NEWS.md

Release notes

bcbioSingleCell 0.7.1 (2023-12-04)

Minor changes:

• plotReadsPerCell: Updated internal code to avoid unwanted type change during leftJoin step.

bcbioSingleCell 0.7.0 (2023-10-05)

Major changes:

• Bumping version, due to significant changes in bcbioBase and Acid Genomics dependency packages.
• Enforcing strict camel case in all function names.

bcbioSingleCell 0.6.4 (2023-08-17)

Major changes:

• Now requiring R 4.3 / Bioconductor 3.17.
• Removed usage of BiocParallel, including BPPARAM from primary bcbioSingleCell generator function.

Minor changes:

• plotReadsPerCell: Updated internal ggplot2 to use .data pronoun instead of !!/sym rlang syntactic sugar approach.

bcbioSingleCell 0.6.3 (2023-02-08)

Minor changes:

• Tightened up package dependencies, requiring Bioconductor 3.16.
• Migrated requireNamespaes in imports from AcidBase to goalie.

bcbioSingleCell 0.6.2 (2022-10-24)

Minor changes:

• Updated calls to import and export, switching from file/dir to simply con. This helps avoid breaking changes with pending pipette package update.
• Updated Docker image URL.

bcbioSingleCell 0.6.1 (2022-06-09)

Minor changes:

• Updated lintr checks and testthat unit tests.

bcbioSingleCell 0.6.0 (2022-05-09)

Major changes:

• Starting a new release series based on R 4.2 / Bioconductor 3.15.
• bcbioSingleCell S4 class check now allows either sessionInfo (from utils package) or session_info (from sessioninfo package) to be slotted in sessionInfo metadata.

bcbioSingleCell 0.5.1 (2022-04-29)

Minor changes:

• Now requiring R 4.2 / Bioconductor 3.15.
• Minor compatibility fixes for Bioconductor 3.15.

bcbioSingleCell 0.5.0 (2022-03-11)

Major changes:

• Split out basejump imports into component packages.

Minor changes:

• Removed unused formalsList from NAMESPACE, which is removed in upcoming basejump package update.
• Removed barcodeRanksPerSample from NAMESPACE.

bcbioSingleCell 0.4.16 (2021-03-12)

Minor changes:

• Updated basejump dependencies and removed unnecessary stringr import.

bcbioSingleCell 0.4.15 (2021-02-22)

Minor changes:

• Maintenance release, providing support for basejump v0.14 release series.

bcbioSingleCell 0.4.14 (2020-10-08)

Minor changes:

• Maintenance release, updating dependency version requirements.

bcbioSingleCell 0.4.13 (2020-07-24)

Minor changes:

• Maintenance release, updating minimum R dependency to 4.0.

bcbioSingleCell 0.4.12 (2020-05-12)

Minor changes:

• Bug fix for integer handling in .importReads following switch to vroom::vroom from data.table::fread.

bcbioSingleCell 0.4.11 (2020-05-11)

Minor changes:

• updateObject: Bug fix release for breaking changes introduced by colData<- assignment on SingleCellExperiment / SummarizedExperiment expecting check = FALSE support for downstream updateObject call. Added ... passthrough that prevents this error in method support for bcbioSingleCell class. This should now be fully compliant with R 4.0 / Bioconductor 3.11 release.
• updateObject: Added verbose argument support, defaulting now to FALSE.

bcbioSingleCell 0.4.10 (2020-02-24)

Minor changes:

• bcbioSingleCell: Removed now defunct spikeNames argument. Refer to makeSummarizedExperiment, makeSingleCellExperiment documentation and release notes in basejump package for details.

bcbioSingleCell 0.4.9 (2020-02-20)

Minor changes:

• Tightened up dependencies in DESCRIPTION in preparation for bioconda release update, which breaks with basejump 0.12.0 conda dependency otherwise.

bcbioSingleCell 0.4.8 (2020-02-19)

Minor changes:

• Changed license from MIT to GPL-3, matching other bcbio and Acid Genomics R packages.

bcbioSingleCell 0.4.7 (2020-01-20)

Minor changes:

• Updated messages to use cli package approach. The same approach is now used in the bcbioRNASeq package as well.
• Updated basejump dependencies to support rename from bioverbs to AcidGenerics.

bcbioSingleCell 0.4.6 (2019-10-30)

Minor changes:

• Updated S4 validity checks and unit tests to support Bioconductor 3.10. Internally, we have to adjust checks against DataFrame class to also look for DFrame class, which has changed in latest S4Vectors update. See related update in bcbioRNASeq package.
• Full backward compatiblity with Bioconductor 3.9 is currently maintained.
• Updated basejump dependency versions.

bcbioSingleCell 0.4.5 (2019-09-17)

Minor changes:

• Switched QC template to use bcb_file as main file input, similar to bcbioRNASeq QC template.
• Updated lintr config.

bcbioSingleCell 0.4.4 (2019-09-09)

Minor changes:

• bcbioSingleCell: Internal generator now calls importSampleData using pipeline = "bcbio" argument, so we don't run into breaking changes when handling user metadata in a future basejump update.
• Updated basejump dependency versions.

bcbioSingleCell 0.4.3 (2019-08-27)

Minor changes:

• NAMESPACE and basejump dependency updates.

bcbioSingleCell 0.4.2 (2019-08-22)

Major changes:

• bcbioSingleCell: Simplifed internal colData handling, calling calculateMetrics after creating SingleCellExperiment with makeSingleCellExperiment. This improves consistency with Chromium package and enables better preparation of rowRanges containing spike-ins and transgenes.

Minor changes:

• Moved metricsCols global to basejump, so we can share with Chromium.
• Improved generator consistency with other basejump and bcbio R packages.

bcbioSingleCell 0.4.1 (2019-08-20)

Minor changes:

• plotReadsPerCell: Reworked internal code to use DataFrame primarily instead of tbl_df, so we can remove dplyr dependency.
• Updated basejump and bcbioBase dependency versions.
• Removed some additional unused dependencies, to lighten the package.

bcbioSingleCell 0.4.0 (2019-08-12)

This update is intended to simplify the package and reduce the amount of plotting code that is defined to bcbioSingleCell class specifically, instead of SingleCellExperiment.

Major changes:

• Offloaded plotting functions to AcidPlots, so we can use some of this code in a shared manner with objects imported from 10X Genomics Chromium.

Minor changes:

• Improved documentation consistency by using shared roxygen from AcidRoxygen package.
• Updated basejump and bcbio R package dependencies.

bcbioSingleCell 0.3.18 (2019-07-29)

Major changes:

• Updated R dependency to 3.6. This now requires Bioconductor 3.9+.
• updateObject: Simplified method support, dropping rowRanges argument. No longer attempting to coerce assays back to a simple list, which doesn't work well on Bioconductor 3.10 Devel currently.

