update markers

camlab-bioml · May 29, 2023 · 5f8888b · 5f8888b
1 parent 33a3b3b
commit 5f8888b
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Showing 5 changed files with 317 additions and 415 deletions.
diff --git a/config/config.yml b/config/config.yml
@@ -1,2 +1,2 @@
 
-version: v6
+version: v8
diff --git a/markers/CyTOF.yml b/markers/CyTOF.yml
@@ -1,36 +1,36 @@
 cell_types:
-  # Eosinophils:
-  #   positive:
-  #     - CD11b
-  #     - SiglecF
+  Eosinophils:
+    positive:
+      - CD11b
+      - SiglecF
 
-  # Plasma Cells:
-  #   positive:
-  #     - IgM
-  #     - CD138
+  # # Plasma Cells:
+  # #   positive:
+  # #     - IgM
+  # #     - CD138
 
-  # pDCs:
-  #   positive:
-  #     - B220
-  #     - 120g8
+  pDCs:
+    positive:
+      - B220
+      - 120g8
 
-  # NKT cells:
-  #   positive:
-  #     - CD3
-  #     - CD49b
-  #   negative:
-  #     - B220
-  #     - 120g8
+  NKT cells:
+    positive:
+      - CD3
+      - CD49b
+    negative:
+      - B220
+      - 120g8
 
-  # mDCs:
-  #   positive:
-  #     - MHCII
-  #     - CD11c
-  #   negative:
-  #     - CD3
-  #     - CD49b
-  #     - B220
-  #     - 120g8
+  # # mDCs:
+  # #   positive:
+  # #     - MHCII
+  # #     - CD11c
+  # #   negative:
+  # #     - CD3
+  # #     - CD49b
+  # #     - B220
+  # #     - 120g8
 
   # Macrophages:
   #   positive:
@@ -42,27 +42,27 @@ cell_types:
   #     - B220
   #     - 120g8
 
-  # Classical Monocytes:
-  #   positive:
-  #     - Ly6C
-  #     - CD11b
-  #   negative:
-  #     - CD43
-  #     - CD3
-  #     - CD49b
-  #     - B220
-  #     - 120g8
+  Classical Monocytes:
+    positive:
+      - Ly6C
+      - CD11b
+    negative:
+      - CD43
+      - CD3
+      - CD49b
+      - B220
+      - 120g8
 
-  # Intermediate Monocytes:
-  #   positive:
-  #     - Ly6C
-  #     - CD43
-  #     - CD11b
-  #   negative:
-  #     - CD3
-  #     - CD49b
-  #     - B220
-  #     - 120g8
+  Intermediate Monocytes:
+    positive:
+      - Ly6C
+      - CD43
+      - CD11b
+    negative:
+      - CD3
+      - CD49b
+      - B220
+      - 120g8
 
   # Non-Classical Monocytes:
   #   positive:
@@ -89,135 +89,135 @@ cell_types:
   #     - B220
   #     - 120g8
 
-  CMP:
-    positive:
-      - cKit
-      - CD34
-    negative:
-      - CD16-32
-      - Sca1
-      - CD115
-      - CD11b
-      - CD3
-      - CD49b
-      - B220
-      - 120g8
-
-  GMP:
-    positive:
-      - CD34
-      - CD16-32
-      - cKit
-    negative:
-      - Sca1
-      - CD115
-      - CD11b
-      - CD3
-      - CD49b
-      - B220
-      - 120g8
-
-  CLP:
-    positive:
-      - CD43
-      - Sca1
-      - cKit
-    negative:
-      - CD115
-      - CD11b
-      - CD3
-      - CD49b
-      - B220
-      - 120g8
-
-  MPP:
-    positive:
-      - CD34
-      - Sca1
-      - cKit
-    negative:
-      - CD115
-      - CD11b
-      - CD3
-      - CD49b
-      - B220
-      - 120g8
-
-  # HSC:
+  # CMP:
   #   positive:
-  #     - Sca1
   #     - cKit
-  #   negative:
   #     - CD34
+  #   negative:
+  #     - CD16-32
+  #     - Sca1
   #     - CD115
   #     - CD11b
   #     - CD3
   #     - CD49b
   #     - B220
   #     - 120g8
 
