NEWS.md

bcbioRNASeq 0.2.5 (2018-06-21)

Minor changes

• Enable support bcbio integration, by modifying bcbioRNASeq() constructor to work with minimal bcbio test data.
• Switched from internal usage of aes_() in favor of consistent usage of aes_string(). This will make the transition to [ggplot2][] v2.3.0 easier in a future update.

bcbioRNASeq 0.2.4 (2018-05-24)

Major changes

• aggregateReplicates() support has been added back. This function returns a RangedSummarizedExperiment instead of a bcbioRNASeq object, containing only an aggregate raw counts matrix in the counts slot of assays().
• The functional analysis [R Markdown][] template has been reworked to use dds_file and organism as new parameter arguments. We've reduced the number of parameters required here to run [clusterProfiler][].
• Made alphaSummary() defunct for bcbioRNASeq object, in favor of DESeqDataSet only. This function is only useful when a proper design formula has been defined.

Minor changes

• metrics() now contains an informative error for datasets that were analyzed using the fast-rnaseq bcbio pipeline.
• DESeqDataSet coercion from bcbioRNASeq object doesn't attempt to run DESeq() command any more, which was unnecessary and improves speed.
• bcbioSingleCell() constructor now supports censorSamples parameter. This is useful for removing known poor quality samples upon loading.
• [ggplot2][] color and fill palettes are now set NULL in the quality control functions. This behavior doesn't change the appearance of the plot colors, which will still default to ggplot2::scale_colour_hue() or ggplot2::scale_fill_hue(). The upcoming [ggplot2][] v2.3.0 update supports global options for color and fill palettes, so these parameters may be deprecated in a future release.
• Reworked the internal code for topTables().

Infrastructure changes

• Added [macOS][] testing to [Travis CI][] build checks.
• Fixed [clusterProfiler][] compilation error on [Travis CI][] by installing libudunits2-dev (Linux).

bcbioRNASeq 0.2.3 (2018-05-10)

Major changes

• Now recommending variance stabilizing transformation (vst) over rlog counts by default in plots, where applicable.

Minor changes

• Tweaked Rory's biotype plots in QC report to match formatting conventions in the package. These plots are now colored.
• Added plotDEGPCA() to default differential expression R Markdown template.
• colData() factors are correctly releveled upon object subset with [. This helps avoid unwanted downstream errors when creating a DESeqDataSet and running differential expression with DESeq2.
• Recommending facet return method by default for plotGene(). Updated the working example to reflect this.
• metrics() now returns interestingGroups column.
• sample label has been removed from axis title for QC plot functions.
• Now using shared ggplot2 convneience functions from bcbioBase 0.2.10: bcbio_geom_abline(), bcbio_geom_label(), and bcbio_geom_label_repel(). These are also used by bcbioSingleCell for improved graphical consistency.
• Removed unused internal legacy ggplot2 code.
• Increased DEGreport, DESeq2, and tximport dependency requirements.

bcbioRNASeq 0.2.2 (2018-04-26)

Minor changes

• Split out assertive imports so we can pin on [bioconda][].
• Improved package documentation.
• Improved label consistency in plotPCA() functions to match plotMeanAverage() and plotVolcano().
• Improved automatic title labeling in plotDEGPCA(), matching the other DEG functions. Also added directionality to plotDEGPCA().
• Added DESeqDataSet method support to plotCorrelationHeatmap(), using the normalized counts.
• reusltsTables() now writes local files to tempdir() when Dropbox mode is enabled using dropboxDir.

bcbioRNASeq 0.2.1 (2018-04-24)

Last set of code fixes before F1000v2 resubmission.

Major changes

• Added rle return support for counts(), which are calculated on the fly.
• Added transgeneNames and spikeNames support to loadRNASeq() function.
• loadRNASeq() now supports organism = NULL again, for datasets with poorly annotated genomes.
• Primary assay() containing raw counts is now named counts instead of raw, for consistency with other SummarizedExperiment objects (e.g. DESeqDataSet) and the bcbioSingleCell S4 class definition.
• Improved internal code for plotGene() and plotGenderMarkers().

