diff --git a/config/config.yml b/config/config.yml index 032e034..13c3f73 100644 --- a/config/config.yml +++ b/config/config.yml @@ -1,2 +1,2 @@ -version: v6 \ No newline at end of file +version: v8 \ No newline at end of file diff --git a/markers/CyTOF.yml b/markers/CyTOF.yml index 24962fe..f055b26 100644 --- 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: @@ -89,66 +89,13 @@ 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 @@ -156,68 +103,121 @@ cell_types: # - 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 diff --git a/markers/scRNASeq-different.yml b/markers/scRNASeq-different.yml index 554b971..141239c 100644 --- a/markers/scRNASeq-different.yml +++ b/markers/scRNASeq-different.yml @@ -1,41 +1,26 @@ cell_types: - Cytotoxic T cell: - positive: - - CD3D - - CD3E - - CD3G - - TRAC - - CD8A - - CD8B - - GZMK - - CCL5 - - NKG7 - negative: - - CD4 - - FCER1G - - CD14+ monocyte: - positive: - - VCAN - - FCN1 - - S100A8 - - S100A9 - - CD14 - - ITGAL - - ITGAM - - CSF3R - - CSF1R - - CX3CR1 - - TYROBP - - LYZ - - S100A12 - negative: - - FCGR3A - - FCGR3B - - CD3D - - CD3E - - CD3G - - TRAC - - NKG7 - - KLRB1 - - KLRD1 + HCC1937: + positive: + - CRABP2 + - FXYD3 + - IFI27 + - KLK5 + - KRT13 + - BTBD16 + - SLPI + - CDKN2A + - KRT7 + negative: + - KRT19 + - EEF1A1 + - LDHA + + MDAMB468: + positive: + - SAT1 + - MAGEA12 + - CSAG1 + - SEC61G + - KRT23 + - EGFR + - LANCL2 diff --git a/markers/scRNASeq-similar.yml b/markers/scRNASeq-similar.yml index 8959b1f..4492706 100644 --- a/markers/scRNASeq-similar.yml +++ b/markers/scRNASeq-similar.yml @@ -1,38 +1,27 @@ cell_types: - Cytotoxic T cell: - positive: - - CD3D - - CD3E - - CD3G - - TRAC - - CD8A - - CD8B - - GZMK - - CCL5 - - NKG7 - negative: - - CD4 - - FCER1G - - Natural killer cell: - positive: - - NCAM1 - - NKG7 - - KLRB1 - - KLRD1 - - KLRF1 - - KLRC1 - - KLRC2 - - KLRC3 - - KLRC4 - - FCGR3A - - FCGR3B - - ITGAL - - ITGAM - - FCER1G - negative: - - CD3D - - CD3E - - CD3G - - CD14 - - TRAC + CAL851: + positive: + - IFI27 + - KRT86 + - RARRES1 + - AKR1B1 + - KRT7 + - CDKN2A + negative: + - SLPI + + HCC1937: + positive: + - CRABP2 + - FXYD3 + - IFI27 + - KLK5 + - KRT13 + - BTBD16 + - SLPI + - CDKN2A + - KRT7 + negative: + - KRT19 + - EEF1A1 + - LDHA diff --git a/markers/scRNASeq.yml b/markers/scRNASeq.yml index 8066d57..5c0e69e 100644 --- a/markers/scRNASeq.yml +++ b/markers/scRNASeq.yml @@ -1,189 +1,117 @@ cell_types: - CD4+ T cell: - positive: - - CD3D - - CD3E - - CD3G - - TRAC - - CD4 - - TCF7 - - CD27 - - IL7R - negative: - - CD8A - - CD8B - - GNLY - - NKG7 - - CST7 - - Cytotoxic T cell: - positive: - - CD3D - - CD3E - - CD3G - - TRAC - - CD8A - - CD8B - - GZMK - - CCL5 - - NKG7 - negative: - - CD4 - - FCER1G - - B cell: - positive: - - CD19 - - MS4A1 - - CD79A - - CD79B - - MZB1 - - IGHD - - IGHM - - Natural killer cell: - positive: - - NCAM1 - - NKG7 - - KLRB1 - - KLRD1 - - KLRF1 - - KLRC1 - - KLRC2 - - KLRC3 - - KLRC4 - - FCGR3A - - FCGR3B - - ITGAL - - ITGAM - - FCER1G - negative: - - CD3D - - CD3E - - CD3G - - CD14 - - TRAC - - CD14+ monocyte: - positive: - - VCAN - - FCN1 - - S100A8 - - S100A9 - - CD14 - - ITGAL - - ITGAM - - CSF3R - - CSF1R - - CX3CR1 - - TYROBP - - LYZ - - S100A12 - negative: - - FCGR3A - - FCGR3B - - CD3D - - CD3E - - CD3G - - TRAC - - NKG7 - - KLRB1 - - KLRD1 - - CD16+ monocyte: - positive: - - FCN1 - - FCGR3A - - FCGR3B - - ITGAL - - ITGAM - - CSF3R - - CSF1R - - CX3CR1 - - CDKN1C - - MS4A7 - negative: - - S100A8 - - S100A9 - - S100A12 - - CD14 - - CD3D - - CD3E - - CD3G - - TRAC - - NKG7 - - KLRB1 - - KLRD1 - - Dendritic cell: - positive: - - HLA-DPB1 - - HLA-DPA1 - - HLA-DQA1 - - ITGAX - - CD1C - - CD1E - - FCER1A - - CLEC10A - - FCGR2B - negative: - - CD3D - - CD3E - - CD3G - - NCAM1 - - CD19 - - CD14 - - MS4A1 - - CD79A - - CD79B - - Plasmacytoid dendritic cell: - positive: - - IL3RA - - GZMB - - JCHAIN - - IRF7 - - TCF4 - - LILRA4 - - CLEC4C - negative: - - ITGAX - - CD3D - - CD3E - - CD3G - - NCAM1 - - CD19 - - CD14 - - MS4A1 - - CD79A - - CD79B - - Megakaryocyte: - positive: - - PF4 - - PPBP - - GP5 - - ITGA2B - - NRGN - - TUBB1 - - SPARC - - RGS18 - - MYL9 - - GNG11 - - - - - - - - - - - - - - - - + AU565: + positive: + - NDUFB9 + - ERBB2 + - DHRS2 + - GSDMB + - DECR1 + - KRT81 + - S100P + - S100A9 + + MCF7: + positive: + - PSMD6 + - BCAS3 + - SPTSSB + - TFF1 + - KRT8 + - AGR2 + + CAMA1: + positive: + - BACH1 + - IGFBP5 + - ANKRD30A + - SERF2 + - GATA3 + + BT483: + positive: + - CRABP2 + - CRIP2 + - SMIM22 + - RAB11FIP1 + - KRT19 + - ITM2B + - FXYD3 + + CAL851: + positive: + - IFI27 + - KRT86 + - RARRES1 + - AKR1B1 + - KRT7 + - CDKN2A + negative: + - SLPI + + HDQP1: + positive: + - AKR1B1 + - RARRES1 + - ITGB1 + - EEF1A1 + - KRT7 + - CDKN2A + - SLPI + - KRT13 + - BTBD16 + negative: + - IFI27 + - KRT86 + + HCC1937: + positive: + - CRABP2 + - FXYD3 + - IFI27 + - KLK5 + - KRT13 + - BTBD16 + - SLPI + - CDKN2A + - KRT7 + negative: + - KRT19 + - EEF1A1 + - LDHA + + JIMT1: + positive: + - LDHA + - PSMD3 + - OXTR + - ARL14EPL + - KRBOX1 + - CD44 + - COTL1 + + MDAMB468: + positive: + - SAT1 + - MAGEA12 + - CSAG1 + - SEC61G + - KRT23 + - EGFR + - LANCL2 + + CAL51: + positive: + - MDK + - PDPN + - ALDH1A1 + - COBLL1 + - HMGA2 + - IFITM3 + - CALD1 + - GSTP1 + - LDHB + - FTL + negative: + - KRT19 + - FXYD3