Minor changes:

• Updated basejump dependencies.
• Improved code coverage over 90%.

bcbioSingleCell 0.3.17 (2019-07-24)

Minor changes:

• Improved internal S4 function naming consistency.
• Updated basejump dependencies.

bcbioSingleCell 0.3.16 (2019-07-17)

Minor changes:

• Updated basejump dependencies.
• Improved Travis CI docker configuration.

bcbioSingleCell 0.3.15 (2019-05-29)

Minor changes:

• Updated barcodeRanksPerSample and plotBarcodeRanks to support DropletUtils update in Bioconductor 3.9.
• Improved Travis and AppVeyor CI configuration.

bcbioSingleCell 0.3.14 (2019-04-25)

• S4 generic reexport documentation fixes.

bcbioSingleCell 0.3.13 (2019-04-23)

Minor changes:

• Now importing ggplot2 code from AcidPlots package.
• plotCellCounts: Improved default appearance, removing black border.
• Updated basejump and bcbio R package dependencies.

bcbioSingleCell 0.3.12 (2019-04-18)

Minor changes:

• Deprecated prepareSingleCellTemplate, in favor of prepareTemplate.
• Switched Travis CI configuration to use singlecell Docker image.

bcbioSingleCell 0.3.11 (2019-04-11)

Major changes:

• Restricted S4 methods back to bcbioSingleCell from SingleCellExperiment where applicable. Generally, this applies to the supported QC plotting functions. Previously, the methods were defined against SingleCellExperiment to also support CellRanger S4 class, which has since been moved to the Chromium package.

Minor changes:

• Improved code coverage by adding additional unit tests.
• Updated internal reexport method for S4 generics, making reexports.Rd file no longer necessary.
• Renamed R Markdown QC template from quality_control to quality-control, using kebab case instead of snake case.

bcbioSingleCell 0.3.10 (2019-04-07)

Major changes:

• updateObject is now fully backward compatible for all objects created by the package, including versions prior to v0.1.
• Tightened up S4 validity class checks for bcbioSingleCell. Similar to bcbioRNASeq class checks, now requiring these elements in metadata: bcbioCommandsLog, bcbioLog, dataVersions, gffFile, lanes, programVersions, projectDir, runDate, wd, and yaml. Previously, these weren't required because we were sharing internal validity code checks with the CellRanger S4 class. CellRanger has since been moved to the new Chromium package, so it's now appropriate to tighten up bcbioSingleCell.
• Extract method [ on bcbioSingleCell class objects no longer alters the version of the object. It only sets subset = TRUE, similar to bcbioRNASeq.

Minor changes:

• Bug fix release for formal rename in emptyRanges from mcolsNames to mcolnames. This has been changed in basejump 0.10.3.

bcbioSingleCell 0.3.9 (2019-04-01)

Minor changes:

• Migrated development code to Acid Genomics.
• Updated basejump dependency to v0.10 release series.

bcbioSingleCell 0.3.8 (2019-03-18)

Minor changes:

• Updated basejump and bcbioBase dependencies.
• Updated documentation.
• Added complete release information in NEWS.

bcbioSingleCell 0.3.7 (2019-02-12)

Minor changes:

• bcbioSingleCell generator: improved internal handling of mapCellsToSamples call. This reworked join step checks the sampleID mapping more carefully.
• Removed plotGene from deprecations. This function has been renamed to plotCounts instead in the basejump package.

bcbioSingleCell 0.3.6 (2019-01-13)

Minor changes:

• Updated basejump and bcbioBase dependencies, to pass build checks.
• Split out imports into a separate R file.

bcbioSingleCell 0.3.5 (2018-12-22)

This release reworks the internal assert checks substantially.

Major changes:

• First release that has fully migrated to using goalie package instead of assertive package internally for checks.
• Reworked bcbioSingleCell S4 validity checks.
• Reworked bcbioSingleCell generator function to use cleaner assert checks.
• Migrated to inheriting S4 generics from bioverbs, where applicable.

Minor changes:

• Reworked documentation to use sentence case instead of title case.

bcbioSingleCell 0.3.4 (2018-12-01)

Major changes:

• metrics: Removed code and consolidated SingleCellExperiment method support in basejump package.

Minor changes:

• Documentation improvements.
• plotQC: Improved validity checks.

bcbioSingleCell 0.3.3 (2018-11-25)

Minor changes:

• Updated basejump and bcbioBase dependencies, to tighten up build checks.
• Documentation and CI configuration fixes.

bcbioSingleCell 0.3.2 (2018-11-19)

Major changes:

• Migrating CellRanger S4 class to separate Chromium R package.
• Migrated additional S4 generics to basejump package (bioverbs).
• Exporting calculateMetrics as a user-accessible function.
• Extract ([) now returns bcbioSingleCell object again.
• filterCells: Reworking to return SingleCellExperiment instead of bcbioSingleCell object.
• Improved plotting functions to inherit params from basejump.

Minor changes:

• Removed barcodePattern global variable.

bcbioSingleCell 0.3.1 (2018-11-14)

Major changes:

• Updated NAMESPACE to inherit from basejump instead of any of the basejump subpackages, which are subject to rework during this release series.
• Renamed example data from cellranger_small to cellranger, and indrops_small to simply indrops.

Minor changes:

• Transitioning to goalie for assert checks in place of assertive package.
• Miscellaneous documentation improvements.
• Updated working examples for plotting functions, using indrops example data.
• Reworked bcbioSingleCell show (print) method.

bcbioSingleCell 0.3.0 (2018-11-06)

Fork of hbc/bcbioSingleCell code base, for additional development and improvements prior to Bioconductor submission. The v0.2 release series is being maintained on the hbc organization page for stability.

The v0.3 release series serves to offload some of the code base to the basejump package, freeing bcbioSingleCell up to be lighterweight and easier to maintain long-term.

Note that v0.2 release series will remain pinned to basejump v0.7 series.

CellRanger code will be split out into a separate Chromium R package in a future update, so some of these SingleCellExperiment-specific methods need to be consolidated into the basejump package.

Major changes:

• aggregateReplicates, cell2sample, combine, plotZerosVsDepth, sampleData, selectSamples, subsetPerSample, topBarcodes: Offloaded to basejump as SingleCellExperiment S4 methods.
• Removed generics offloaded to basejump.
• barcodeRanksPerSample: Reworked internal code, using improved countsPerSample and ranks calculations.
• Updated extract method to work on SingleCellExperiment, so it can also be inherited for CellRanger S4 class.
• Reorganized metricsPerSample code approach.