Minor changes

• Improved AppVeyor CI support to test against bioc-devel using R 3.5.
• Improved support and unit testing for updateObject() method.
• DESeq2 normalized counts are always slotted in assays(), even when rlog and vst transformations are skipped.
• Exporting [[<-, assays<-, colData<-, interestingGroups<-, and metadata<- assignment methods, to avoid unwanted coercion to SummarizedExperiment. Objects extending RangedSummarizedExperiment shouldn't be doing this, so we may need to file a bug report with Bioconductor or check our class definition in the package.
• Now importing specific functions from S4Vectors and methods rather than importing everything.
• Switched back to using stop(), warning() and message() rather than the alternate rlang functions abort(), warn(), and inform().
• Objects with invalid metadata now print which slots are invalid to the console.

bcbioRNASeq 0.2.0 (2018-03-22)

Major changes

• bcbioRNASeq S4 class object is now extending RangedSummarizedExperiment instead of SummarizedExperiment. Consequently, the row annotations are now stored in the rowRanges slot as GRanges class, instead of in the rowData slot as a DataFrame. The rowData() accessor still works and returns a data frame of gene/transcript annotations, but these are now coerced from the internally stored GRanges. The GRanges object is acquired automatically from [Ensembl][] using basejump::ensembl(). By default, GRanges are acquired from [Ensembl][] using AnnotationHub and [ensembldb][]. Legacy GRCh37 genome build is supported using the [EnsDb.Hsapiens.v75][] package.
• assays() now only slot matrices. We've moved the [tximport][] data from the now defunct bcbio() slot to assays. This includes the lengths matrix from [tximport][]. Additionally, we are optionally slotting [DESeq2][] variance-stabilized counts ("rlog", "vst"). [DESeq2][] normalized counts and [edgeR][] TMM counts are calculated on the fly and no longer stored inside the bcbioRNASeq object.
• colData() now defaults to returning as data.frame instead of DataFrame, for easy piping to [tidyverse][] functions.
• bcbio() slot is now defunct.
• FASTA spike-ins (e.g. EGFP, ERCCs) can be defined using the isSpike argument during the loadRNASeq() data import step.
• Melted counts are now scaled to log2 in the relevant quality control functions rather than using log10. This applies to plotCountsPerGene() and plotCountDensity(). Note that we are subsetting the nonzero genes as defined by the raw counts here.
• Simplified internal tximport() code to no longer attempt to strip transcript versions. This is required for working with C. elegans transcripts.
• Minimal working example dataset is now derived from GSE65267, which is also used in the F1000 paper.
• Added as(object, "DESeqDataSet") coercion method support for bcbioRNASeq class. This helps us set up the differential expression analysis easily.
• counts() function now returns [DESeq2][] normalized counts (normalized = TRUE) and [edgeR][] TMM counts (normalized = "tmm") on the fly, as suggested by the F1000 reviewers.
• Design formula can no longer be slotted into bcbioRNASeq object, since we're not stashing a DESeqDataSet any more.
• Updated Functional Analysis R Markdown template.

Minor changes

• validObject() is now required for all plotting functions. This check is also called in the R Markdown template. Legacy objects can be updated using updateObject().
• metrics() now returns columns sorted alphabetically.
• Added contrastName() as a generic function.
• plotDEGHeatmap() and plotDEGPCA() generics no longer have counts defined in the signature. The counts argument is now only defined in the methods.
• prepareRNASeqTemplate() has been converted from a generic to a standard function.
• Improved metadata() validity checks.
• plotCorrelationHeatmap() matrix method has been moved to basejump package, for improved consistency with the other heatmap code.
• plotGenderMarkers() internal code has been reworked to match plotGene().
• Default plotMA() appearance has changed, providing a line at the 0 y-intercept, similar to DESeqDataSet method.
• Internal example datasets have been renamed (e.g. bcb_small instead of bcb).
• Added AppVeyor CI support for code testing on Windows.
• Made Travis CI checks stricter, added BiocCheck().
• Internal .sampleDirs() code is now exported in bcbioBase as a generic.
• gene2symbol() and interestingGroups() method support are now defined for SummarizedExperiment in the bcbioBase package.

