Files in roryk/bcbioSinglecell

Single-Cell RNA-Seq Utilities

.Rbuildignore

.gitignore

.lintr

.travis.yml

CONTRIBUTING.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/AllClasses.R R/AllGenerics.R R/bcbioSingleCell-package.R R/datasets.R R/deprecated.R R/globals.R R/internal-assert.R R/internal-cellularBarcodes.R R/internal-general.R R/internal-new.R R/internal-plotQCMetric.R R/internal-sparseCounts.R R/mapCellsToSamples.R R/methods-aggregateReplicates.R R/methods-barcodeRanksPerSample.R R/methods-cell2sample.R R/methods-cellCountsPerCluster.R R/methods-cellTypesPerCluster.R R/methods-clusterCellCountsPerSample.R R/methods-coerce.R R/methods-diffExp.R R/methods-extract.R R/methods-fetchData.R R/methods-filterCells.R R/methods-knownMarkersDetected.R R/methods-metrics.R R/methods-metricsPerSample.R R/methods-plotBarcodeRanks.R R/methods-plotCellCounts.R R/methods-plotCellTypesPerCluster.R R/methods-plotDimensionalReduction.R R/methods-plotDot.R R/methods-plotFeature.R R/methods-plotGene.R R/methods-plotGenesPerCell.R R/methods-plotMarker.R R/methods-plotMitoRatio.R R/methods-plotMitoVsCoding.R R/methods-plotNovelty.R R/methods-plotPCElbow.R R/methods-plotQC.R R/methods-plotReadsPerCell.R R/methods-plotUMIsPerCell.R R/methods-plotUMIsVsGenes.R R/methods-plotViolin.R R/methods-plotZerosVsDepth.R R/methods-sampleData.R R/methods-sanitizeMarkers.R R/methods-selectSamples.R R/methods-seurat-SingleCellExperiment.R R/methods-seurat-bcbio.R R/methods-show.R R/methods-subsetPerSample.R R/methods-topBarcodes.R R/methods-topMarkers.R R/methods-updateObject.R R/prepareSingleCellTemplate.R R/readCellRanger.R R/readCellTypeMarkers.R R/reexports.R README.md

_pkgdown.yml

bcbioSingleCell.Rproj

data-raw/01_indrops.R data-raw/02_cellranger.R data-raw/03_seurat.R data-raw/extdata-cell_type_markers.R data-raw/markers.R

