bcbioSingleCell 0.0.19

  • Renamed main object class from bcbioSCDataSet to bcbioSingleCell.
  • Cell filtering with filterCells() will now slot a named logical vector into metadata(object)[["filteredCells"]], which will be used to dynamically subset the slotted internal SummarizedExperiment data. Now that we’re using this approach, we can return a modified bcbioSingleCell object rather than defining a separate bcbioSCFiltered class.
  • Renamed loadSingleCellRun() to loadSingleCell(), to match bcbioRNASeq package.
  • Now allowing implicit integers in our function code.
  • Added support for plotting technical replicates. This is handled by sampleNameAggregate in the sample metadata.
  • Now using ridgeline plots in place of histograms where applicable.
  • Travis CI checks take too long when loading SummarizedExperiment. Hopefully this will be fixed in the 3.6 release later this month.
  • New internal dark theme (darkTheme()), based on the Seurat theme.
  • Initial commit of plotDot() function, based on Seurat::DotPlot().
  • Added new tSNE plots that allow for consistent cluster labeling.
  • Providing legacy support for bcbioSCDataSet and bcbioSCFiltered, which will be deprecated in a future release.
  • Offloaded some internal code to basejump, for improved consistency with bcbioRNASeq package: internal-projectDir.R, internal-readSampleMetadataFile.R, internal-sampleDirs.R. We may want to provide this code as a shared bcbio core package (e.g. bcbioBase) in the future.
  • Added internal utility to check for valid marker genes (.validMarkers()).
  • Improved Ensembl release version support (ensemblVersion).

bcbioSingleCell 0.0.18

  • Renamed plotClusters() to plotMarkers(). Added soft deprecation.
  • Added viridis color support in tSNE plots and heatmaps.
  • Converted loadSingleCellRun() and loadCellRanger() from S4 generics back to standard functions.
  • Added t-SNE utility functions: fetchTSNEData(), fetchTSNEExpressionData(), and plotTSNEExpressionData(). This enable plotting of geometric mean values of desired marker genes.
  • Updated NEWS to Markdown, with hyperlinks.
  • Offloaded generics that would otherwise conflict with bcbioRNASeq to the basejump package.
  • Improved roxygen documentation. Moved as much documentation as possible to the methods files.
  • Updated cellCycleMarkers and cellTypeMarkers data. Now supports Drosophila.
  • Sample IDs are now sanitized using make.names() instead of camel(). This avoids undesirable coercion of some IDs (e.g. group1_1 into group11).
  • Added recommended package syntax guidelines.
  • lintr checks now allow implicit integers (e.g. 1 instead of 1L).
  • Added Seurat as dependency in DESCRIPTION file. The package now attaches Seurat automatically.
  • Package no longer imports mononcle or suggests scater, scde, or scone. We’re planning on adding these back in a future update, but build checks on Travis CI otherwise take too long.
  • Added new quantileHeatmap() function.
  • Improved Markdown header support across functions, where applicable.
  • Improved bcbioSCFiltered to seurat coercion to slot relevant bcbio metadata.

bcbioSingleCell 0.0.17

  • Renamed package from bcbioSinglecell to bcbioSingleCell.
  • Added viridis color palette support to quality control plots.
  • Added cell-cycle marker genes for human and mouse.
  • Slotted organism in bcbioSCDataSet metadata, in addition to genomeBuild.
  • Updated bcbioSCFiltered to seurat coercion method to also run FindVariableGenes() and ScaleData() by default.
  • Added cell-cycle regression into Seurat clustering RMarkdown template.
  • Improved pkgdown settings and website appearance.