Updating legacy objects < v0.2.0

• Use updateObject() in combination with the rowRanges argument, which requires a GRanges object. GRanges can be obtained from [Ensembl][] using the basejump::ensembl() function or the [ensembldb][] package.

Deprecations

• bcbio() slot is now defunct, since we have moved all data into the SummarizedExperiment container.
• Deprecated plot5x3Bias() in favor of plot5Prime3PrimeBias(). This is less confusing as to what this function plots.
• flatFiles() has been deprecated in favor of as(object, "list") coercion method. See bcbioBase package for SummarizedExperiment method support.
• Defunct: design(), download(), meltLog10(), txi().
• Legacy bcbioRNADataSet method support has been removed.

bcbioRNASeq 0.1.8 (2018-04-03)

• Bug fix for gene2symbol argument not renaming rows in plotDEGHeatmap().

bcbioRNASeq 0.1.7 (2018-02-28)

• Bug fix for [ subset method dropping metrics in metadata.
• Simplified unit testing for Dropbox mode enabled in resultsTables().

bcbioRNASeq 0.1.6 (2018-02-20)

• Bug fix for gene-to-symbol mappings in plotDEGHeatmap().
• Added support for quickly plotting differentially expressed genes (DEG) in a PCA plot with plotDEGPCA().
• Added support for Dropbox shared links to resultsTables(), for use with the [Stem Cell Commons][] database.
• Added assert checks internally for all functions.
• Improved internal code for plotGene() and plotGenderMarkers() to run faster.
• Deprecated data frame methods based on metrics for QC functions.

bcbioRNASeq 0.1.5 (2018-01-31)

• Import shared dependency functions from bcbioBase instead of basejump.
• Added method support for selectSamples().
• organism and genomeBuild parameters are now user-definable in the main loadRNASeq() import function.
• Fixed gene subsetting method on S4 object, which handles genes using intersect() in the featureCounts matrix.
• Removed internal aggregateReplicates() code. This needs to be reworked and added back in a future release.
• Improve method for handling a missing normalized counts matrix in the assays slot. This can occur when the user opts to skip the CPU-intensive DESeq2 normalizations.
• Improved internal code for the quality control functions. Improved the if statements to be more class specific.
• Renamed plotCorrelationHeatmap() transform argument to normalized, for consistency with the counts() generic.
• Added title support to plots, where applicable.
• Updated internal code for plotDEGHeatmap().
• Updated internal marker handling code for plotGenderMarkers().
• resulsTables() function now defaults to summary = TRUE.

bcbioRNASeq 0.1.4 (2018-11-27)

• Migrated all basejump function imports to bcbioBase package.

bcbioRNASeq 0.1.3 (2017-12-03)