Minor changes:

• Consolidated S4 validity check code into AllClasses.R file.
• Updated Travis and AppVeyor CI configuration.
• Split out some internal code into barcodes-internal.R. This includes .nCount and .rawMetrics.
• Improved documentation for bcbioSingleCell generator function.
• Reorganized internal CellRanger processing functions.
• Improved documentation for CellRanger generator function.
• Reworked plotting function code to integrate with basejump package.
• Split out plotting code methods into internal functions (e.g. plotMitoVsCoding.SingleCellExperiment).

bcbioSingleCell 0.2.1 (2018-08-19)

Major changes:

• Moved clustering and marker templates to pointillism package, since all clustering code has been moved there. The quality control template using the filterCells function is still provided here.

Minor changes:

• prepareSingleCellTemplate: Improved internal code to use updated prepareTemplate, which has been migrated to basejump package.
• Added back the cellranger_small example dataset.

bcbioSingleCell 0.2.0 (2018-08-09)

This is a significant maintenance release designed to simplify the package for long-term stability. Here we are removing code support for Seurat and visualization of cell clustering. This functionality has been moved to the new pointillism package. We have streamlined bcbioSingleCell to simply import bcbio single-cell data using the bcbioSingleCell constructor or Cell Ranger data with the readCellRanger function. The package continues to provide quality control visualization (see plotQC) and low-quality cell removal with the filterCells function.

Major changes:

• Moved clustering and seurat object support to pointillism: cellCountsPerCluster, cellTypesPerCluster, clusterCellCountsPerSample, fetchData functions, plotFeature functions, plotGene functions, plotMarker functions, plotPCA, plotTSNE, plotUMAP.
• Now requiring bcbioBase v0.4+ and basejump v0.7+.

Defunct functions:

• Removed from exports (for simplicifcation): plotClusters, plotFeatures, quantileHeatmap, readMarkers, readMarkersFile.

Minor changes:

• No longer exporting mapCellsToSamples. This is now only called internally.
• Updated documentation to use roxygen2 v6.1.

bcbioSingleCell 0.1.18 (2018-07-31)

Major changes:

• Now recommending BiocManager instead of BiocInstaller to install.
• filterCells now supports zinbwave = TRUE for automatic zero-inflation weights calculation, using the zinbwave package.
• Now requiring in bcbioSingleCell object validity checks that all sampleData columns are defined in colData, and that the factor levels also match. If you run into an error because of this change, post an issue on GitHub and we'll sort it out. The validity check method now also checks to make sure that all metricsCols are defined in colData.
• aggregateReplicates now keeps track of interesting groups metadata better and returns a SingleCellExperiment containing this information.
• seurat to SingleCellExperiment now keeps track of rowRanges, if they have been stashed inside the seurat object.
• Minimal bcbioSingleCell (indrops_small) and SingleCellExperiment (cellranger_small) objects now contain dimensionality reduction information calculated with Seurat. See the scripts in data-raw/ for how this was performed.
• metrics: SingleCellExperiment method now just returns colData with interestingGroups column defined internally with uniteInterestingGroups. Previously we updated the sampleData to long format here dynamically, but this is no longer needed now that colData always must contain sample data in long format.
• sampleData<- assignment method now dynamically updates the sample metadata in colData to match.
• Simplified SingleCellExperiment method extension for seurat objects.
• Added support for global ggplot2 discrete color palettes using bcbio.discrete.color and bcbio.discrete.fill with options.

Minor changes:

• Marker functions are no longer exported as generics, since they only currently apply to Seurat and may be deprecated in the future.
• Improved documentation, specifying the accepted classes for each argument. This matches the conventions now used in bcbioBase and bcbioRNASeq.
• Now using roxygen2 v6.1 for documentation.
• metrics matrix method now uses rowRanges instead of rowData.
• mapCellsToSamples is no longer exported and has been switched to an internal function.
• Improved filterCells return to include the counts per sample, which makes visual inspection and confirmation with plotCellCounts easier.
• Added assert checks to plotting functions to stop if interestingGroups = NULL. Adding support for NULL handling may be a good idea in a future release but isn't a priority at the moment.
• Improved factor level handling in plotCellCounts and plotZerosVsDepth to avoid warnings if colData and sampleData levels don't match exactly. This can happen if the sample order is different in sampleData than in colData.

bcbioSingleCell 0.1.17 (2018-07-21)

Major changes:

• readCellRanger now supports HDF5 data (.h5 files) or MatrixMarket Exchange Format explicitly, using the format argument. The function also now supports user-requested import of raw whitelisted cellular barcodes, using the filtered argument. By default, filtered counts from Cell Ranger are imported.
• Removed support for zingeR in diffExp. We will consider adding this functionality back in a future update, once the package is available on Bioconductor. For now, we're recommending usage of zinbwave.
• filterCells now supports nCells argument for hard cutoffs, applied after other QC filtering cutoffs using nUMI.
• Internal data has been renamed to snake_case format, for improved consistency. Note that cell_cycle_markers is used in place of cellCycleMarkers, and cell_type_markers in place of cellTypeMarkers. There's no easy way to link these files as aliases, so this is a necessary breaking change.

Minor changes:

• Improved R Markdown template defaults for quality control and clustering.
• Now importing functions related to differential expression into the package NAMESPACE, including DESeq2, edgeR, and zinbwave.
• Parallelization is no longer used to load samples, improving handling in an HPC cluster environment. We will consider using BiocParallel in a future update.
• Now requiring ggplot2 v3.0. Switched to using aes instead of aes_string internally, using new tidyeval syntax.
• Removed additional single-cell toolkit packages in Suggests, including scater and scran. This helps speed up build checks on Travis CI.
• Reexported functions have been moved to the bcbioBase package.
• Improved internal consistency between the bcbioSingleCell and readCellRanger data import functions.

Additional notes:

• Package still works with Bioconductor 3.6 / R 3.4, but we will be migrating to Bioconductor 3.7 / R 3.5 when conda r-base is updated to 3.5.1.

bcbioSingleCell 0.1.16 (2018-06-20)

New functions:

• cellCountsPerCluster and clusterCellCountsPerSample.

R Markdown templates:

• Now recommending 1000 UMIs by default, and a maximum of 10% mitochondrial transcripts.
• Seurat clustering now calculates multiple resolutions, suggesting 0.4, 0.8, and 1.2 by default. Dimensional reduction plots have been updated to support looping of these multiple resolutions.

