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.gitignore
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# # Compiled source #
# ###################
# *.com
# *.class
# *.dll
# *.exe
# *.o
# *.so
# # Packages #
# ############
# # it's better to unpack these files and commit the raw source
# # git has its own built in compression methods
# *.7z
# *.dmg
# *.gz
# *.iso
# *.jar
# *.rar
# *.tar
# *.zip
# # Logs and databases #
# ######################
# *.log
# *.sql
# *.sqlite
# # OS generated files #
# ######################
.DS_Store
# .DS_Store?
# ._*
# .Spotlight-V100
# .Trashes
# ehthumbs.db
# Thumbs.db
#Ignore .vscode folder
/.vscode/
.vscode/settings.json
#R stuff to be ignored:
.RData
.Rhistory
CyTOF_DataAnalysis.Rproj
.Rproj.user/
#Directories to ignore:
# #Data directory:
Raw_Data/Raw/
Raw_Data/Tests/
Raw_Data/UNNAMED/
Raw_Data/Umap/
# #Pycache
code/aux/__pycache__/
# #Inputs
# Ignore the output folders:
Preprocessed_Data/Tests/
Preprocessed_Data/UNNAMED/
Analysis/UMAP_input/Tests/
Analysis/UMAP_output/Tests/
Analysis/EMD_input/Tests/
Analysis/EMD_output/Tests/
Analysis/DREMI_input/Tests/
Analysis/DREMI_output/Tests/
Preprocessed_Data/test_zoom/
Analysis/Vis_Heatmap/EMD_testingemd_zoom.txt
Analysis/EMD_output/testingemd_zoom/
Analysis/EMD_input/Pro_TOBis01_Organoids.fcs
Analysis/EMD_input/Pro_TOBis02_Organoids.fcs
Analysis/EMD_input/Pro_TOBis03_Organoids.fcs
Analysis/EMD_input/Pro_TOBis04_Organoids.fcs
Analysis/EMD_input/Pro_TOBis05_Organoids.fcs
Analysis/EMD_input/test_zoom_panel_markers.csv
# Ignore User Data
# 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
Analysis/EMD_output/UNNAMED/
Allpackages_includingbaselibs.csv
Utils_Data/output/opt6_renameMIN/UNNAMED/