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karbalayghareh · Feb 21, 2023 · e086ee7 · e086ee7
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diff --git a/README.md b/README.md
@@ -14,4 +14,4 @@ You need three files to run ENCODE-E2G models:
 
 [tss](https://github.com/karbalayghareh/ENCODE-E2G/tree/main/tss) contains the TSS file we have used. [crispri](https://github.com/karbalayghareh/ENCODE-E2G/tree/main/data/crispri) has the CRISPRi datasets for training the ENCODE-E2G and ENCODE-E2G_Extended models. Feature tables are binary matrices which specify the features to be used in each model. We have included the the full and ablated models of ENCODE-E2G and ENCODE-E2G_Extended in [feature_table](https://github.com/karbalayghareh/ENCODE-E2G/tree/main/data/feature_table).
 
-This [demo](https://github.com/karbalayghareh/ENCODE-E2G/blob/main/demo.ipynb) file show step-by-step how to run the ENCODE-E2G models, save them, predict the CRISPRi E-G pair, plot the analysis figures, and perform the genome-wide predictions for the provided E-G pairs for every ENCODE cell types. 
+This [demo](https://github.com/karbalayghareh/ENCODE-E2G/blob/main/demo.ipynb) file shows step-by-step how to run the ENCODE-E2G models, save them, predict the CRISPRi E-G pair, plot the analysis figures, and perform the genome-wide predictions for the provided E-G pairs for every ENCODE cell types. 
diff --git a/demo.ipynb b/demo.ipynb
@@ -31,7 +31,7 @@
    "outputs": [],
    "source": [
     "# True for ENCODE-E2G_Extended / False for  ENCODE-E2G\n",
-    "extented = True"
+    "extented = False"
    ]
   },
   {

diff --git a/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_Precision.pdf b/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_Precision.pdf
diff --git a/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_auPR.pdf b/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_auPR.pdf
diff --git a/figs/ENCODE-E2G_PR_curve_0-10k.pdf b/figs/ENCODE-E2G_PR_curve_0-10k.pdf
diff --git a/figs/ENCODE-E2G_PR_curve_100k-2500k.pdf b/figs/ENCODE-E2G_PR_curve_100k-2500k.pdf
diff --git a/figs/ENCODE-E2G_PR_curve_10k-100k.pdf b/figs/ENCODE-E2G_PR_curve_10k-100k.pdf
diff --git a/figs/ENCODE-E2G_PR_curve_all.pdf b/figs/ENCODE-E2G_PR_curve_all.pdf
diff --git a/figs/ENCODE-E2G_SHAP_scores_barplot.pdf b/figs/ENCODE-E2G_SHAP_scores_barplot.pdf
diff --git a/figs/ENCODE-E2G_SHAP_scores_dotplot.pdf b/figs/ENCODE-E2G_SHAP_scores_dotplot.pdf
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Expand Up		@@ -14,4 +14,4 @@ You need three files to run ENCODE-E2G models:

		[tss](https://github.com/karbalayghareh/ENCODE-E2G/tree/main/tss) contains the TSS file we have used. [crispri](https://github.com/karbalayghareh/ENCODE-E2G/tree/main/data/crispri) has the CRISPRi datasets for training the ENCODE-E2G and ENCODE-E2G_Extended models. Feature tables are binary matrices which specify the features to be used in each model. We have included the the full and ablated models of ENCODE-E2G and ENCODE-E2G_Extended in [feature_table](https://github.com/karbalayghareh/ENCODE-E2G/tree/main/data/feature_table).

		This [demo](https://github.com/karbalayghareh/ENCODE-E2G/blob/main/demo.ipynb) file show step-by-step how to run the ENCODE-E2G models, save them, predict the CRISPRi E-G pair, plot the analysis figures, and perform the genome-wide predictions for the provided E-G pairs for every ENCODE cell types.
		This [demo](https://github.com/karbalayghareh/ENCODE-E2G/blob/main/demo.ipynb) file shows step-by-step how to run the ENCODE-E2G models, save them, predict the CRISPRi E-G pair, plot the analysis figures, and perform the genome-wide predictions for the provided E-G pairs for every ENCODE cell types.