Minor changes:

• as(object, "SingleCellExperiment") coercion now slots stashed metadata into SingleCellExperiment, if defined.
• Simplified the internal code for sampleData. seurat objects now share the same code as SingleCellExperiment, and return NULL if the sample data is not defined. The metrics function continues to slot empty metadata in sampleID, sampleName, and interestingGroups if not defined.
• SingleCellExperiment is used as default method over seurat where applicable: fetchData family, plotDimensionalReduction family, plotMarker family, plotFeature family, plotGene family, and plotCellTypesPerCluster. The internal code hasn't changed, it just is defined primarily for SingleCellExperiment.
• dimRed argument has been renamed to reduction, where applicable.
• topBarcodes can now return either a data.frame or list, containing the top barcodes grouped by sample.

bcbioSingleCell 0.1.15 (2018-06-13)

Minor changes:

• Updated internal code to use text as primary argument in markdownHeader calls.
• Updated example datasets and unit tests to match.
• Working on using pbmc4k as example dataset for vignette.

bcbioSingleCell 0.1.14 (2018-06-05)

Major changes:

• Multiplexed Cell Ranger barcodes are now reformatted to be more readable and compatible with the mapCellsToSamples utility function. This change helps simplify the internal code for cell2sample. For example in the pbmc4k dataset, the barcode IDs are sanitized from TTTGGTTTCGCTAGCG-1 to "pbmc4k_1_TTTGGTTTCGCTAGCG". The "1" here denotes 1 sample in the matrix, which is how Cell Ranger denotes multiplexed samples in a single counts matrix. Note that the "-" character is illegal in names, so we consistently sanitize barcodes to contain "_" instead. See help("make.names") for more information on syntactically valid names in R.
• readCellRanger no longer requires reference data defined by refdataDir, although this is still recommended.

Minor changes:

• Resaved example datasets.
• Switched the example cellranger_small and seurat_small datasets to the publicly available pbmc4k dataset from 10X Genomics. Here we've subset the top 500 cells and genes by abundance. We'll use either the pbmc4k or pbmc8k dataset for the vignette in a future update.
• bcbioSingleCell and readCellRanger functions now consistently default to not requiring sampleMetadataFile, which is now NULL by default. For bcbioSingleCell, if a custom sample metadata file is not provided, the function reads from the bcbio YAML metadata. For readCellRanger, the function uses minimalSampleData internally to return minimal metadata, containing sampleName and description columns.
• Broke out internal .sampleDirs function to bcbioSingleCell and readCellRanger functions.
• Improved plotMarker documentation examples to use mitochondrial genes.
• Using seurat_small in place of Seurat::pbmc_small in working examples.

Internal code changes:

• Now consistently using dplyr for piped data.frame as much as possible, where applicable. Code is being updated to use tidyeval.

bcbioSingleCell 0.1.13 (2018-05-29)

Minor changes:

• t-SNE and UMAP plot improvements.

bcbioSingleCell 0.1.12 (2018-05-25)

Major changes:

• No longer using automatic camel case sanitization for metrics or fetchData return column names.
• Improved R Markdown clustering and marker templates to optionally support UMAP and dark mode in the YAML parameters.

Minor changes:

• Using original Seurat mapping names for data: tSNE_1, tSNE_2, PC1, PC2, UMAP1, UMAP2.
• Ensure transcript-level counts always have stripTranscriptVersions command applied, to remove the Ensembl transcript versions if present.
• No longer using labels (e.g. A, B, C, D) on ggplot grid return.
• Note that "phase" has been renamed to "Phase" in the R Markdown clustering for cell-cycle regression PCA.

bcbioSingleCell 0.1.11 (2018-05-23)

New functions:

• UMAP is now supported. This functionality is provided in: plotUMAP, plotMarkerUMAP, and plotFeatureUMAP. Corresponding fetch functions, fetchUMAPData and fetchUMAPExpressionData, have also been added.
• plotGene: Added seurat method support. If advanced customization of the plot is needed, use plotDot or plotViolin instead, or refer to the Seurat documentation for alternates.

Major changes:

• Dimensional reduction and marker plots no longer use dark mode by default. The default color palette support for marker plots has been improved to consistently use viridis.
• diffExp: improved internal code to work directly on SingleCellExperiment, removing the need to pass design and group parameters internally. Also added unit testing against zinbwave, zingeR, and edgeR support. DESeq2 is supported but runs slowly.
• Reworked plotFeature and plotMarker family of functions. Improved the color palette support when dark = FALSE, now using a flipped viridis plasma color palette.
• aggregateReplicates function has been reworked to return a SingleCellExperiment object instead of bcbioSingleCell. The v0.2.4 update of bcbioRNASeq behaves similarly with this generic.

Minor changes:

• Reworked the internal handling of some seurat SingleCellExperiment method support, using as(x, "SingleCellExperiment") internally, which uses the new Seurat::Convert function.
• Made some previously deprecated functions now defunct: plotClusters, plotTSNEExpressionData, loadSingleCellRun, darkTheme, pcCutoff, quantileHeatmap, plotKnownMarkers, readMarkers, readMarkersFile.
• Made plotFeatures, plotMarker, and plotMarkers functions defunct.
• plotPCElbow now returns a plot grid.
• sanitizeMarkers: improved internal code for supported bcbio stashed metadata, including rowRanges.

bcbioSingleCell 0.1.10 (2018-05-19)

Minor changes:

• plotCellTypesPerCluster is using dark = TRUE by default again.
• Fixed cell2sample handling for multiplexed Cell Ranger data loaded up with readCellRanger. Need to use stashed cell2sample factor saved in metadata, rather than attempting to calculate on the fly with mapCellsToSamples.
• Updated Travis CI build checks to include bioc-release on macOS.

bcbioSingleCell 0.1.9 (2018-05-18)

Major changes:

• No longer attempting to sanitize the rownames for seurat objects in coercion method. This helps maintain the gene symbol appearance in plotting functions for genes with hyphens in the names.

Minor changes:

• Using BiocParallel::SerialParam internally for zinbwave in diffExp.
• Simplified cell2sample internal code to always use mapCellsToSamples instead of attempting to use a stashed vector inside metadata for SingleCellExperiment method.
• Removed internal .applyFilterCutoffs, which is no longer necessary since this functionality is supported in the S4 subset method.
• Simplified assert checks inside fetchGene functions.
• plotCellTypesPerCluster: revert back to dark = TRUE by default.
• Consolidated plotMarker and plotFeature functions in the documentation.
• sanitizeMarkers: Improved gene identifier matching.
• topMarkers now defaults to coding = FALSE by default, since not all datasets will contain biotype information.

bcbioSingleCell 0.1.8 (2018-05-16)

Minor changes:

• Initial updateObject method support for bcbioSingleCell class.
• Relaxed validObject validity check to not require sample-level metadata in colData yet.

bcbioSingleCell 0.1.7 (2018-05-15)

New functions:

• Added support for Uniform Manifold Approximation and Projection (UMAP) with the plotUMAP and fetchUMAPData functions. These work similarly to the other plotDimensionalReduction and fetchData functions.

Major changes:

• Now adding sample-level metadata into colData slot, for better downstream compatibility with other packages that work with SingleCellExperiment container class. Unique per-sample rows are still saved internally in the sampleData slot.
• Now recommending ECDF as the default geom for quality control plots, where applicable.
• filterCells now supports minUMIs = c("knee", "inflection") for automatic filtering based on the cellular barcode ranks. Internally this is handled by DropletUtils::barcodeRanks.

