Recombinant:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
Red Blood Cell Lysis:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
Software:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
Purification:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
Staining:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
cDNA Synthesis:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
Gene Expression:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
Microscopy:
Article Title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Pediatric patient tumor tissue This paper, UZ Ghent ss Chemicals, peptides, and recombinant proteins b-mercaptoethanol Sigma-Aldrich Cat# M3148 Collagenase A Sigma-Aldrich Cat# 11088793001 DAPI Invitrogen Cat# D1306; RIDD: AB_2629482 DMSO Fisher Scientific Cat# 10103483 Dnase I Sigma-Aldrich Cat# 04 536 282 001 EDTA Westburg Cat# 51234 FcBlock 2.4G2 Bioceros N/A FCS Merck Life Science Cat# F0804 Fixable Viability due Live/Dead - eFluor780 eBioscience Cat# 65-0865-18 RPMI 1640 Gibco Cat# 52400-025 RBC lysis buffer BioLegend Cat# 420302 Deposited data Manuscript code This study https://github.com/VIBTOBIlab/NBAtlas_manuscript In-house data This study GEO: GSE253865 In-house data This study EGA: EGAD50000000328 NBAtlas reference atlas data This study Mendeley Data: https://doi.org/10.17632/yhcf6787yp.1 NBAtlas reference atlas visualization This study R2 platform: https://hgserver2.amc.nl/cgi-bin/r2/ main.cgi?dscope=NBSCA&option=about_dscope NBAtlas reference atlas visualization This study https://single-cell.be/nbatlas/ Software and algorithms AUCell (v1.20.2) Aibar et al.59 https://www.bioconductor.org/packages/release/ bioc/html/AUCell.html CellRanger (v6.1.2) 10x Genomics http://www.10xgenomics.com ClusterProfiler (v4.4.4) Wu et al.115 https://bioconductor.org/packages/release/bioc/ html/clusterProfiler.html CopyKAT (v1.1.0) Gao et al.116 https://github.com/navinlabcode/copykat FastCAR (v0.1.0) Berg et al.117 https://github.com/LungCellAtlas/FastCAR fgsea (v1.22.0) ss https://bioconductor.org/packages/release/bioc/ html/fgsea.html ggplot2 ss https://cran.r-project.org/web/packages/ggplot2/ Harmony (v0.1.0) Korsunsky et al.36 https://github.com/immunogenomics/harmony infercnvpy (v0.4.2) ss https://github.com/icbi-lab/infercnvpy NMF (v0.24.0) ss https://cran.r-project.org/web/packages/NMF scanpy (v1.8.1) Wolf et al.118 https://github.com/scverse/scanpy scDblFinder (v1.10.0) Germain et al.119 https://github.com/plger/scDblFinder SCEVAN (v1.0.1) De Falco et al.38 https://github.com/AntonioDeFalco/SCEVAN scvi-tools (v0.16.4) Gayoso et al.34 https://github.com/scverse/scvi-tools Seurat (v4.1.0) Stuart et al.,120 Hao et al.121 https://github.com/satijalab/seurat SingleR (v1.10.0) Aran et al.122 https://github.com/dviraran/SingleR UCell (v2.0.1) Andreatta et al.58 https://github.com/carmonalab/UCell (Continued on next page) Cell Reports 43, 114804, October 22, 2024 21
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