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 July 19, 2018, 3:33 a.m.