Minor changes:

• Attempting to re-enable libgsl-dev installation for zinbwave on Travis CI.
• Suggesting BiocParallel for zinbwave call in diffExp.
• Now importing Seurat functions into NAMESPACE.
• Consolidated fetchData functions in the documentation.
• Consolidated plotDimensionalReduction functions in the documentation.
• Updated aggregateReplicates internal code. This function again only supports aggregation of bcbioSingleCell objects that have been filtered using the filterCells function.
• Now using Seurat::Convert internally to coerce seurat class object to SingleCellExperiment, using as(seurat, "SingleCellExperiment"). This utility function was added to Seurat v2.3.1.

Internal changes:

• Tweaked metrics SingleCellExperiment method code to always merge colData and sampleData.
• Updated readCellRanger internal code to match bcbioSingleCell constructor, specifically handling sample-level metadata in colData.

bcbioSingleCell 0.1.6 (2018-05-09)

Minor changes:

• Updated default QC R Markdown template.
• Added trendline option to QC scatter plot functions.
• Simplified internal handling of interestingGroups in plotQC.
• Using readYAMLSampleData internally instead of defunct sampleYAMLMetadata.
• Added sampleNames method support for seurat.
• Now importing rmarkdown, sessioninfo, tidyverse for R Markdown reports, rather than suggesting. Similar update applied to bcbioRNASeq.
• Suggesting scater and scran.

bcbioSingleCell 0.1.5 (2018-05-04)

Major changes:

• Overhauled inflection and knee point labeling support in plotUMIsPerCell. Now uses the point argument and always labels per sample. Currently requires the geom = "ecdf" argument for labeling.
• Updated default quality control template.
• Added plotBarcodeRanks.

Minor changes:

• Added barcode rank support for seurat class objects.
• QC plots now have titles by default, matching the conventions used in bcbioRNASeq.
• Fixed y-axis scale for histogram geom in QC plots.
• Prefiltering of very low quality barcodes with no UMIs or genes is now always applied. This helps avoid unwanted downstream errors with zero count barcodes.
• Added boxplot geom support for plotReadsPerCell().
• plotQC geom argument is now more consistent across the paneled plots.
• Fixed facet wrapping for aggregate samples in the QC plots.
• Added interestingGroups support to plotZerosVsDepth, matching the other QC functions.

bcbioSingleCell 0.1.4 (2018-04-30)

• Updated sampleData S4 methods to match update in bcbioBase. Now supports clean argument, which returns non-blacklisted factor columns only. See bcbioBase::metadataBlacklist for the blacklist.
• Improved axis scale appearance on dimensionality reduction plots using scales::pretty_breaks internally.
• Added grid argument to plots, where applicable.
• Renamed example dataset from bcb_small to indrops_small.
• Removed unnecessary method support for interestingGroups and metadata. These extend from SummarizedExperiment correctly now.
• Fixed x-axis label centering for plotCellCounts and plotReadsPerCell.
• Simplified seurat method support for SingleCellExperiment-like methods, where applicable. This includes rowData, gene2symbol, and interestingGroups.
• Improved dark mode color support for plotDot, plotFeatureTSNE, plotMarker.
• Updated sample metadata example in README.

bcbioSingleCell 0.1.3 (2018-04-25)

Minor changes:

• Improved summary statistics output during filterCells call.
• Miscellaneous documentation improvements, most notably to bcbioSingleCell constructor function.
• plotViolin now uses a color border by default.
• Improved cell2sample mapping internally for readCellRanger.
• Improved Bioconductor 3.7 installation instructions.

bcbioSingleCell 0.1.2 (2018-04-24)

Major changes:

• Now using bcbioSingleCell instead of loadSingleCell as the main constructor function to create a bcbioSingleCell object. loadSingleCell is deprecated and still works, but will warn the user.
• Renamed loadCellRanger to readCellRanger for better name consistency.
• Quality control function color palettes now default to ggplot2 colors instead of using viridis palettes. This is defined using scale_color_hue instead of scale_color_viridis for example. The viridis color palette is still used by default for marker expression plots.
• Use "aggregate" instead of "sampleNameAggregate" to define aggregate/grouped samples in metadata.

Minor changes:

• Reexporting relevant ggplot2 and viridis color palettes.
• Renamed references to "inDrops" from "inDrop", where applicable.
• Consistently using sym in place of .data internally for tidy code.
• Updated seurat blacklist for sampleData generic.
• plotCellTypesPerCluster and plotMarkerTSNE now use an automatic color palette by default, which enables for dynamic color palette support when dark = TRUE. Internally this is handled with the theme_midnight and theme_paperwhite ggplot2 themes.
• Updated installation instructions to support Bioconductor 3.7.

Internal changes:

• metrics method support now defaults to matrix and works similarly for dgCMatrix sparse matrices. This is used in place of calculateMetrics to generate the per cell quality control metrics.
• Reworked and improved aggregateReplicates internal code.
• Fixed facet wrapping when aggregate is defined in metadata for quality control plots.
• Improved internal code for sanitizeMarkers to use map the gene annotations from rowRanges better.

bcbioSingleCell 0.1.1 (2018-04-16)

Major changes:

• Added support for calculating barcodeRanks and barcodeRanksPerSample.
• Now exporting plotMarker in addition to plotMarkers.
• Primary counts matrix slotted into assay is named counts instead of raw, for better consistency with SingleCellExperiment class. The counts generic requires that the primary assay slot is named counts to work correctly. Nothing else here has changed, just the name.
• loadCellRanger now returns a SingleCellExperiment object instead of a bcbioSingleCell object.
• Added support for transgeneNames and spikeNames when loading up a dataset.
• Datasets from a poorly annotated genome can now be loaded up using organism = NULL during the loadSingleCell call.
• Methods now dispatch on SingleCellExperiment rather than bcbioSingleCell where applicable, providing support for SingleCellExperiment objects created elsewhere.

Minor changes:

• Added support for labeling barcode ranks, such as elbow or inflection point on UMI counts per cell plots.
• Added support for plotting metrics using an empirical distribution function (ECDF) plot.
• Use theme_midnight and theme_paperwhite internally for dimensionality reduction plots.
• TSNE and PCA plots now use an aspect ratio of 1 by default.
• Improved imports from Matrix, S4Vectors, and methods.
• Switched back to using base stop, warning, and message.
• inflectionPoint has been made defunct, in favor of using barcodeRanks.
• Moved internal constructors into S4 methods, where applicable.

bcbioSingleCell 0.1.0 (2018-04-04)

Major changes:

• bcbioSingleCell S4 class now extends SingleCellExperiment instead of SummarizedExperiment. This requires definition of rowRanges inside the object instead of rowData. Similar functionality was added to the bcbioRNASeq package. Upgrade support will be provided using updateObjectin a future release.
• Added a differential expression utility function named diffExp, which uses zingeR/edgeR internally to calculate gene expression changes across cell groups.