bcbioSingleCell 0.0.16

  • Support for CRAN release of Seurat.
  • Improved documentation of package NAMESPACE in bcbioSinglecell-package.R file.
  • Offloaded download() functionality to basejump package, to avoid collisions with bcbioRNASeq package. Function has been renamed to externalFile().
  • Removed function deprecations to simplify the NAMESPACE.
  • Improved Cell Ranger sample matching. With these changes the internal .detectPipeline() function is no longer needed.
  • Improved sample directory matching in internal .sampleDirs() function.
  • Updated paths to Cell Ranger MatrixMarket files in internal .readSparseCounts() function.
  • Updated use of packageSE() to prepareSE(), matching the corresponding basejump function change.
  • Renamed internal use of filter() to tidy_filter(), to avoid future NAMESPACE collisions with ensembldb package.
  • Renamed bcbioSCSubset class to bcbioSCFiltered class.
  • Fixed memory issue in plotZeroesVsDepth() for datasets with high cell counts.
  • Improved sample matching for selectSamples(). Will attempt to migrate this to bracket-based subsetting in a future update.
  • Restricted sample selection with selectSamples() to only work on bcbioSCFiltered class for the time being. We can add bracket-based subsetting or S4 method support in selectSamples() to properly work on bcbioSCDataSet class in a future update.
  • Updated RMarkdown template settings and simplified the setup chunks.
  • Initial support for bcbioSCFiltered class coercion to monocle CellDataSet class.
  • Suggest scater and scone packages for additional quality control and visualization.
  • Require monocle >= 2.5.0.
  • Added initial support for viridis color palette in quality control plots.
  • Suggest rmarkdown and scde packages.
  • Initial commit of subsetPerSample() function.
  • Miscellaneous RMarkdown template improvements.

bcbioSingleCell 0.0.15

  • Renamed functions in lowerCamelCase from snake_case.
  • Draft support for monocle, scater, and scone.
  • Package now depends on SummarizedExperiment.
  • Renamed loadRun() to loadSingleCellRun() for improved compatibility with bcbioRNASeq package. This helps avoid NAMESPACE collisions between packages.
  • Improved support for custom GTF files.
  • Split out Cell Ranger import into a separate utility function named loadCellRanger().
  • Added plotZerosVsDepth() by @roryk.
  • Renamed filteringCriteria to filterParams in @metadata slot.
  • Miscellaneous documentation fixes.

bcbioSingleCell 0.0.14

  • Migrated plotting functions to S4 methods.
  • Improved sample metadata handling.
  • Updated sample name and cellular barcode sanization.
  • Initial commit of Seurat utility functions.
  • Initial commit of YAML parameters for RMarkdown templates.
  • Draft support for Seurat v2 pre-release.
  • Initial support for SureCell UMIs.

bcbioSingleCell 0.0.13

  • Integrated [bcbio][] and Cell Ranger workflows into load_run().

bcbioSingleCell 0.0.12

bcbioSingleCell 0.0.11

bcbioSingleCell 0.0.10

bcbioSingleCell 0.0.9

  • Compatibility update for basejump S4 NAMESPACE changes.
  • Improved plots for quality control and filtering.

bcbioSingleCell 0.0.8

  • Renamed mitochondrial plot functions.
  • Changed presentation of mitochondrial abundance as ratio instead of percentage.
  • Simplified NAMESPACE by offloading dependencies to basejump.

bcbioSingleCell 0.0.7

  • Initial support for loading of 10x Genomics Cell Ranger output.
  • Add detection of droplet method based on the metadata file.
  • Draft support for import of inDrop i5 index barcode counts.

bcbioSingleCell 0.0.6

  • Modified load_run() function for improved consistency with bcbioRNASeq package.
  • Initial incorporation of scater package into workflow.
  • Initial commit of RMarkdown template skeletons.

bcbioSingleCell 0.0.5

  • Improvements to run object based on code in bcbioRNASeq package.
  • Better handling in plots for datasets with many samples.
  • Labeled quality control cutoffs on the plots.

bcbioSingleCell 0.0.4

  • Prepared package for tidyverse dependency updates.
  • Updated HPC server detection.

bcbioSingleCell 0.0.3

  • NAMESPACE consolidation and function cleanup.

bcbioSingleCell 0.0.2

  • Added quality control plotting functions.
  • Converted all functions to standard evaluation.

bcbioSingleCell 0.0.1

  • Initial draft release.