cell_relabelling

data/cell_relabelling.csv

@@ -0,0 +1,67 @@
+cell_type_original;cell_type;source;cell_type_color;cell_type_color_hex;cell_type_shape;cell_subtype;cell_subtype_color;cell_subtype_color_hex
+B;B;van Galen et al., 2019;green;#4FC384;12;B;green;#4FC384
+CD10+ B cells;B;Oetjen et al., 2018;green;#4FC384;12;B;green;#4FC384
+CD20+ B cells;B;Oetjen et al., 2018;green;#4FC384;12;B;green;#4FC384
+ProB;B;van Galen et al., 2019;green;#4FC384;12;B;green;#4FC384
+Mono;Mono;van Galen et al., 2019;darkorange;#F09040;13;Mono;darkorange;#F09040
+CD14+ monocytes;Mono;Oetjen et al., 2018;darkorange;#F09040;13;Mono;darkorange;#F09040
+CD16+ monocytes;Mono;Oetjen et al., 2018;darkorange;#F09040;13;Mono;darkorange;#F09040
+Mono-like;Mono;van Galen et al., 2019;darkorange;#F09040;13;Mono;darkorange;#F09040
+ProMono;Mono;van Galen et al., 2019;darkorange;#F09040;13;pro_Mono;orange;#F0AD40
+Monocyte progenitors;Mono;Oetjen et al., 2018;darkorange;#F09040;13;pro_Mono;orange;#F0AD40
+ProMono-like;Mono;van Galen et al., 2019;darkorange;#F09040;13;pro_Mono;orange;#F0AD40
+T;T;van Galen et al., 2019;blue;#4F92EE;12;CD4_T;lightblue;#4FCCEE
+CD4+ memory T cells;T;Oetjen et al., 2018;blue;#4F92EE;12;CD4_T;lightblue;#4FCCEE
+CD4+ naive T cells;T;Oetjen et al., 2018;blue;#4F92EE;12;CD4_T;lightblue;#4FCCEE
+CD8+ effector T cells;T;Oetjen et al., 2018;blue;#4F92EE;12;CD8_T;blue;#4F92EE
+CD8+ naive T cells;T;Oetjen et al., 2018;blue;#4F92EE;12;CD8_T;blue;#4F92EE
+CTL;T;van Galen et al., 2019;blue;#4F92EE;12;CD8_T;blue;#4F92EE
+pDC;DC;van Galen et al., 2019;brown;#854701;15;pDC;darkbrown;#854701
+Plasmacytoid dendritic cells;DC;Oetjen et al., 2018;brown;#854701;15;pDC;darkbrown;#854701
+cDC;DC;van Galen et al., 2019;brown;#854701;15;cDC;brown;#B95D10
+Dendritic cells;DC;Oetjen et al., 2018;brown;#854701;15;cDC;brown;#B95D10
+cDC-like;DC;van Galen et al., 2019;brown;#854701;15;cDC;brown;#B95D10
+earlyEry;Ery;van Galen et al., 2019;red;#F72E3A;19;early_Ery;red;#F72E3A
+Early erythrocytes;Ery;Oetjen et al., 2018;red;#F72E3A;19;early_Ery;red;#F72E3A
+Early erythroid progenitors;Ery;Oetjen et al., 2018;red;#F72E3A;19;early_Ery;red;#F72E3A
+lateEry;Ery;van Galen et al., 2019;red;#F72E3A;19;late_Ery;darkred;#C72D37
+Late erythrocytes;Ery;Oetjen et al., 2018;red;#F72E3A;19;late_Ery;darkred;#C72D37
+Late erythroid progenitors;Ery;Oetjen et al., 2018;red;#F72E3A;19;early_Ery;red;#F72E3A
+Megakaryocytes;Megakaryocytes;Oetjen et al., 2018;beige;#C89B7A;13;Megakaryocytes;beige;#C89B7A
+NK;NK;van Galen et al., 2019;darkblue;#4F64EE;17;NK;darkblue;#4F64EE
+Natural killer cells;NK;Oetjen et al., 2018;darkblue;#4F64EE;17;NK;darkblue;#4F64EE
+Plasma;B;van Galen et al., 2019;green;#4FC384;9;Plasma;darkgreen;#317E54