Minor changes:

• Added plotCumulativeUMIsPerCell utility. This may be removed in a future update in favor of adding this plot into plotUMIsPerCell using an ECDF plot.
• Now using readCellTypeMarkers to load marker data.frames, instead of readCellTypeMarkersFile. This matches the conventions used in the bcbioBase package.

bcbioSingleCell 0.0.32 (2018-03-12)

• Fixes for object subsetting and loadSingleCell organism calls

bcbioSingleCell 0.0.31 (2018-02-21)

• Improved handling of old Ensembl release version for Cell Ranger output.
• Switched R Markdown templates to consistent snake case formatting for variables and file names.
• prepareSingleCellTemplate now uses _setup.R instead of setup.R.
• Updated unit tests to work with new assert checks.
• Export mapCellsToSamples instead of cell2sample. cell2sample now simply acts as an accessor function, returning the internally stored cell2sample mappings rather than trying to calculate. mapCellsToSamples performs the actual mapping from cellular barcodes to sample identifiers.
• Export metricsPerSample
• Now using BiocParallel::bpmapply to loop across the sparse matrix files per sample internally in the .sparseCountsList function, which is shared between loadSingleCell and loadCellRanger.
• Updated assert checks.
• Updated prepareSingleCellTemplate to explicitly state which files to include for each R Markdown template, rather than inheriting from bcbioBase::prepareTemplate.
• selectSamples now fails on a sample mismatch, rather than warning.
• Improved internal code for subset method, adding a drop = FALSE argument to the cellular barcode matching call.
• Made all file loads in working examples a single line.
• Simplified R Markdown directory paths.
• Made all loads in unit tests a single line.
• Renamed programs metadata slot to programVersions, to improve consistency with bcbioRNASeq package.
• Updated internal sample metadata sanitization to ensure all columns are factors.

bcbioSingleCell 0.0.30 (2018-01-26)

• Fixes for QC plot labeling of bcbioSingleCell object with different per sample filtering cutoffs applied.
• Added new fetchGeneData function, that wraps the functionality of Seurat::FetchData for specific genes.
• Improved internal dimensionality reduction plotting code. The main function has been renamed to .plotDR internally.
• Simplified the code for fetchTSNEExpressionData to return a standard data.frame with the cellular barcodes as rows, instead of the previously grouped tibble method. Now this function returns aggregate gene marker calculations in the mean, median, and sum columns. Since this method has way fewer rows than the grouped tibble, the ggplot2 code for plotMarkerTSNE now runs faster.
• Explicitly declare viridis:: for color palettes, where applicable.
• colorPoints argument has been renamed to expression for plotMarkerTSNE.
• Dynamic gene symbol to ensgene conversion has been removed from the plotting functions, for greater simplicity. Now the genes argument simply matches against the rownames in the counts matrix of the object.
• Decreased the default minCumPct argument for plotPCElbow from 0.9 to 0.8. This is more conservative and will return slightly fewer principal components for dimensionality reduction, by default.
• plotTSNE, plotPCA, and the other dimensionality reduction-related plotting functions now default to a smaller point size (0.5) and slight alpha transparency (0.8), to make super imposed points more obvious for large datasets with many cells.
• Added a working example for subsetPerSample.
• Internally switched from .onLoad to .onAttach method for automatically loading required dependency packages.
• plotPCA now uses phase instead of Phase plotting cell cycle regression as an interestingGroup (see Seurat clustering template). Previously some of the Seurat metadata columns were not consistently sanitized to lowerCamelCase (e.g. Phase, res.0.8, orig.ident).
• Suppress package startup messages in R Markdown templates.

bcbioSingleCell 0.0.29 (2018-01-24)

• Switched to rlang methods for errors, messages, and warnings: abort, inform, and warn.
• Updated filterCells function to enable per sample filtering cutoffs. This works by passing in a named numeric vector, where the names must match the internal sampleID metadata column (not sampleName).
• Improved internal sanitization of metrics available with the metrics accessor. Now all count columns (e.g. nUMI) are consistently integers, and all character vector columns are consistently coerced to factors.
• Seurat metadata available through the bcbioSingleCell generics are now consistently sanitized in lowerCamelCase. This applies to orig.ident and the res.* metadata columns.
• Explicit integers are now consistently used in all of the function parameter arguments.

bcbioSingleCell 0.0.28 (2018-01-22)

• Manually define functions used to read barcodes and matrices. This improves the functionality of the internal .readSparseCounts function.
• Improved sample directory matching for Cell Ranger output.
• Fixed sample metadata subsetting based on cell2sample factor levels in the internal subset code.
• Added tabbed histogram, violin, and barplots for appropriate quality control functions in the R Markdown code.

bcbioSingleCell 0.0.27 (2018-01-18)

• Migrated core dependency imports from basejump to bcbioBase.
• Improved colnames and rownames handling for internal .readSparseCounts function.
• Reworked loadCellRanger function. refDataDir parameter has been renamed to refdataDir.
• Added organism and genomeBuild options to loadSingleCell, to override the metadata set in the bcbio run, if necessary.
• Improved if statement data class checks, where applicable.
• Renamed internal .sparseCountsTx2Gene to .transcriptToGeneLevelCounts.
• Updated geomean bind method in fetchTSNEExpressionData.
• Changed minNovelty default from 0.8 to 0.75.
• Improved seurat class support for plotDot.
• Improved parameter names for plotKnownMarkersDetected. Now uses tsneColor, violinFill, and dotColor. Also added pointsAsNumbers parameter.
• Added subtitle parameter for plotMarkerTSNE.
• Added tsneColor, violinFill, dotColor, and dark parameters for plotMarkers.
• Improved looping method for plotTopMarkers so that it renders correctly in R Markdown calls.
• Added method support for plotViolin.
• Improved internal cell2sample handling in subset method code.

bcbioSingleCell 0.0.26 (2017-12-18)

• Renamed readMarkersFile to readCellTypeMarkersFile.
• Improved internal handling of multiplexed CellRanger samples. These are count matrices with cellular barcodes ending in -2, for example.
• Updated aggregateReplicates code to work with basejump generic, which uses groupings instead of cells as the grouping parameter.
• Added method support for detectOrganism.
• Improved filtering parameter output in filterCells.
• Updated gene2symbol method support for bcbioSingleCell and seurat objects.
• Fixed working example in knownMarkersDetected.
• Reworked internal code for plotCellTypesPerCluster.
• Improved internal checks for facet wrapping and color palette parameter arguments, where applicable.
• Offloaded base plotQuantileHeatmap functionality into basejump, for use in bcbioRNASeq package.
• Added unit test data for loadSingleCell().
• Added additional unit tests to improve code coverage.

