cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12413783.v1
title: Additional file 5 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 5. CNVcalling MCF7 CNV calling results for MCF7.
DOI: 10.6084/m9.figshare.12413792.v1
title: Additional file 7 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 7. CNVcalling SKBR3–1 cell CNV calling results for SKBR3–1 cell.
DOI: 10.6084/m9.figshare.12413771
title: Additional file 3 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 3. CNVcalling HCC1187 CNV calling results for HCC1187.
DOI: 10.6084/m9.figshare.12413771.v1
title: Additional file 3 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 3. CNVcalling HCC1187 CNV calling results for HCC1187.
DOI: 10.6084/m9.figshare.12413762
title: Additional file 2 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 2. CCLs knownCNVs Supplementary table containing genes per cancer cell line, incl. Copy number, segment length and evaluation length.
DOI: 10.6084/m9.figshare.12413777.v1
title: Additional file 4 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 4. CNVcalling HCC2218 CNV calling results for HCC2218.
DOI: 10.6084/m9.figshare.12413759
title: Additional file 1 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 1. MetaCNV Readme Manual to run MetaCNV.
DOI: 10.6084/m9.figshare.12413762.v1
title: Additional file 2 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 2. CCLs knownCNVs Supplementary table containing genes per cancer cell line, incl. Copy number, segment length and evaluation length.
DOI: 10.6084/m9.figshare.12413747
title: Additional file 12 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 12. CNVcalling SKBR3–6 cells CNV calling results for SKBR3–6 cells.
DOI: 10.6084/m9.figshare.12413759.v1
title: Additional file 1 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 1. MetaCNV Readme Manual to run MetaCNV.
DOI: 10.6084/m9.figshare.12413744
title: Additional file 1 of Ipilimumab or FOLFOX with Nivolumab and Trastuzumab in previously untreated HER2-positive locally advanced or metastatic EsophagoGastric Adenocarcinoma - the randomized phase 2 INTEGA trial (AIO STO 0217)

description: Additional file 1.
DOI: 10.6084/m9.figshare.12413747.v1
title: Additional file 12 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 12. CNVcalling SKBR3–6 cells CNV calling results for SKBR3–6 cells.
DOI: 10.6084/m9.figshare.12413735
title: Additional file 10 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 10. CNVcalling SKBR3–4 cells CNV calling results for SKBR3–4 cells.
DOI: 10.6084/m9.figshare.12413732
title: Additional file 9 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 9: Table S7. Genes differentially expressed between methanol-fixed and freshly profiled cold-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413738
title: Additional file 11 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 11. CNVcalling SKBR3–5 cells CNV calling results for SKBR3–5 cells.
DOI: 10.6084/m9.figshare.12413744.v1
title: Additional file 1 of Ipilimumab or FOLFOX with Nivolumab and Trastuzumab in previously untreated HER2-positive locally advanced or metastatic EsophagoGastric Adenocarcinoma - the randomized phase 2 INTEGA trial (AIO STO 0217)

description: Additional file 1.
DOI: 10.6084/m9.figshare.12413726
title: Additional file 7 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 7: Table S5. Genes differentially expressed between cryopreserved and freshly profiled cold-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413735.v1
title: Additional file 10 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 10. CNVcalling SKBR3–4 cells CNV calling results for SKBR3–4 cells.
DOI: 10.6084/m9.figshare.12413738.v1
title: Additional file 11 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data

