diff --git a/README.md b/README.md index 3a90c7f..6ff0f84 100644 --- 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. \ No newline at end of file +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. \ No newline at end of file diff --git a/demo.ipynb b/demo.ipynb index c08c30d..1aa9c50 100644 --- 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 index bef6a93..8d7a64b 100644 Binary files a/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_Precision.pdf and b/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_Precision.pdf differ diff --git a/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_auPR.pdf b/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_auPR.pdf index bc115f5..7cfa82a 100644 Binary files a/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_auPR.pdf and b/figs/ENCODE-E2G_Model_Ablation_Barplot_Delta_auPR.pdf differ diff --git a/figs/ENCODE-E2G_PR_curve_0-10k.pdf b/figs/ENCODE-E2G_PR_curve_0-10k.pdf index b7a586f..6ddf835 100644 Binary files a/figs/ENCODE-E2G_PR_curve_0-10k.pdf and b/figs/ENCODE-E2G_PR_curve_0-10k.pdf differ diff --git a/figs/ENCODE-E2G_PR_curve_100k-2500k.pdf b/figs/ENCODE-E2G_PR_curve_100k-2500k.pdf index 0ba49a3..6e7b964 100644 Binary files a/figs/ENCODE-E2G_PR_curve_100k-2500k.pdf and b/figs/ENCODE-E2G_PR_curve_100k-2500k.pdf differ diff --git a/figs/ENCODE-E2G_PR_curve_10k-100k.pdf b/figs/ENCODE-E2G_PR_curve_10k-100k.pdf index a99e023..c15050c 100644 Binary files a/figs/ENCODE-E2G_PR_curve_10k-100k.pdf and b/figs/ENCODE-E2G_PR_curve_10k-100k.pdf differ diff --git a/figs/ENCODE-E2G_PR_curve_all.pdf b/figs/ENCODE-E2G_PR_curve_all.pdf index de4cdb9..1beed42 100644 Binary files a/figs/ENCODE-E2G_PR_curve_all.pdf and b/figs/ENCODE-E2G_PR_curve_all.pdf differ diff --git a/figs/ENCODE-E2G_SHAP_scores_barplot.pdf b/figs/ENCODE-E2G_SHAP_scores_barplot.pdf index e1001ba..1dafc99 100644 Binary files a/figs/ENCODE-E2G_SHAP_scores_barplot.pdf and b/figs/ENCODE-E2G_SHAP_scores_barplot.pdf differ diff --git a/figs/ENCODE-E2G_SHAP_scores_dotplot.pdf b/figs/ENCODE-E2G_SHAP_scores_dotplot.pdf index 8bdefb1..cb62813 100644 Binary files a/figs/ENCODE-E2G_SHAP_scores_dotplot.pdf and b/figs/ENCODE-E2G_SHAP_scores_dotplot.pdf differ