bcbioSingleCell 0.0.25 (2017-12-11)

• Prepared a minimal working example dataset.
• Added some initial unit tests.
• Renamed plotKnownMarkers to plotKnownMarkersDetected.
• Renamed readMarkers to readMarkersFile.
• Added gene2symbol method support.
• Moved plotDot generic to basejump package.
• Added internal .checkFormat function, which will check for ensgene or symbol input.
• Added internal .convertGenesToSymbols utility function, for mapping Ensembl gene identifiers to gene symbols.
• Use explicit calls to Seurat functions interally, for clarity.
• Simplified bcbioSingleCell object return in loadSingleCell function.
• Added seurat class method support for annotable function.
• Added bcbio<- assignment method support for seurat class objects.
• calculateMetrics function now uses annotable = TRUE as default, instead of using missing method.
• Added method support for cell2sample for seurat class objects.
• cellTypesPerCluster now uses min and max default arguments that don't remove any rows.
• Added method support for seurat class objects to counts function. This defaults to returning the raw counts (normalized = FALSE), but can also return log-normalized (normalized = TRUE) and scaled (normalized = "scaled") counts.
• Added Ensembl gene identifier mapping support to fetchTSNEExpressionData.
• filterCells now simply works in a destructive manner. We've removed the drop parameter. The messages displayed to the user during this function call have been improved, and now include more statistics on the step where the majority of cells are filtered.
• Initial commit of gene2symbol method support for bcbioSingleCell and seurat class objects.
• Improved interestingGroups<- assignment method support for seurat class objects.
• Color palettes now default to viridis instead of inferno palette, where applicable.
• Added Ensembl gene identifier support for plotDot function.
• plotFeatureTSNE now uses a plural features parameter instead of feature, which is consistent with the syntax used in the other functions.
• Added Ensembl gene identifier support to plotMarkerTSNE. The format argument still defaults to "symbol", for consistency with previous behavior. However, in the future we recommend that users pass in stable Ensembl gene identifiers here if possible, for better reproducibility.
• plotMarkers now supports Ensembl gene identifiers.
• plotPCElbow now silently returns the sequence of principal components (PCs) that we recommend to use for dimensionality reduction.
• We're now using "glm" instead of "gam" for geom_smooth plotting, where applicable. See the plotQC function code.
• Improved the defaults for plotQuantileHeatmap to enable faster plotting. Now the dendrogram calculations are skipped by default, which take a long time for large datasets.
• Removed the draft plotStressGenes function for now. Will try to add this in a future update.
• Fixed Markdown header handling for plotTopMarkers if headerLevel = NULL.
• Simplified selectSamples code to rely upon output of our bracket-based subsetting method. See subset.R file for more details.
• Improved metadata update in bracket-based subsetting method.
• subsetPerSample function now defaults to saving in the working directory.
• Updated topBarcodes function to rank by nUMI instead of nCount column, so it works with data from either bcbioSingleCell or seurat objects.
• Minor tweaks to seurat coercion from bcbioSingleCell object. Here we've improved the metadata slotting.
• Initial commit of example data script in the data-raw/ directory!

bcbioSingleCell 0.0.24 (2017-11-27)

• Raw cellular barcodes are now slotted in object@cellularBarcodes as a data.frame instead of a per sample list. This makes downstream subsetting operations on the barcodes simpler.
• Bug fixes for cell2sample mapping.
• Switched back to stable CRAN version of roxygen2 (6.0.1) for documentation.
• Renamed pcCutoff to plotPCElbow. The function now returns a PC sequence from 1 to the cutoff (e.g. 1:10) instead of just the final PC cutoff value. The R Markdown clustering template has been updated to reflect this change.
• Renamed quantileHeatmap to plotQuantileHeatmap, for consistency with other plotting functions.
• Initial support for customized bracket based subsetting, which now acts upon the raw cellular barcode counts stashed in the object@bcbio slot.
• Moved darkTheme to basejump package and reworked as midnightTheme, with improved colors and axis appearance.
• Added pointsAsNumbers parameter to plotTSNE and plotPCA functions, to match the functionality in plotMarkerTSNE.
• Overhauled loadCellRanger to support multiplexed Cell Ranger matrix output. Cell Ranger adds a numeric suffix to the end of multiplexed barcodes (e.g. AAACCTGGTTTACTCT-1 denotes cellular barcode AAACCTGGTTTACTCT is assigned to sample 1).
• Improved cell2sample mapping in aggregateReplicates function, which uses the sampleNameAggregate column in sample metadata to define the aggregate sample pairings. The summarize step at line 101 is slow for datasets with many samples and should be changed in the future to speed things up.
• Improved internal cell2sample code to handle NULL stashed mappings better.
• Updated TNSE plotting functions to use midnightTheme instead of darkTheme.
• Added user-defined point and label sizes for plotMarkerTSNE.
• Fixed typo in plotMitoRatio where maxGenes cutoff was plotted instead of maxMitoRatio.
• Added legend parameter argument to plotQC function. Also improved handling of NULL return for plotReadsPerCell, which can happen with Cell Ranger output.
• Updated facet wrapping in plotZeroesVsDepth to match the behavior in the other plotting functions.
• Initial methods support for custom bracket-based subsetting.

bcbioSingleCell 0.0.23 (2017-11-22)

