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 title: CPT 1
 emoji: 🌌
 colorFrom: gray
-colorTo: pink
+colorTo: indigo
 sdk: streamlit
-sdk_version: 1.19.0
+sdk_version: 1.15.2
 app_file: app.py
 pinned: false
 license: bsd-3-clause
diff --git a/app.py b/app.py
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index 0000000000000000000000000000000000000000..d6b3f2c8c547e6ce313dcbafd7bb3af668c936c6
--- /dev/null
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+import streamlit as st
+import pandas as pd
+from os import listdir
+import plotly.graph_objects as go
+
+gene_names_eve = [file.split('_')[0] for file in listdir('./CPT1_score_EVE_set/')]
+gene_names_no_eve1 = [file.split('_')[0] for file in listdir('./CPT1_score_no_EVE_set1/')]
+gene_names_no_eve2 = [file.split('_')[0] for file in listdir('./CPT1_score_no_EVE_set2/')]
+
+st.subheader('CPT-1')
+st.markdown('Cross-protein transfer learning for variant effect prediction')
+st.markdown('This is a lookup tool for the variant effect preditions of CPT-1 for 18,602 human proteins, initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects (2022)".')
+
+# Input query gene
+gene = st.selectbox(
+    'Which gene/protein are you interested in?',
+    gene_names_eve + gene_names_no_eve1 + gene_names_no_eve2)
+
+if st.button('Show results'):
+    # Read the gene file
+    if gene in gene_names_eve:
+        pred = pd.read_csv('./CPT1_score_EVE_set/' + gene + '_HUMAN.csv.gz', compression = 'gzip')
+    elif gene in gene_names_no_eve1:
+        pred = pd.read_csv('./CPT1_score_no_EVE_set1/' + gene + '_HUMAN.csv.gz', compression = 'gzip')
+    else:
+        pred = pd.read_csv('./CPT1_score_no_EVE_set2/' + gene + '_HUMAN.csv.gz', compression = 'gzip')
+    
+    # Plot heatmap
+    mat = pred.copy()
+    mat['Mutant amino acid'] = mat['mutant'].str[-1]
+    mat['Position on protein sequence'] = mat['mutant'].str[:-1]
+    mat = mat.set_index('mutant')
+    mat['Position on protein sequence'] = pd.Categorical(
+        mat['Position on protein sequence'],
+        categories = mat['Position on protein sequence'].unique(),
+        ordered = True)
+    mat = mat.pivot(index='Mutant amino acid', columns='Position on protein sequence', values = mat.columns[0])
+    fig = go.Figure()
+    fig.add_trace(
+        go.Heatmap(z = mat, y = mat.index, x = mat.columns,
+                   colorbar = dict(title='Variant effect'),
+                   colorscale=[[0, '#6FA8DC'],
+                               [0.3, '#CFE2F3'],
+                               [0.5, '#FFFFFF'],
+                               [0.7, '#F4CCCC'],
+                               [1.0, '#BA1111']],
+                   hovertemplate='Wild-type amino acid and position: %{x}\
+                       <br>Mutant amino acid: %{y}\
+                       <br>Prediction: %{z}<extra></extra>')
+    )
+    fig.update_layout(
+        title_text = "CPT-1 variant effect prediction for " + gene + " (red: pathogenic, blue: benign)",
+        xaxis = dict(
+            title = 'Position on protein sequence',
+            rangeslider = dict(visible=True)
+        ),
+        yaxis = dict(
+            title = 'Mutant amino acid'
+        ),
+        yaxis_nticks = mat.shape[0],
+        height = 600
+    )
+    st.plotly_chart(fig, theme = "streamlit", use_container_width = True, height = 600)
+    
+    # Generate download link
+    st.download_button('Download CSV', 
+                       pred.set_index('mutant').to_csv().encode('utf-8'),
+                       gene + '_CPT_score.csv',
+                       'text/csv')
+    
+# Citation
+st.markdown('</br>'
+            '<h5> Citation </h5>'
+'Jagota, M.\*, Ye, C.\*, Rastogi, R., Albors, C., Koehl, A., Ioannidis, N., and Song, Y.S.&dagger;'
+'"Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", '
+'bioRxiv (2022)  </br>'
+'\*These authors contributed equally to this work.  </br>'
+'&dagger; To whom correspondence should be addressed:  yss@berkeley.edu  </br>'
+'DOI: https://doi.org/10.1101/2022.11.15.516532', 
+    unsafe_allow_html = True)
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfa2e593eddc9abeeff3dbbb113aca29770b4edb
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,2 @@
+pandas
+plotly
\ No newline at end of file