description: Additional file 11. CNVcalling SKBR3–5 cells CNV calling results for SKBR3–5 cells.
DOI: 10.6084/m9.figshare.12413729
title: Additional file 8 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 8: Table S6. Genes differentially expressed between cryopreserved and freshly profiled warm-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413732.v1
title: Additional file 9 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 9: Table S7. Genes differentially expressed between methanol-fixed and freshly profiled cold-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413726.v1
title: Additional file 7 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 7: Table S5. Genes differentially expressed between cryopreserved and freshly profiled cold-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413729.v1
title: Additional file 8 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 8: Table S6. Genes differentially expressed between cryopreserved and freshly profiled warm-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413714
title: Additional file 4 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 4: Table S3. Differentially expressed genes with higher expression in cell populations of warm-dissociated kidneys (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413717
title: Additional file 5 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 5: Table S4. Differentially expressed genes with higher expression in cell populations of cold-dissociated kidneys (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413717.v1
title: Additional file 5 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 5: Table S4. Differentially expressed genes with higher expression in cell populations of cold-dissociated kidneys (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413708
title: Additional file 3 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 3: Table S2. Cell type labels assigned to cells and nuclei in this study. aLOH: ascending loop of Henle; CD_IC: intercalated cells of collecting duct; CD_IC_A: type A intercalated cells of collecting duct; CD_IC_B: type B intercalated cells of collecting duct; CD_PC: principal cells of collecting duct; CD_Trans: transitional cells; CNT: connecting tubule; DCT: distal convoluted tubule; dLOH: descending loop of Henle; MC: mesangial cells; MPH: macrophages; PT: proximal tubule.
DOI: 10.6084/m9.figshare.12413714.v1
title: Additional file 4 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 4: Table S3. Differentially expressed genes with higher expression in cell populations of warm-dissociated kidneys (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413708.v1
title: Additional file 3 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 3: Table S2. Cell type labels assigned to cells and nuclei in this study. aLOH: ascending loop of Henle; CD_IC: intercalated cells of collecting duct; CD_IC_A: type A intercalated cells of collecting duct; CD_IC_B: type B intercalated cells of collecting duct; CD_PC: principal cells of collecting duct; CD_Trans: transitional cells; CNT: connecting tubule; DCT: distal convoluted tubule; dLOH: descending loop of Henle; MC: mesangial cells; MPH: macrophages; PT: proximal tubule.
DOI: 10.6084/m9.figshare.12413690
title: Additional file 21 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 21: Table S19. Extended reference dataset used for scMatch annotation.
DOI: 10.6084/m9.figshare.12413684
title: Additional file 20 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 20: Table S18. Cell type gene signatures for refined annotation.
DOI: 10.6084/m9.figshare.12413690.v1
title: Additional file 21 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 21: Table S19. Extended reference dataset used for scMatch annotation.
DOI: 10.6084/m9.figshare.12413678
title: Additional file 1 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 1: Table S1. Genes differentially expressed between bulk RNA-seq profiles of cold- and warm-dissociated kidney single-cell suspensions (FDR 2, edgeR exact test [27]); includes results of functional analysis with ToppGene [28] and Gene Ontology Biological Process for differentially expressed genes with higher expression in warm-dissociated kidneys.
DOI: 10.6084/m9.figshare.12413684.v1
title: Additional file 20 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 20: Table S18. Cell type gene signatures for refined annotation.
DOI: 10.6084/m9.figshare.12413678.v1
title: Additional file 1 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 1: Table S1. Genes differentially expressed between bulk RNA-seq profiles of cold- and warm-dissociated kidney single-cell suspensions (FDR 2, edgeR exact test [27]); includes results of functional analysis with ToppGene [28] and Gene Ontology Biological Process for differentially expressed genes with higher expression in warm-dissociated kidneys.
DOI: 10.6084/m9.figshare.12413669
title: Additional file 19 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 19: Table S17. Public reference dataset used for the first scMatch run.
DOI: 10.6084/m9.figshare.12413663
title: Additional file 18 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 18: Table S16. Cell viability.
DOI: 10.6084/m9.figshare.12413669.v1
title: Additional file 19 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 19: Table S17. Public reference dataset used for the first scMatch run.
DOI: 10.6084/m9.figshare.12413657
title: Additional file 17 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 17: Table S15. Mice used and workflows tested. The experiments were performed in three batches separated in time. For each batch, we used kidneys from mice available at that time and the workflows were used with modifications as indicated in this table.
DOI: 10.6084/m9.figshare.12413663.v1
title: Additional file 18 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 18: Table S16. Cell viability.
DOI: 10.6084/m9.figshare.12413651
title: Additional file 16 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 16: Table S14. Genes differentially expressed between single-cell and single-nuclei libraries in Balb/c male mice profiled with v2 10x chemistry (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413651.v1
title: Additional file 16 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 16: Table S14. Genes differentially expressed between single-cell and single-nuclei libraries in Balb/c male mice profiled with v2 10x chemistry (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413657.v1
title: Additional file 17 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 17: Table S15. Mice used and workflows tested. The experiments were performed in three batches separated in time. For each batch, we used kidneys from mice available at that time and the workflows were used with modifications as indicated in this table.
DOI: 10.6084/m9.figshare.12413642
title: Additional file 14 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 14: Table S12. Number of cells in each cell population across single-cell and single-nuclei experiments and BSEQ-sc estimates for bulk RNA-seq libraries.
DOI: 10.6084/m9.figshare.12413642.v1
title: Additional file 14 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 14: Table S12. Number of cells in each cell population across single-cell and single-nuclei experiments and BSEQ-sc estimates for bulk RNA-seq libraries.
DOI: 10.6084/m9.figshare.12413645
title: Additional file 15 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 15: Table S13. Genes differentially expressed between bulk RNA-seq profiles of intact kidneys and cold-dissociated single-cell suspensions; includes results of functional analysis with ToppGene [28] for genes with higher expression in intact kidneys.
DOI: 10.6084/m9.figshare.12413633
title: Additional file 13 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 13: Table S11. Genes differentially expressed in each cell type between SN_sucrose and SN_FANS_3x500g protocols (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413645.v1
title: Additional file 15 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 15: Table S13. Genes differentially expressed between bulk RNA-seq profiles of intact kidneys and cold-dissociated single-cell suspensions; includes results of functional analysis with ToppGene [28] for genes with higher expression in intact kidneys.
DOI: 10.6084/m9.figshare.12413624
title: Additional file 12 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 12: Table S10. Genes differentially expressed in each cell type between SN_FANS_1x2000g and SN_sucrose protocols (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413633.v1
title: Additional file 13 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 13: Table S11. Genes differentially expressed in each cell type between SN_sucrose and SN_FANS_3x500g protocols (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413618
title: Additional file 10 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 10: Table S8. Genes differentially expressed between methanol-fixed and freshly profiled warm-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413621
title: Additional file 11 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 11: Table S9. Genes differentially expressed in each cell type between SN_FANS_1x2000g and SN_FANS_3x500g protocols (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413624.v1
title: Additional file 12 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 12: Table S10. Genes differentially expressed in each cell type between SN_FANS_1x2000g and SN_sucrose protocols (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413621.v1
title: Additional file 11 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 11: Table S9. Genes differentially expressed in each cell type between SN_FANS_1x2000g and SN_FANS_3x500g protocols (Seurat Wilcoxon test [30] with thresholds of logFC = 0.5, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413618.v1
title: Additional file 10 of Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