• Improved facet wrapping of aggregated samples (sampleNameAggregate present in sample metadata), but removing code support for wrapping by multiplexed FASTQ description.
• Simplified handling of bcbioSingleCell objects with filterCells applied. This information is stored in the metadata slot as 3 variables: (1) filterParams, numeric vector of the parameters used to define the cell filtering cutoffs; (2) filterCells, character vector of the cellular barcode IDs that passed filtering; (3) filterGenes, character vector of the Ensembl gene identifiers that have passed filtering, as determined by the minCellsPerGene parameter.
• For filterCells return, we're now defaulting to a destructive operation, where the columns (cells) and rows (genes) of the object are adjusted to match the cells and genes that have passed filtering. Currently this can be adjusted with the drop argument for testing, but should generally be left as drop = TRUE.
• We're now slotting a cell2sample named factor in the metadata slot, which makes downstream quality control operations faster. This is generated on the fly for previously saved objects that don't have a stashed cell2sample.
• Initial commit of plotQC utility function, which plots multiple quality control functions for easy visualization. This defaults to output as a cowplot grid (return = "grid"), but can alternatively be set to return R Markdown code (return = "markdown").
• aggregateReplicates operation has been improved to properly slot raw cellular barcodes in object@bcbio$cellularBarcodes. The filterCells vector is adjusted, and sampleMetadata factors should be properly releveled.
• The counts accessor simply returns the sparse matrix contained in the assay slot. The filterCells argument has been removed.
• Messages have been added to the filterCells function, to help the user determine at which step the majority of cells are being filtered. We're keeping a non-destructive option using drop = FALSE for the time being, but this will likely be removed for improved simplicity in a future update.
• Updated the internal code for metrics to use a simpler join operation on the colData, cell2sample and sampleMetadata.
• Updated facet wrap code in quality control plots to not facet multiplexed FASTQ descriptions and simply check for sampleNameAggregate.
• Improved appearance of plotReadsPerCell labels and legends. Additionally, plotReadsPerCell more efficiently handles the stashed values in the nCount column of colData, for faster plotting that having to rely on manipulation of the raw cellularBarcodes list stashed in object@bcbio$cellularBarcodes.
• sampleMetadata return is now consistently sanitized for bcbioSingleCell and seurat objects.
• Minor tweaks to quality control template and setup.R files.
• Added plotFeatureTSNE utility function. This improves on Seurat::FeaturePlot and enables the user to overlay the cluster identifiers on top of the t-SNE plot. plotFeatures is now deprecated in favor of this function.
• Improved internal handling of Seurat data in the .fetchDimDataSeurat function. This now keeps the cell ID as the rowname.
• Allow the user to define the color palette (color), as well as pointSize and labelSize for plotPCA and plotTSNE.
• Factors are now correctly releveled in cell2sample return.
• Improved internal code for fetchTSNEExpressionData.
• Bug fix for metrics accessor not including the cell ID as rownames.
• Clustering template fixes. Now uses plotFeatureTSNE to assess quality control metrics on t-SNE.

bcbioSingleCell 0.0.22 (2017-11-17)

• Now internally stashing a cell2sample data.frame, which helps speed up operations on cellular barcode metrics calculations for quality control plots.
• Improved support for optional annotable, ensemblVersion, gtfFile, and sampleMetadataFile arguments in loadSingleCell function.
• Simplified some of the messages shown during sample loading, in an attempt to make them clearer and more informative. Also improved messages shown to the user during a filterCells function call.
• The metrics function will now look for a stashed cell2sample data.frame, which speeds up operations for quality control plots.
• Improved handling of sample metadata columns as factors. In particular, levels should be correctly updated using droplevels in a selectSamples call. The bcbioRNASeq package has also been updated to work in a similar fashion, where all columns in the sample metadata data.frame are now defined as factors.
• Simplified bcbioSingleCell to seurat object coercion to stash all of the bcbio metadata, and simply return the basic seurat object, rather than trying to also perform normalization and scaling. These steps have instead been added back to the Seurat R Markdown clustering template.
• Updated cell cycle and cell type markers from our master copy on Google Sheets.
• Added a troubleshooting section to the GitHub README, with a note on maximum DLLs.

bcbioSingleCell 0.0.21 (2017-11-08)

• Updated package imports to match Bioconductor 3.6.
• Initial support for plotCellTypesPerCluster.
• Initial support for plotMitoVsCoding. I broke this code out from plotMitoRatio. We could opt to keep this in plotMitoRatio with a geom = "scatterplot" argument.
• Initial commit of .applyFilterCutoffs internal function, used to subset the object to contain only cells and genes that have passed quailty control filtering.
• Improved Seurat FindAllMarkers sanitization.
• Made the quality control plots more modular. Now they support multiple geoms, including boxplot, histogram, ridgeline, and violin (default). Median labels are applied with the internal .medianLabels function.
• Updated error message for Cell Ranger directory structure.
• Cellular barcode columns are no longer split with an underscore. Instead, they are kept as a single ACGT string. We're now generating cellID to sampleID matching with a different method. In the future, we'll stash a cell2sample data.frame inside the object, that makes this operation faster than the current mclapply code.
• Updated annotable support in loadSingleCell and loadCellRanger.
• Added support for handling both gene- and transcript-level counts. The updated release of the bcbio single-cell pipeline now outputs at gene level.
• Initial quality control plot support for seurat objects.
• Added support for return of only filtered cells and genes with the counts(filterCells = TRUE) function.
• Added assignment support for interestingGroups<-.
• Initial support for sample metadata generation from seurat object.
• Improved internal code for selectSamples.
• Updated topMarkers to match Seurat v2.1 update.
• Improved bcbioSingleCell to seurat coercion method with setAs.

bcbioSingleCell 0.0.20 (2017-10-24)

• Upgraded to basejump 0.1.0 and Seurat 2.1.0 dependencies.
• Improved documentation of NAMESPACE imports per function.
• Switched to base grep functions where applicable (grepl, gsub).
• Use GTF in package documentation rather than GFF. Applies primarily to the loadSingleCell import function.
• Restrict class support in S4 methods to bcbioSingleCell. Legacy bcbioSCDataSet class can be upgraded to bcbioSingleCell class using as(bcb, "bcbioSingleCell") coercion.
• Use filtered cell output for metrics and quality control functions by default.
• Updated the quality control R Markdown to include filterCells = FALSE where applicable.
• Draft support for aggregated technical replicates in quality control functions using sampleNameAggregate column in sample metadata. This doesn't change the actual counts values. It only applies to visualization in the quality control plots currently.
• Miscellaneous R Markdown template updates. Primarily improvements to the setup chunk object loading workflow.
• Removed lintr checks from testthat. This is breaking devtools::test.

bcbioSingleCell 0.0.19 (2017-10-12)

• 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 t-SNE 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 (2017-09-17)

• Renamed plotClusters to plotMarkers. Added soft deprecation.
• Added viridis color support in t-SNE 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 roxygen2 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 (2017-09-03)

• 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 R Markdown template.
• Improved pkgdown settings and website appearance.

bcbioSingleCell 0.0.16 (2017-08-25)

• 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 R Markdown 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 (2017-08-11)

• 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 (2017-07-26)

• 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 (2017-07-10)

• Integrated bcbio and Cell Ranger workflows into load_run.

bcbioSingleCell 0.0.12 (2017-06-28)

• Initial support for S4 object creation using SummarizedExperiment.

bcbioSingleCell 0.0.11 (2017-06-24)

• Added testthat, lintr, and covr support for code coverage.

bcbioSingleCell 0.0.10 (2017-06-15)

• Updated RMarkdown templates.

bcbioSingleCell 0.0.9 (2017-06-12)

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

bcbioSingleCell 0.0.8 (2017-05-28)

• 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 (2017-05-13)

• 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 (2017-05-10)

• 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 (2017-05-08)

• 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 (2017-04-26)

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

bcbioSingleCell 0.0.3 (2017-04-20)

• NAMESPACE consolidation and function cleanup.

bcbioSingleCell 0.0.2 (2017-04-12)

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

bcbioSingleCell 0.0.1 (2017-03-01)

• Initial draft release.