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🎨 remove centering
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- just does not look good in table of contents
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Henry Webel committed May 29, 2024
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6 changes: 3 additions & 3 deletions scripts/2_Run_CLASTER.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"## <center> Training CLASTER <center>\n",
"## Training CLASTER\n",
"The model can be trained by running the following command:\n",
"\n",
"```bash\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"## <center> Testing CLASTER <center>\n",
"## Testing CLASTER\n",
"\n",
"> _Note:_ \n",
">\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"## <center> Predicting _in silico_ perturbed chromatin landscapes <center>\n",
"## Predicting _in silico_ perturbed chromatin landscapes\n",
"\n",
">Note: Make sure to create the output folder beforehand: ./runs/perturbation_runs/gene_expression_only_chrom_pure_conv/"
]
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6 changes: 3 additions & 3 deletions scripts/3_Data_analysis.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"## <center> Model performance on the baseline prediction task <center>\n",
"## Model performance on the baseline prediction task\n",
"**Figure 1 and related supplementary figures**\n",
"\n",
"> Note: ⏰ This took 42 min when analysing all genes and enhancers in chr4:\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"## <center> _In silico_ perturbations <center>\n",
"## _In silico_ perturbations\n",
"\n",
"**Figure 2 and related supplementary figures**\n",
"\n"
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"cell_type": "markdown",
"metadata": {},
"source": [
"# <center> Attributions <center>\n",
"# Attributions\n",
"\n",
"Now we will compute the attribution scores for every input position (4,10.001) towards every output (401). This mechanism tells how important is every input position (i.e. a given bin in each input track in the landscape or a given bin in a Micro-C matrix) for the prediction of the EU-seq levels at the position described by a given target node (401 targets). It also tells us the direction of the association.\n",
"The original paper can be found at:\n",
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