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isoform_differentiation/Untitled1.ipynb

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"import pandas as pd\n",
"import numpy as np\n",
"import plotly.express as px\n",
"import plotly.graph_objects as go"
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"filename = \"/project/Neurodifferentiation_System/IsoformsAll/isoformSwitches0_01.csv\"\n",
"df = pd.read_csv(filename)\n",
"genes = list(df[\"gene_name\"])\n",
"genes.sort()"
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"filename = \"/home/annaldas/projects/nanopore-transcriptome-analysis/Results/Quantification/transcript_stats.csv\"\n",
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"df_group = df.groupby(\"gene_name\")\n",
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"for gene,data in df_group:\n",
" day0 = data[data[\"day0_mean\"] == max(data[\"day0_mean\"])][\"transcript_id\"].iloc[0]\n",
" day2 = data[data[\"day2_mean\"] == max(data[\"day2_mean\"])][\"transcript_id\"].iloc[0]\n",
" day4 = data[data[\"day4_mean\"] == max(data[\"day4_mean\"])][\"transcript_id\"].iloc[0]\n",
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" if (not ((day0 == day2) and (day2 == day4))):\n",
" interesting.append(gene)\n",
" '''\n",
" means=data.iloc[:,3:6]\n",
" stds=data.iloc[:,6:9]\n",
" labels=data.iloc[:,1]\n",
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],
"source": [
"df_group = df.groupby(\"gene_name\")\n",
"\n",
"for gene,data in df_group:\n",
" means=data.iloc[:,3:6]\n",
" stds=data.iloc[:,6:9]\n",
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" z=data.shape[0]\n",
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},
{
"cell_type": "code",
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},
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"most_interesting = [\"ACSL4\",\"ACYP2\",\"ADARB2\",\"ADGRL2\",\"AFAP1\",\"ALG11\",\"APP\",\"BBS9\",\"CCDC9\",\"COX20\",\"DPYD\",\"DPYSL3\",\"ELOVL6\",\"ERC1\",\"IGSF1\",\"KMT5B\",\"MEF2D\",\"PCGF2\",\"PDGFRA\",\"PECR\",\"RHOF\",\"SESN1\",\"TBC1D23\",\"USP36\",\"\"]\n",
"\n",
"len(interesting)\n",
"len(genes)"
]
},
{
"cell_type": "code",
"execution_count": 57,
"metadata": {},
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"name": "stdout",
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"text": [
"ACSL4\n",
"ACYP2\n",
"ADARB2\n",
"ADGRL2\n",
"AFAP1\n",
"ALG11\n",
"APP\n",
"BBS9\n",
"CCDC9\n",
"COX20\n",
"DPYD\n",
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"ELOVL6\n",
"ERC1\n",
"IGSF1\n",
"KMT5B\n",
"MEF2D\n",
"PCGF2\n",
"PDGFRA\n",
"PECR\n",
"RHOF\n",
"SESN1\n",
"TBC1D23\n",
"USP36\n",
"\n"
]
}
],
"source": [
"for g in most_interesting:\n",
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]
},
{
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"source": [
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"df_group = df.groupby(\"gene_name\")\n",
"\n",
"for gene,data in df_group:\n",
" means=data.iloc[:,3:6]\n",
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]
},
{
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"source": [
"ADGRL2\n",
"AFAP1\n",
"APP\n",
"COX20\n",
"ELOVL6\n",
"ERC1\n",
"IGSF1\n",
"KMT5B\n",
"MEF2D\n",
"PCGF2\n",
"PECR\n",
"TBC1D23\n",
"USP36"
]
}
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