• Combined examples (bcb, dds, res, etc.) into a single examples object. This helps avoid accidental use of example bcb in an analysis.
• Moved ggplot imports from internal-ggplot.R to above each function.
• Renamed maxSamples parameter in loadRNASeq() to transformationLimit. If there are more samples than this limit, then the DESeq2 transformations will be skipped. In this case, rlog and vst will not be slotted into assays().
• Added a colData sanitization step in loadRNASeq() to ensure rows are in the same order as the columns in the counts matrix. Otherwise, DESeq will report an error at the DESeqDataSetFromTximport() step. We're also ensuring the factor levels get updated here.
• Now using glimpse() instead of str() in examples, where applicable.
• Added colData<- assignment method support. This requires a DataFrame class object. Upon assignment, the internal colData at bcbio(object, "DESeqDataSet"), assays(object)[["rlog"]] and assays(object)[["vst"]] are also updated to match.
• Initial assignment support for design, which will update the internal DESeqDataSet.
• Added method support for gene2symbol() generic, which will now return a 2 column data.frame with ensgene and symbol columns. This is helpful for downstream gene to symbol mapping operations.
• Added working example for interestingGroups<- in the documentation.
• Added some code to improve factor releveling, where applicable. See internal-meltLog10.R for example.
• Now explicitly defining the custom color palettes (e.g. viridis::scale_fill_viridis(discrete = TRUE). This makes it clearer to the user in the documentation where these palettes are located.
• Improved axis label support in plotGene().
• plotHeatmap() now uses internal gene2symbol mappings from stashed annotable, instead of always querying Ensembl. The user can define custom mappings with the gene2symbol argument, if desired.
• plotPCA() now supports custom color palettes. The shapes parameter has been removed because it doesn't work well and is limited to datasets with few samples. This behavior matches the PCA functionality in DESeq2.
• Improved internal code for plotVolcano(). Added support for gene2symbol argument, like in plotHeatmap(). If left missing, the function will query Ensembl for the gene2symbol mappings. We're now using data instead of stats as the main data source.
• Improved legibility of subset method code.
• Added some additional reexports, which are used for the package documentation and website.
• Simplified legacy object coercion method code.
• Updated Bioconductor installation method code. We're now using the dependencies argument, which allows for automatic install of suggested packages along with imports.

bcbioRNASeq 0.1.2 (2017-11-08)

• Updated package imports to match Bioconductor 3.6.
• Added support for interesting groups assignment with interestingGroups<-.
• Renamed plotGeneHeatmap() to simply plotHeatmap().
• Added gender marker support for Homo sapiens.
• Improved support for multiple interesting groups in quality control plots. Now interestingGroups is defined as a column in the metrics data.frame that is used to specify the plot color/fill. This matches the convention in the bcbioSingleCell 0.0.22 update.
• Sample metadata columns are now consistently set as factors.

bcbioRNASeq 0.1.1 (2017-10-26)

• Added support for coloring of multiple interesting groups in quality control plots.

bcbioRNASeq 0.1.0 (2017-10-23)

• Updated version and author information to match the F1000 Research workflow.
• Added an f1000v1 branch containing the reproducible code used to generate the figures in our workflow.
• Modified plotMA() to support vertical or horizontal layout return. Also added an argument to remove the color legend, which is typically not that informative.
• Added custom color palette support to the quality control functions.
• Upgrading from bcbioRNADataSet (< 0.1.0) to bcbioRNASeq class object is now possible using as() coercion method.
• Object oriented methods are now restricted to use bcbioRNASeq object. Legacy bcbioRNADataSet objects must be upgraded to bcbioRNASeq class.

bcbioRNASeq 0.0.28 (2017-10-17)

• Added support for output of unstructured data inside bcbioRNASeq S4 object using flatFiles() function.
• Added bcbioRNASeq method support for annotable() generic.

bcbioRNASeq 0.0.27 (2017-10-10)

• Renamed bcbioRNADataSet S4 class to bcbioRNASeq. This matches the naming conventions in the bcbioSingleCell package.
• Renamed loadRNASeqRun() to simply loadRNASeq().
• Switched loadRNASeq() from using S4 dispatch to a standard function.
• Added a parameter argument to loadRNASeq() that enables request of a specific Ensembl release version for gene annotations.
• Renamed interestingGroup argument in quality control functions to interestingGroups for better consistency.
• Improved handling of sample metrics in plotPCACovariates().
• Added functional analysis R Markdown template.
• Offloaded some core functionality shared between [bcbioRNASeq][] and bcbioSingleCell to the basejump package. This included some code to handle sample metadata YAML and file loading. This helps provide a consistent experience across both packages.