data-raw/pbmc4k.R

data/all_markers_small.rda

data/cellCycleMarkers.rda

data/cellTypeMarkers.rda

data/cellranger_small.rda

data/indrops_small.rda

data/known_markers_small.rda

data/seurat_small.rda

docs/CONTRIBUTING.html

docs/LICENSE-text.html

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/extra.css

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/aggregateReplicates.html

docs/reference/all_markers_small.html

docs/reference/barcodeRanksPerSample.html

docs/reference/bcbio.html

docs/reference/bcbioSingleCell-package.html

docs/reference/bcbioSingleCell.html

docs/reference/cell2sample.html

docs/reference/cellCountsPerCluster.html

docs/reference/cellCycleMarkers.html

docs/reference/cellTypeMarkers.html

docs/reference/cellTypesPerCluster.html

docs/reference/cellranger_small.html

docs/reference/clusterCellCountsPerSample.html

docs/reference/coerce.html

docs/reference/defunct.html

docs/reference/deprecated.html

docs/reference/diffExp.html

docs/reference/extract.html

docs/reference/fetchData.html

docs/reference/filterCells.html

docs/reference/general.html

docs/reference/index.html

docs/reference/indrops_small.html

docs/reference/knownMarkersDetected.html

docs/reference/known_markers_small.html

docs/reference/mapCellsToSamples.html

docs/reference/metrics.html

docs/reference/metricsPerSample.html

docs/reference/plotBarcodeRanks-1.png

docs/reference/plotBarcodeRanks.html

docs/reference/plotCellCounts-1.png

docs/reference/plotCellCounts.html

docs/reference/plotCellTypesPerCluster-1.png

docs/reference/plotCellTypesPerCluster.html

docs/reference/plotDimensionalReduction-1.png

docs/reference/plotDimensionalReduction-2.png

docs/reference/plotDimensionalReduction-3.png

docs/reference/plotDimensionalReduction-4.png

docs/reference/plotDimensionalReduction-5.png

docs/reference/plotDimensionalReduction.html

docs/reference/plotDot-1.png

docs/reference/plotDot.html

docs/reference/plotFeature-1.png

docs/reference/plotFeature-2.png

docs/reference/plotFeature.html

docs/reference/plotGene-1.png

docs/reference/plotGene-2.png

docs/reference/plotGene.html

docs/reference/plotGenesPerCell-1.png

docs/reference/plotGenesPerCell.html

docs/reference/plotMarker-1.png

docs/reference/plotMarker-2.png

docs/reference/plotMarker-3.png

docs/reference/plotMarker-4.png

docs/reference/plotMarker-5.png

docs/reference/plotMarker-6.png

docs/reference/plotMarker.html

docs/reference/plotMitoRatio-1.png

docs/reference/plotMitoRatio.html

docs/reference/plotMitoVsCoding-1.png

docs/reference/plotMitoVsCoding.html

docs/reference/plotNovelty-1.png

docs/reference/plotNovelty.html

docs/reference/plotPCElbow-1.png

docs/reference/plotPCElbow.html

docs/reference/plotQC-1.png

docs/reference/plotQC-2.png

docs/reference/plotQC-3.png

docs/reference/plotQC.html

docs/reference/plotReadsPerCell-1.png

docs/reference/plotReadsPerCell-2.png

docs/reference/plotReadsPerCell.html

docs/reference/plotUMIsPerCell-1.png

docs/reference/plotUMIsPerCell-2.png

docs/reference/plotUMIsPerCell-3.png

docs/reference/plotUMIsPerCell-4.png

docs/reference/plotUMIsPerCell-5.png

docs/reference/plotUMIsPerCell.html

docs/reference/plotUMIsVsGenes-1.png

docs/reference/plotUMIsVsGenes.html

docs/reference/plotViolin-1.png

docs/reference/plotViolin.html

docs/reference/plotZerosVsDepth-1.png

docs/reference/plotZerosVsDepth.html

docs/reference/prepareSingleCellTemplate.html

docs/reference/readCellRanger.html

docs/reference/readCellTypeMarkers.html

docs/reference/reexports.html

docs/reference/sampleData.html

docs/reference/sanitizeMarkers.html

docs/reference/selectSamples.html

docs/reference/seurat-SingleCellExperiment.html

docs/reference/seurat_small.html

docs/reference/show.html

docs/reference/subsetPerSample.html

docs/reference/topBarcodes.html

docs/reference/topMarkers.html

docs/reference/updateObject.html

inst/extdata/cell_type_markers.csv

inst/extdata/cellranger/filtered_gene_bc_matrices/GRCh38/barcodes.tsv

inst/extdata/cellranger/filtered_gene_bc_matrices/GRCh38/genes.tsv

inst/extdata/cellranger/filtered_gene_bc_matrices/GRCh38/matrix.mtx

inst/extdata/indrops/2018-01-01_bcbio/bcbio-nextgen-commands.log

inst/extdata/indrops/2018-01-01_bcbio/bcbio-nextgen.log

inst/extdata/indrops/2018-01-01_bcbio/programs.txt

inst/extdata/indrops/2018-01-01_bcbio/project-summary.yaml

inst/extdata/indrops/metadata.csv

inst/extdata/indrops/multiplexed-AAAAAAAA/multiplexed-AAAAAAAA-barcodes.tsv

inst/extdata/indrops/multiplexed-AAAAAAAA/multiplexed-AAAAAAAA.mtx

inst/extdata/indrops/multiplexed-AAAAAAAA/multiplexed-AAAAAAAA.mtx.colnames

inst/extdata/indrops/multiplexed-AAAAAAAA/multiplexed-AAAAAAAA.mtx.rownames

inst/rmarkdown/fragments/indrop_sample_preparation.Rmd inst/rmarkdown/shared/_footer.Rmd inst/rmarkdown/shared/_header.Rmd

inst/rmarkdown/shared/_output.yaml

inst/rmarkdown/shared/_setup.R

inst/rmarkdown/shared/bibliography.bib

inst/rmarkdown/templates/quality_control/skeleton/skeleton.Rmd

inst/rmarkdown/templates/quality_control/template.yaml

inst/rmarkdown/templates/seurat_clustering/skeleton/skeleton.Rmd

inst/rmarkdown/templates/seurat_clustering/template.yaml

inst/rmarkdown/templates/seurat_markers/skeleton/skeleton.Rmd

inst/rmarkdown/templates/seurat_markers/template.yaml

inst/rmarkdown/templates/seurat_per_cluster_analysis/skeleton/skeleton.Rmd

inst/rmarkdown/templates/seurat_per_cluster_analysis/template.yaml

man/aggregateReplicates.Rd man/all_markers_small.Rd man/barcodeRanksPerSample.Rd man/bcbio.Rd man/bcbioSingleCell-package.Rd man/bcbioSingleCell.Rd man/cell2sample.Rd man/cellCountsPerCluster.Rd man/cellCycleMarkers.Rd man/cellTypeMarkers.Rd man/cellTypesPerCluster.Rd man/cellranger_small.Rd man/clusterCellCountsPerSample.Rd man/coerce.Rd man/defunct.Rd man/deprecated.Rd man/diffExp.Rd man/extract.Rd man/fetchData.Rd man/filterCells.Rd man/general.Rd man/indrops_small.Rd man/knownMarkersDetected.Rd man/known_markers_small.Rd man/mapCellsToSamples.Rd man/metrics.Rd man/metricsPerSample.Rd man/plotBarcodeRanks.Rd man/plotCellCounts.Rd man/plotCellTypesPerCluster.Rd man/plotDimensionalReduction.Rd man/plotDot.Rd man/plotFeature.Rd man/plotGene.Rd man/plotGenesPerCell.Rd man/plotMarker.Rd man/plotMitoRatio.Rd man/plotMitoVsCoding.Rd man/plotNovelty.Rd man/plotPCElbow.Rd man/plotQC.Rd man/plotReadsPerCell.Rd man/plotUMIsPerCell.Rd man/plotUMIsVsGenes.Rd man/plotViolin.Rd man/plotZerosVsDepth.Rd man/prepareSingleCellTemplate.Rd man/readCellRanger.Rd man/readCellTypeMarkers.Rd man/reexports.Rd man/sampleData.Rd man/sanitizeMarkers.Rd man/selectSamples.Rd man/seurat-SingleCellExperiment.Rd man/seurat_small.Rd man/show.Rd man/subsetPerSample.Rd man/topBarcodes.Rd man/topMarkers.Rd man/updateObject.Rd

pkgdown/extra.css

tests/testthat.R

tests/testthat/.gitignore

tests/testthat/test_clustering_functions.R tests/testthat/test_coercion_methods.R tests/testthat/test_data_functions.R tests/testthat/test_differential_expression_functions.R tests/testthat/test_plot_functions.R tests/testthat/test_quality_control_functions.R tests/testthat/test_read_functions.R tests/testthat/test_rmarkdown_functions.R tests/testthat/test_s4_object.R

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.