TAPE-Lab
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@@ -83,7 +83,77 @@ Analysis/EMD_input/Pro_TOBis05_Organoids.fcs
 Analysis/EMD_input/test_zoom_panel_markers.csv
 
 # Ignore User Data
-Preprocessed_Data/
-Analysis/
+# Preprocessed_Data/
+# Analysis/
 Utils_Data/input/opt1_concatenation/Tests/
 Utils_Data/output/opt1_concatenation/UNNAMED/
+Analysis/EMD_input/Pro_wholetrain_nonresp.txt
+Analysis/EMD_input/Pro_wholetrain_resp.txt
+Analysis/EMD_input/UNNAMED_panel_markers.csv
+Analysis/EMD_output/UNNAMED/EMD_ref-wholenonresp.txt
+Analysis/UMAP_input/Pro_TOBis01_Organoids.fcs
+Analysis/UMAP_input/Pro_TOBis01_Organoids.fcs.txt
+Analysis/UMAP_input/Pro_TOBis02_Organoids.fcs
+Analysis/UMAP_input/Pro_TOBis02_Organoids.fcs.txt
+Analysis/UMAP_input/Pro_TOBis03_Organoids.fcs
+Analysis/UMAP_input/Pro_TOBis03_Organoids.fcs.txt
+Analysis/UMAP_input/Pro_TOBis04_Organoids.fcs
+Analysis/UMAP_input/Pro_TOBis04_Organoids.fcs.txt
+Analysis/UMAP_input/Pro_TOBis05_Organoids.fcs
+Analysis/UMAP_input/Pro_TOBis05_Organoids.fcs.txt
+Analysis/UMAP_input/UNNAMED_panel_markers.csv
+Analysis/UMAP_output/UNNAMED/markers_for_UNNAMED.csv
+Analysis/UMAP_output/UNNAMED/merged_UMAP_UNNAMED.txt
+Analysis/UMAP_output/UNNAMED/Pro_TOBis01_Organoids_UMAP_UNNAMED.txt
+Analysis/UMAP_output/UNNAMED/Pro_TOBis02_Organoids_UMAP_UNNAMED.txt
+Analysis/UMAP_output/UNNAMED/Pro_TOBis03_Organoids_UMAP_UNNAMED.txt
+Analysis/UMAP_output/UNNAMED/Pro_TOBis04_Organoids_UMAP_UNNAMED.txt
+Analysis/UMAP_output/UNNAMED/Pro_TOBis05_Organoids_UMAP_UNNAMED.txt
+Analysis/UMAP_output/UNNAMED/UNNAMED_downsampled_IDs.csv
+Analysis/Vis_Heatmap/EMD_ref-wholenonresp.txt
+Analysis/Vis_PCA/EMD_ref-wholenonresp.txt
+Preprocessed_Data/PDO21_ALLrep2/PDO21_ALLrep2_panel_markers.csv
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_0ng_2.Apoptosis.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_0ng_2.G0.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_0ng_2.G1.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_0ng_2.G2.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_0ng_2.M_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_0ng_2.S_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_1.25ng_2.Apoptosis.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_1.25ng_2.G0.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_1.25ng_2.G1.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_1.25ng_2.G2.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_1.25ng_2.M_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_1.25ng_2.S_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_2.5ng_2.Apoptosis.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_2.5ng_2.G0.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_2.5ng_2.G1.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_2.5ng_2.G2.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_2.5ng_2.M_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_2.5ng_2.S_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_5ng_2.Apoptosis.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_5ng_2.G0.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_5ng_2.G1.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_5ng_2.G2.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_5ng_2.M_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_5ng_2.S_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_7.5ng_1.Apoptosis.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_7.5ng_1.G0.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_7.5ng_1.G1.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_7.5ng_1.G2.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_7.5ng_1.M_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_7.5ng_1.S_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_10ng_1.Apoptosis.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_10ng_1.G0.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_10ng_1.G1.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_10ng_1.G2.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_10ng_1.M_Phase.txt
+Preprocessed_Data/PDO21_ALLrep2/Pro_20200109__EGF__Test__P21_10ng_1.S_Phase.txt
+Preprocessed_Data/PDO21_UNTrep2/PDO21_UNTrep2_panel_markers.csv
+Preprocessed_Data/PDO21_UNTrep2/Pro_20200109__EGF__Test__P21_0ng_2.Apoptosis.txt
+Preprocessed_Data/PDO21_UNTrep2/Pro_20200109__EGF__Test__P21_0ng_2.G0.txt
+Preprocessed_Data/PDO21_UNTrep2/Pro_20200109__EGF__Test__P21_0ng_2.G1.txt
+Preprocessed_Data/PDO21_UNTrep2/Pro_20200109__EGF__Test__P21_0ng_2.G2.txt
+Preprocessed_Data/PDO21_UNTrep2/Pro_20200109__EGF__Test__P21_0ng_2.M__Phase.txt
+Preprocessed_Data/PDO21_UNTrep2/Pro_20200109__EGF__Test__P21_0ng_2.S__Phase.txt
+Preprocessed_Data/maria_bothtxtfcs.7z