input"
]
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <style>\n",
" /* to remove the background color in dark mode */\n",
" div#flip-card .output.text_html {\n",
" background-color: transparent;\n",
" }\n",
" .flip-card-q1 {\n",
" background-color: transparent;\n",
" width: 350px;\n",
" height: 200px;\n",
" perspective: 1000px;\n",
" display: inline-block;\n",
" margin: 10px;\n",
" text-align: center;\n",
" padding: 10px;\n",
" }\n",
" .flip-card-inner-q1 {\n",
" position: relative;\n",
" width: 100%;\n",
" height: 100%;\n",
" text-align: center;\n",
" transition: transform 0.6s;\n",
" transform-style: preserve-3d;\n",
" transform-origin: center;\n",
" }\n",
" .flip-card-q1:hover .flip-card-inner-q1 {\n",
" transform: rotateY(180deg);\n",
" }\n",
" .flip-card-front-q1, .flip-card-back-q1 {\n",
" position: absolute;\n",
" width: 100%;\n",
" height: 100%;\n",
" min-height: 200px;\n",
" backface-visibility: hidden;\n",
" display: flex;\n",
" align-items: center;\n",
" justify-content: center;\n",
" font-weight: bold;\n",
" color: white;\n",
" padding: 20px;\n",
" border-radius: 15px;\n",
" box-sizing: border-box;\n",
" overflow: hidden;\n",
" text-align: center;\n",
" }\n",
" .flip-card-front-q1 {\n",
" background-color: #3965a3;\n",
" font-size: 20px;\n",
" }\n",
" .flip-card-back-q1 {\n",
" background-color: #a8d480;\n",
" transform: rotateY(180deg);\n",
" font-size: 13px;\n",
" }\n",
" </style>\n",
"\n",
" <div class=\"flip-card-q1\">\n",
" <div class=\"flip-card-inner-q1\">\n",
" <div class=\"flip-card-front-q1\">\n",
" Where does the high variability of AIRs stem from?\n",
" </div>\n",
" <div class=\"flip-card-back-q1\">\n",
" Junctional diversity adds random nucleotides. Peripheral diversity motivates rapid amino acid switches specific to the host organ. Combinatorial diversity of different gene segments. Inherited diversity genetically encodes multiple AIRs.\n",
" </div>\n",
" </div>\n",
" </div>\n",
" <noscript>\n",
" <p><strong>Q:</strong> Where does the high variability of AIRs stem from?</p>\n",
" <p><strong>Answer:</strong> Junctional diversity adds random nucleotides. Peripheral diversity motivates rapid amino acid switches specific to the host organ. Combinatorial diversity of different gene segments. Inherited diversity genetically encodes multiple AIRs.</p>\n",
" </noscript>\n",
" "
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"\n",
" <style>\n",
" /* to remove the background color in dark mode */\n",
" div#flip-card .output.text_html {\n",
" background-color: transparent;\n",
" }\n",
" .flip-card-q2 {\n",
" background-color: transparent;\n",
" width: 350px;\n",
" height: 200px;\n",
" perspective: 1000px;\n",
" display: inline-block;\n",
" margin: 10px;\n",
" text-align: center;\n",
" padding: 10px;\n",
" }\n",
" .flip-card-inner-q2 {\n",
" position: relative;\n",
" width: 100%;\n",
" height: 100%;\n",
" text-align: center;\n",
" transition: transform 0.6s;\n",
" transform-style: preserve-3d;\n",
" transform-origin: center;\n",
" }\n",
" .flip-card-q2:hover .flip-card-inner-q2 {\n",
" transform: rotateY(180deg);\n",
" }\n",
" .flip-card-front-q2, .flip-card-back-q2 {\n",
" position: absolute;\n",
" width: 100%;\n",
" height: 100%;\n",
" min-height: 200px;\n",
" backface-visibility: hidden;\n",
" display: flex;\n",
" align-items: center;\n",
" justify-content: center;\n",
" font-weight: bold;\n",
" color: white;\n",
" padding: 20px;\n",
" border-radius: 15px;\n",
" box-sizing: border-box;\n",
" overflow: hidden;\n",
" text-align: center;\n",
" }\n",
" .flip-card-front-q2 {\n",
" background-color: #3965a3;\n",
" font-size: 20px;\n",
" }\n",
" .flip-card-back-q2 {\n",
" background-color: #a8d480;\n",
" transform: rotateY(180deg);\n",
" font-size: 20px;\n",
" }\n",
" </style>\n",
"\n",
" <div class=\"flip-card-q2\">\n",
" <div class=\"flip-card-inner-q2\">\n",
" <div class=\"flip-card-front-q2\">\n",
" What properties does a productive AIR have?\n",
" </div>\n",
" <div class=\"flip-card-back-q2\">\n",
" It spans over the V- to the J-gene with a CDR3 regions contained. It contains a start codon in the leading region.\n",
" </div>\n",
" </div>\n",
" </div>\n",
" <noscript>\n",
" <p><strong>Q:</strong> What properties does a productive AIR have?</p>\n",
" <p><strong>Answer:</strong> It spans over the V- to the J-gene with a CDR3 regions contained. It contains a start codon in the leading region.</p>\n",
