Software:Article Title: Comprehensive integration of single-cell data
Article Snippet: .. Mouse cortex – sci-ATAC-seq Cusanovich et al., 2018 http://atlas.gs.washington.edu/mouse-atac/data/ Human PBMCs – scATAC-seq 10x Genomics https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_pbmc_10k Human PBMCs – scRNA-seq 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3 Mouse cortex – Drop-seq Saunders et al., 2018 http://dropviz.org/ Software and Algorithms Seurat v3.0.0.9000 This paper https://github.com/satijalab/seurat/tree/release/3.0 Seurat v2.3.3 Butler et al., 2018 https://github.com/satijalab/seurat/releases/tag/v2.3.3 Scran v1.6.9 Lun et al., 2016 https://bioconductor.org/packages/release/bioc/html/scran.html Scanorama commit b83e1ba87e6635825e155046b884dee2154c5d34 Hie et al., 2018 https://github.com/brianhie/scanorama scmap v1.1.5 Kiselev et al., 2018 http://bioconductor.org/packages/scmap Scrublet v0.1 Wolock et al., 2018 https://github.com/AllonKleinLab/scrublet CellRanger v2.2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation CITE-seq-count v1.2 Patrick Roelli https://github.com/Hoohm/CITE-seq-Count Drop-seq tools v2.0.0 McCarroll Lab https://github.com/broadinstitute/Drop-seq deepTools v3.1.2 Ramirez et al., 2016 https://github.com/deeptools/deepTools GOstats v2.44.0 Falcon and Gentleman, 2007 https://github.com/deeptools/deepTools Homer v4.10 Heinz et al., 2010 http://homer.ucsd.edu/homer/ R R Core https://www.r-project.org/ Python Python Software Foundation https://www.python.org/ Open in a separate window Highlights Seurat v3 identifies correspondences between cells in different experiments These ‘anchors’ can be used to harmonize datasets into a single reference Reference labels and data can be projected onto query datasets Extends beyond RNA-seq to single-cell protein, chromatin, and spatial data A platform that integrates diverse modalities associated with single cell sequencing datasets can be used to better understand cellular identity and function. ..
RNA Sequencing:Article Title: Comprehensive integration of single-cell data
Article Snippet: .. Mouse cortex – sci-ATAC-seq Cusanovich et al., 2018 http://atlas.gs.washington.edu/mouse-atac/data/ Human PBMCs – scATAC-seq 10x Genomics https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_pbmc_10k Human PBMCs – scRNA-seq 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3 Mouse cortex – Drop-seq Saunders et al., 2018 http://dropviz.org/ Software and Algorithms Seurat v3.0.0.9000 This paper https://github.com/satijalab/seurat/tree/release/3.0 Seurat v2.3.3 Butler et al., 2018 https://github.com/satijalab/seurat/releases/tag/v2.3.3 Scran v1.6.9 Lun et al., 2016 https://bioconductor.org/packages/release/bioc/html/scran.html Scanorama commit b83e1ba87e6635825e155046b884dee2154c5d34 Hie et al., 2018 https://github.com/brianhie/scanorama scmap v1.1.5 Kiselev et al., 2018 http://bioconductor.org/packages/scmap Scrublet v0.1 Wolock et al., 2018 https://github.com/AllonKleinLab/scrublet CellRanger v2.2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation CITE-seq-count v1.2 Patrick Roelli https://github.com/Hoohm/CITE-seq-Count Drop-seq tools v2.0.0 McCarroll Lab https://github.com/broadinstitute/Drop-seq deepTools v3.1.2 Ramirez et al., 2016 https://github.com/deeptools/deepTools GOstats v2.44.0 Falcon and Gentleman, 2007 https://github.com/deeptools/deepTools Homer v4.10 Heinz et al., 2010 http://homer.ucsd.edu/homer/ R R Core https://www.r-project.org/ Python Python Software Foundation https://www.python.org/ Open in a separate window Highlights Seurat v3 identifies correspondences between cells in different experiments These ‘anchors’ can be used to harmonize datasets into a single reference Reference labels and data can be projected onto query datasets Extends beyond RNA-seq to single-cell protein, chromatin, and spatial data A platform that integrates diverse modalities associated with single cell sequencing datasets can be used to better understand cellular identity and function. ..
