diff --git a/scripts/2_Run_CLASTER.ipynb b/scripts/2_Run_CLASTER.ipynb index b93f142..a41227f 100644 --- a/scripts/2_Run_CLASTER.ipynb +++ b/scripts/2_Run_CLASTER.ipynb @@ -5617,7 +5617,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "##
Training CLASTER
\n", + "## Training CLASTER\n", "The model can be trained by running the following command:\n", "\n", "```bash\n", @@ -5689,7 +5689,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "##
Testing CLASTER
\n", + "## Testing CLASTER\n", "\n", "> _Note:_ \n", ">\n", @@ -5776,7 +5776,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "##
Predicting _in silico_ perturbed chromatin landscapes
\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/" ] diff --git a/scripts/3_Data_analysis.ipynb b/scripts/3_Data_analysis.ipynb index 94966ea..2aebdbe 100644 --- a/scripts/3_Data_analysis.ipynb +++ b/scripts/3_Data_analysis.ipynb @@ -958,7 +958,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "##
Model performance on the baseline prediction task
\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", @@ -1256,7 +1256,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "##
_In silico_ perturbations
\n", + "## _In silico_ perturbations\n", "\n", "**Figure 2 and related supplementary figures**\n", "\n" @@ -1962,7 +1962,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "#
Attributions
\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",