-  # Basophils:
+  # GMP:
   #   positive:
-  #     - FceR1a
-  #     - CD49b
+  #     - CD34
+  #     - CD16-32
+  #     - cKit
   #   negative:
-  #     - NKp46
+  #     - Sca1
+  #     - CD115
+  #     - CD11b
   #     - CD3
-  #     - B220
-  #     - 120g8
-
-  # NK cells:
-  #   positive:
-  #     - NKp46
   #     - CD49b
-  #   negative:
-  #     - FceR1a
-  #     - CD3
   #     - B220
   #     - 120g8
 
-  # CD4 T cells:
+  # CLP:
   #   positive:
-  #     - CD4
-  #     - TCRb
-  #     - CD3
+  #     - CD43
+  #     - Sca1
+  #     - cKit
   #   negative:
-  #     - CD8
-  #     - TCRgd
+  #     - CD115
+  #     - CD11b
+  #     - CD3
   #     - CD49b
   #     - B220
   #     - 120g8
-
-  # CD8 T cells:
+      
+  # MPP:
   #   positive:
-  #     - CD8
-  #     - TCRb
-  #     - CD3
+  #     - CD34
+  #     - Sca1
+  #     - cKit
   #   negative:
-  #     - CD4
-  #     - TCRgd
+  #     - CD115
+  #     - CD11b
+  #     - CD3
   #     - CD49b
   #     - B220
   #     - 120g8
 
-  # gd T cells:
+  # # HSC:
+  # #   positive:
+  # #     - Sca1
+  # #     - cKit
+  # #   negative:
+  # #     - CD34
+  # #     - CD115
+  # #     - CD11b
+  # #     - CD3
+  # #     - CD49b
+  # #     - B220
+  # #     - 120g8
+
+  # Basophils:
   #   positive:
-  #     - TCRgd
-  #     - CD3
-  #   negative:
-  #     - TCRb
+  #     - FceR1a
   #     - CD49b
+  #   negative:
+  #     - NKp46
+  #     - CD3
   #     - B220
   #     - 120g8
 
-  # IdD pos IgM pos B cells:
-  #   positive:
-  #     - IgM
-  #     - IgD
-  #     - B220
-  #   negative:
-  #     - CD43
-  #     - 120g8
+  NK cells:
+    positive:
+      - NKp46
+      - CD49b
+    negative:
+      - FceR1a
+      - CD3
+      - B220
+      - 120g8
+
+  CD4 T cells:
+    positive:
+      - CD4
+      - TCRb
+      - CD3
+    negative:
+      - CD8
+      - TCRgd
+      - CD49b
+      - B220
+      - 120g8
+
+  CD8 T cells:
+    positive:
+      - CD8
+      - TCRb
+      - CD3
+    negative:
+      - CD4
+      - TCRgd
+      - CD49b
+      - B220
+      - 120g8
+
+  # # gd T cells:
+  # #   positive:
+  # #     - TCRgd
+  # #     - CD3
+  # #   negative:
+  # #     - TCRb
+  # #     - CD49b
+  # #     - B220
+  # #     - 120g8
+
+  IgDpos IgMpos B cells:
+    positive:
+      - IgM
+      - IgD
+      - B220
+    negative:
+      - CD43
+      - 120g8
 
   IgD- IgMpos B cells:
     positive:
@@ -237,10 +237,10 @@ cell_types:
       - CD43
       - 120g8
 
-  B-cell Frac A-C (pro-B cells):
-    positive:
-      - CD43
-      - B220
-    negative:
-      - 120g8
+  # B-cell Frac A-C (pro-B cells):
+  #   positive:
+  #     - CD43
+  #     - B220
+  #   negative:
+  #     - 120g8