+Plasma cells;B;Oetjen et al., 2018;green;#4FC384;9;Plasma;darkgreen;#317E54
+HSC;HSPC;van Galen et al., 2019;magenta;#D040F0;12;HSPC;magenta;#D040F0
+HSPCs;HSPC;Oetjen et al., 2018;magenta;#D040F0;12;HSPC;magenta;#D040F0
+Prog;HSPC;van Galen et al., 2019;magenta;#D040F0;12;HSPC;magenta;#D040F0
+GMP;HSPC;van Galen et al., 2019;magenta;#D040F0;12;HSPC;magenta;#D040F0
+HSC-like;HSPC;van Galen et al., 2019;magenta;#D040F0;12;HSPC;magenta;#D040F0
+Prog-like;HSPC;van Galen et al., 2019;magenta;#D040F0;12;HSPC;magenta;#D040F0
+GMP-like;HSPC;van Galen et al., 2019;magenta;#D040F0;12;HSPC;magenta;#D040F0
+CD4+ T;T;Lasry et al., 2022;blue;#4F92EE;12;CD4_T;lightblue;#4FCCEE
+CD8+ T;T;Lasry et al., 2022;blue;#4F92EE;12;CD8_T;blue;#4F92EE
+CD16+ monocyte;Mono;Lasry et al., 2022;darkorange;#F09040;13;Mono;darkorange;#F09040
+cDC2;DC;Lasry et al., 2022;brown;#854701;15;cDC;brown;#B95D10
+B;B;Lasry et al., 2022;green;#4FC384;12;B;green;#4FC384
+CD14+ monocyte;Mono;Lasry et al., 2022;darkorange;#F09040;13;Mono;darkorange;#F09040
+NK;NK;Lasry et al., 2022;darkblue;#4F64EE;17;NK;darkblue;#4F64EE
+cDC1;DC;Lasry et al., 2022;brown;#854701;15;cDC;brown;#B95D10
+HLA-II+ monocyte;Mono;Lasry et al., 2022;darkorange;#F09040;13;Mono;darkorange;#F09040
+HSC;HSPC;Lasry et al., 2022;magenta;#D040F0;12;HSPC;magenta;#D040F0
+MAIT;T;Lasry et al., 2022;blue;#4F92EE;12;MAIT;deepskyblue4;#00688B
+CD11c+;Mono;Lasry et al., 2022;darkorange;#F09040;13;Mono;darkorange;#F09040
+Pre-B;B;Lasry et al., 2022;green;#4FC384;12;B;green;#4FC384
+Pro-B;B;Lasry et al., 2022;green;#4FC384;12;B;green;#4FC384
+DC precursor;DC;Lasry et al., 2022;brown;#854701;15;pDC;darkbrown;#854701
+Granulocyte;Gran;Lasry et al., 2022;darkorange3;#CD6600;15;Gran;darkorange3;#CD6600
+MPP;HSPC;Lasry et al., 2022;magenta;#D040F0;12;HSPC;magenta;#D040F0
+pDC;DC;Lasry et al., 2022;brown;#854701;15;pDC;darkbrown;#854701
+MEP;HSPC;Lasry et al., 2022;magenta;#D040F0;12;HSPC;magenta;#D040F0
+gd T;T;Lasry et al., 2022;blue;#4F92EE;12;gd_T;deepskyblue;#00BFFF
+GMP;HSPC;Lasry et al., 2022;magenta;#D040F0;12;HSPC;magenta;#D040F0
+Plasmablast;B;Lasry et al., 2022;green;#4FC384;9;Plasma;darkgreen;#317E54
+Perivascular cell;PeriVasc;Lasry et al., 2022;gray;#BEBEBE;17;PeriVasc;gray;#BEBEBE
+LymP;LymP;Lasry et al., 2022;darkolivegreen;#556B2F;12;LymP;darkolivegreen;#556B2F
+Plasma cell;B;Lasry et al., 2022;green;#4FC384;9;Plasma;darkgreen;#317E54
+Ery;Ery;Lasry et al., 2022;red;#F72E3A;19;Ery;darkred;#C72D37

src/data_preprocessing/Lasry/1.preprocess_data.ipynb

@@ -13848,7 +13848,7 @@
    "mimetype": "text/x-r-source",
    "name": "R",
    "pygments_lexer": "r",
-   "version": "4.2.3"
+   "version": "4.1.2"
   },
   "toc": {
    "base_numbering": 1,