update README

Author: zouter

README.md

@@ -36,15 +36,25 @@ Of note, the "mCherry-BCXX" barcodes were used internally to design the cell lin
     <tr><td>7<strong>b-c</strong></td><td><a href="code/10_Combinations/4-state_bias.ipynb">10_Combinations/4-state_bias.ipynb</a></td></tr>
     <tr><td>7<strong>d</strong></td><td><a href="code/10_Combinations/3-pairwise_dosage.ipynb">10_Combinations/3-pairwise_dosage.ipynb</a></td></tr>
     <tr><td>7<strong>e</strong></td><td><a href="code/10_Combinations/5-unique_state_enrichment.ipynb">10_Combinations/5-unique_state_enrichment.ipynb</a></td></tr>
+    <tr><th colspan="2" border="1">Extended Data Figure 1</th></tr>
+    <tr><td>ED1<strong>a-b</strong></td><td><a href="code/01_Preprocessing_and_integration/">01_Preprocessing_and_integration/</a></td></tr>
+    <tr><td>ED1<strong>c</strong></td><td><a href="code/08_RNAscope_quantification/1.1_plot_qupath_measurements_mCherry.R">08_RNAscope_quantification/1.1_plot_qupath_measurements_mCherry.R</a></td></tr>
     <tr><th colspan="2" border="1">Extended Data Figure 2</th></tr>
     <tr><td>ED2<strong>a-d</strong></td><td><a href="code/05_Other_overexpression_studies/dose_comparison.py">05_Other_overexpression_studies/dose_comparison.py</a></td></tr>
-    <tr><td>ED2<strong>e</strong></td><td><a href="code/09_Cell_cycle">09_Cell_cycle</a></td></tr>
+    <tr><th colspan="2" border="1">Extended Data Figure 3</th></tr>
+    <tr><td>ED3<strong>a-d</strong></td><td><a href="code/02_Clustering_DE_and_GSEA/">02_Clustering_DE_and_GSEA</a></td></tr>
     <tr><th colspan="2" border="1">Extended Data Figure 4</th></tr>
     <tr><td>ED4<strong>a-b,d</strong></td><td><a href="code/04_Dose_sensitivity_and_reprogramming_capacity/1.3_protein_features_enrichment.R">04_Dose_sensitivity_and_reprogramming_capacity/1.3_protein_features_enrichment.R</a></td></tr>
     <tr><td>ED4<strong>c</strong></td><td><a href="code/07_Endogenous_dose/2-create_figures.ipynb">07_Endogenous_dose/2-create_figures.ipynb</a></td></tr>
     <tr><td>ED4<strong>e</strong></td><td><a href="code/04_Dose_sensitivity_and_reprogramming_capacity/Power/power.ipynb">04_Dose_sensitivity_and_reprogramming_capacity/Power/power.ipynb</a></td></tr>
     <tr><td>ED4<strong>f</strong></td><td><a href="code/04_Dose_sensitivity_and_reprogramming_capacity/Power/power.ipynb">04_Dose_sensitivity_and_reprogramming_capacity/Power/power.ipynb</a></td></tr>
     <tr><td>ED4<strong>g</strong></td><td><a href="code/04_Dose_sensitivity_and_reprogramming_capacity/Power/power.ipynb">04_Dose_sensitivity_and_reprogramming_capacity/Power/power.ipynb</a></td></tr>
+    <tr><th colspan="2" border="1">Extended Data Figure 6</th></tr>
+    <tr><td>ED6<strong>a-f</strong></td><td><a href="code/02_Clustering_DE_and_GSEA">02_Clustering_DE_and_GSEA</a></td></tr>
+    <tr><th colspan="2" border="1">Extended Data Figure 7</th></tr>
+    <tr><td>ED7<strong>a-l</strong></td><td><a href="code/04_Dose_sensitivity_and_reprogramming_capacity">04_Dose_sensitivity_and_reprogramming_capacity</a></td></tr>
+    <tr><th colspan="2" border="1">Extended Data Figure 8</th></tr>
+    <tr><td>ED7<strong>a-f</strong></td><td><a href="code/09_Cell_cycle">09_Cell_cycle</a></td></tr>
     <tr><th colspan="2" border="1">Extended Data Figure 9</th></tr>
     <tr><td>ED9<strong>a</strong></td><td><a href="code/10_Combinations/5-unique_state_enrichment.ipynb">10_Combinations/5-unique_state_enrichment.ipynb</a></td></tr>
     <tr><td>ED9<strong>b</strong></td><td><a href="code/10_Combinations/3-pairwise_dosage.ipynb">10_Combinations/3-pairwise_dosage.ipynb</a></td></tr>