Single Cell:Article Title: Comprehensive integration of single-cell data
Article Snippet: .. Mouse cortex – sci-ATAC-seq Cusanovich et al., 2018 http://atlas.gs.washington.edu/mouse-atac/data/ Human PBMCs – scATAC-seq 10x Genomics https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_pbmc_10k Human PBMCs – scRNA-seq 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3 Mouse cortex – Drop-seq Saunders et al., 2018 http://dropviz.org/ Software and Algorithms Seurat v3.0.0.9000 This paper https://github.com/satijalab/seurat/tree/release/3.0 Seurat v2.3.3 Butler et al., 2018 https://github.com/satijalab/seurat/releases/tag/v2.3.3 Scran v1.6.9 Lun et al., 2016 https://bioconductor.org/packages/release/bioc/html/scran.html Scanorama commit b83e1ba87e6635825e155046b884dee2154c5d34 Hie et al., 2018 https://github.com/brianhie/scanorama scmap v1.1.5 Kiselev et al., 2018 http://bioconductor.org/packages/scmap Scrublet v0.1 Wolock et al., 2018 https://github.com/AllonKleinLab/scrublet CellRanger v2.2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation CITE-seq-count v1.2 Patrick Roelli https://github.com/Hoohm/CITE-seq-Count Drop-seq tools v2.0.0 McCarroll Lab https://github.com/broadinstitute/Drop-seq deepTools v3.1.2 Ramirez et al., 2016 https://github.com/deeptools/deepTools GOstats v2.44.0 Falcon and Gentleman, 2007 https://github.com/deeptools/deepTools Homer v4.10 Heinz et al., 2010 http://homer.ucsd.edu/homer/ R R Core https://www.r-project.org/ Python Python Software Foundation https://www.python.org/ Open in a separate window Highlights Seurat v3 identifies correspondences between cells in different experiments These ‘anchors’ can be used to harmonize datasets into a single reference Reference labels and data can be projected onto query datasets Extends beyond RNA-seq to single-cell protein, chromatin, and spatial data A platform that integrates diverse modalities associated with single cell sequencing datasets can be used to better understand cellular identity and function. ..
Sequencing:Article Title: Comprehensive integration of single-cell data
Article Snippet: .. Mouse cortex – sci-ATAC-seq Cusanovich et al., 2018 http://atlas.gs.washington.edu/mouse-atac/data/ Human PBMCs – scATAC-seq 10x Genomics https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_pbmc_10k Human PBMCs – scRNA-seq 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3 Mouse cortex – Drop-seq Saunders et al., 2018 http://dropviz.org/ Software and Algorithms Seurat v3.0.0.9000 This paper https://github.com/satijalab/seurat/tree/release/3.0 Seurat v2.3.3 Butler et al., 2018 https://github.com/satijalab/seurat/releases/tag/v2.3.3 Scran v1.6.9 Lun et al., 2016 https://bioconductor.org/packages/release/bioc/html/scran.html Scanorama commit b83e1ba87e6635825e155046b884dee2154c5d34 Hie et al., 2018 https://github.com/brianhie/scanorama scmap v1.1.5 Kiselev et al., 2018 http://bioconductor.org/packages/scmap Scrublet v0.1 Wolock et al., 2018 https://github.com/AllonKleinLab/scrublet CellRanger v2.2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation CITE-seq-count v1.2 Patrick Roelli https://github.com/Hoohm/CITE-seq-Count Drop-seq tools v2.0.0 McCarroll Lab https://github.com/broadinstitute/Drop-seq deepTools v3.1.2 Ramirez et al., 2016 https://github.com/deeptools/deepTools GOstats v2.44.0 Falcon and Gentleman, 2007 https://github.com/deeptools/deepTools Homer v4.10 Heinz et al., 2010 http://homer.ucsd.edu/homer/ R R Core https://www.r-project.org/ Python Python Software Foundation https://www.python.org/ Open in a separate window Highlights Seurat v3 identifies correspondences between cells in different experiments These ‘anchors’ can be used to harmonize datasets into a single reference Reference labels and data can be projected onto query datasets Extends beyond RNA-seq to single-cell protein, chromatin, and spatial data A platform that integrates diverse modalities associated with single cell sequencing datasets can be used to better understand cellular identity and function. ..
Comparison:Article Title: A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells
Article Snippet: .. The bottom two tracks represent ACRs from cell type and whole-root bulk resolutions, respectively. (C) Pairwise Jaccard similarity (fraction of overlapping ACRs versus the union of ACR sets) for ACR calls among various scATAC-seq technologies and resolutions. (D) Relative chromatin accessibility across sci-ATAC-seq-based and 10X Genomics scATAC-seq-based cell types and 50 394 ACRs. (E) Comparison of beta values from likelihood ratio tests of the contribution of cell type membership toward ACR chromatin accessibility status between sci-ATAC-seq and 10X Genomics scATAC-seq. (F) Distributions of ACR distance to the nearest TSS for cell-type-specific and non-specific ACRs. ..
|