description: Additional file 10: Table S8. Genes differentially expressed between methanol-fixed and freshly profiled warm-dissociated kidney single-cell suspensions (Seurat Wilcoxon test [30] with thresholds of logFC = 1, minimum detection rate 0.5, FDR
DOI: 10.6084/m9.figshare.12413522
title: Additional file 6 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 6 This file contains the detailed comparison of experimental setup D, E and F with previous tools.
DOI: 10.6084/m9.figshare.12413525
title: Additional file 7 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 7 This file contains the dataset for DeepHF.
DOI: 10.6084/m9.figshare.12413519
title: Additional file 5 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 5 This file contains the detailed comparison of experimental setup A, B and C with previous tools.
DOI: 10.6084/m9.figshare.12413525.v1
title: Additional file 7 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 7 This file contains the dataset for DeepHF.
DOI: 10.6084/m9.figshare.12413519.v1
title: Additional file 5 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 5 This file contains the detailed comparison of experimental setup A, B and C with previous tools.
DOI: 10.6084/m9.figshare.12413522.v1
title: Additional file 6 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 6 This file contains the detailed comparison of experimental setup D, E and F with previous tools.
DOI: 10.6084/m9.figshare.12413504
title: Additional file 2 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 2 This file contains the DeepCRISPR data for cell HEK293.
DOI: 10.6084/m9.figshare.12413510
title: Additional file 3 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 3 This file contains the DeepCRISPR data for cell HeLa.
DOI: 10.6084/m9.figshare.12413513
title: Additional file 4 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 4 This file contains the DeepCRISPR data for cell HL60.
DOI: 10.6084/m9.figshare.12413513.v1
title: Additional file 4 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 4 This file contains the DeepCRISPR data for cell HL60.
DOI: 10.6084/m9.figshare.12413504.v1
title: Additional file 2 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 2 This file contains the DeepCRISPR data for cell HEK293.
DOI: 10.6084/m9.figshare.12413510.v1
title: Additional file 3 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 3 This file contains the DeepCRISPR data for cell HeLa.
DOI: 10.6084/m9.figshare.12413498
title: Additional file 1 of CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning

description: Additional file 1 This file contains the DeepCRISPR data for cell HCT116.