" </noscript>\n",
" "
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"\n",
" <style>\n",
" /* to remove the background color in dark mode */\n",
" div#flip-card .output.text_html {\n",
" background-color: transparent;\n",
" }\n",
" .flip-card-q3 {\n",
" background-color: transparent;\n",
" width: 350px;\n",
" height: 200px;\n",
" perspective: 1000px;\n",
" display: inline-block;\n",
" margin: 10px;\n",
" text-align: center;\n",
" padding: 10px;\n",
" }\n",
" .flip-card-inner-q3 {\n",
" position: relative;\n",
" width: 100%;\n",
" height: 100%;\n",
" text-align: center;\n",
" transition: transform 0.6s;\n",
" transform-style: preserve-3d;\n",
" transform-origin: center;\n",
" }\n",
" .flip-card-q3:hover .flip-card-inner-q3 {\n",
" transform: rotateY(180deg);\n",
" }\n",
" .flip-card-front-q3, .flip-card-back-q3 {\n",
" position: absolute;\n",
" width: 100%;\n",
" height: 100%;\n",
" min-height: 200px;\n",
" backface-visibility: hidden;\n",
" display: flex;\n",
" align-items: center;\n",
" justify-content: center;\n",
" font-weight: bold;\n",
" color: white;\n",
" padding: 20px;\n",
" border-radius: 15px;\n",
" box-sizing: border-box;\n",
" overflow: hidden;\n",
" text-align: center;\n",
" }\n",
" .flip-card-front-q3 {\n",
" background-color: #3965a3;\n",
" font-size: 20px;\n",
" }\n",
" .flip-card-back-q3 {\n",
" background-color: #a8d480;\n",
" transform: rotateY(180deg);\n",
" font-size: 20px;\n",
" }\n",
" </style>\n",
"\n",
" <div class=\"flip-card-q3\">\n",
" <div class=\"flip-card-inner-q3\">\n",
" <div class=\"flip-card-front-q3\">\n",
" What cells should be identified for potential filtering?\n",
" </div>\n",
" <div class=\"flip-card-back-q3\">\n",
" Cells with high count of AIR sequence reads, cells with incomplete AIR information, etc.\n",
" </div>\n",
" </div>\n",
" </div>\n",
" <noscript>\n",
" <p><strong>Q:</strong> What cells should be identified for potential filtering?</p>\n",
" <p><strong>Answer:</strong> Cells with high count of AIR sequence reads, cells with incomplete AIR information, etc.</p>\n",
" </noscript>\n",
" "
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import sys\n",
"\n",
"Where does the high variability of AIRs stem from?\n",
"- \\+ Junctional diversity adds random nucleotides.\n",
"- Peripheral diversity motivates rapid amino acid switches specific to the host organ.\n",
"- \\+ Combinatorial diversity of different gene segments.\n",
"- Inherited diversity genetically encodes multiple AIRs.\n",
"sys.path.append(\"../src\")\n",
"\n",
"What properties does a productive AIR have?\n",
"- \\+ It spans over the V- to the J-gene with an CDR3 regions contained.\n",
"- It contains a stop codon in the D-gene.\n",
"- There exist multiple different sequences for the same AIR chains.\n",
"- \\+ It contains a start codon in the leading region.\n",
"from lib import flip_card\n",
"\n",
"What cells should be identified for potential filtering?\n",
"- Cells with a high count of AIR sequence reads.\n",
"- \\+ Cells with incomplete AIR information.\n",
"- \\+ Cells with multiple AIRs indicating doublets.\n",
"- Cells with specific motifs in the CDR3 region."
"flip_card(\n",
" \"q1\",\n",
" \"Where does the high variability of AIRs stem from?\",\n",
" \"Junctional diversity adds random nucleotides. Peripheral diversity motivates rapid amino acid switches specific to the host organ. Combinatorial diversity of different gene segments. Inherited diversity genetically encodes multiple AIRs.\",\n",
" back_font_size=13,\n",
")\n",
"flip_card(\n",
" \"q2\",\n",
" \"What properties does a productive AIR have?\",\n",
" \"It spans over the V- to the J-gene with a CDR3 regions contained. It contains a start codon in the leading region.\",\n",
")\n",
"flip_card(\n",
" \"q3\",\n",
" \"What cells should be identified for potential filtering?\",\n",
" \"Cells with high count of AIR sequence reads, cells with incomplete AIR information, etc.\",\n",
")"
]
},
{
Expand All @@ -3265,7 +3529,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.10.5 64-bit",
"display_name": "book",
"language": "python",
"name": "python3"
},
Expand All @@ -3279,12 +3543,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.8"
},
"vscode": {
"interpreter": {
"hash": "e7370f93d1d0cde622a1f8e1c04877d8463912d04d973331ad4851f04de6915a"
}
"version": "3.11.8"
}
},
"nbformat": 4,
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