bcbioRNASeq 0.0.26 (2017-09-09)

• Renamed package from bcbioRnaseq to bcbioRNASeq.
• Improved website appearance.
• Added [viridis][] color palette support to quality control functions.
• Improved subset operations on bcbioRNADataSet object.
• Fixed setup chunk loading of bcbioRNADataSet in differential expression [R Markdown][] template.

bcbioRNASeq 0.0.25 (2017-08-11)

• Added S4 methods support for plots, allowing the user to use either bcbioRNADataSet or a metrics data.frame and manual interesting_group declaration for visualization.
• Migrated function and variable names from snake_case to camelCase.
• Offloaded small RNA functionality to a separate package named bcbioSmallRNA.

bcbioRNASeq 0.0.24 (2017-07-13)

• Reworked [R Markdown][] templates to improve YAML defaults and add more comments.
• Modified default path variables in setup.R to use *_dir instead of *_out.
• Updated NEWS file to use [Markdown][] syntax.

bcbioRNASeq 0.0.23 (2017-07-03)

• Slotted DESeqDataSet using design = formula(~1) for quality control. This enables automatic generation of rlog and vst transformed counts.
• Documentation fixes and website updates.
• Renamed S4 class from bcbioRnaDataSet to bcbioRNADataSet (case sensitive).
• Adjusted the number of exported functions.

bcbioRNASeq 0.0.22 (2017-06-21)

• Added [testthat][] checking with [lintr][].
• Initial setup of code coverage using [covr][].

bcbioRNASeq 0.0.21 (2017-06-16)

• Prepared draft of [F1000][] workflow document.

bcbioRNASeq 0.0.20 (2017-06-09)

• Added [Travis-CI][] support for automatic rendering of quality control report.

bcbioRNASeq 0.0.19 (2017-06-07)

• bcbioRnaDataSet S4 definition updates.
• Updates to plot_pca() and gene-level heatmaps.

bcbioRNASeq 0.0.18 (2017-05-24)

• Simplified count pooling functions.

bcbioRNASeq 0.0.17 (2017-05-21)

• Reduced number of exports and improved documentation.

bcbioRNASeq 0.0.16 (2017-05-18)

• Draft migration of bcbio run object into S4 bcbioRnaDataSet.
• Created a new variant of load_run() that saves to S4 object instead of list.

bcbioRNASeq 0.0.15 (2017-05-15)

• Reworked and re-organized internal functions.

bcbioRNASeq 0.0.14 (2017-05-10)

• Defaulted to loading run using project summary YAML file.
• Initial commit of [R Markdown][] templates (e.g. quality control).
• Added support for dynamic file downloads from [HBC][] website.
• Draft build of website using pkgdown::build_site().

bcbioRNASeq 0.0.13 (2017-05-08)

• Improved [RDAVIDWebService][] utility functions to work with [dplyr][] 0.6.0.

bcbioRNASeq 0.0.12 (2017-05-01)

• Reworked metadata and summary metrics functions to obtain information from project-summary.yaml saved in the final run directory.

bcbioRNASeq 0.0.11 (2017-04-27)

• Reduced number of depdencies.
• Initial commit of modified volcano plot from CHBUtils package.
• Internal code updates for upcoming [dplyr][] 0.6.0/[tidyeval][] update.
• Updated [Ensembl][] biomaRt annotations to use live site, currently release 88.

bcbioRNASeq 0.0.10 (2017-04-19)

• Renamed import_* functions to read_*.

bcbioRNASeq 0.0.9 (2017-04-13)

• Consolidated NAMESPACE imports.
• Defaulted to writing count matrices with gzip compression, to save disk space.

bcbioRNASeq 0.0.8 (2017-04-12)

• Renamed internal parameters for better readability.
• Improved documentation and consolidate functions by group.

bcbioRNASeq 0.0.7 (2017-04-10)

• NAMESPACE simplification using basejump package.

bcbioRNASeq 0.0.6 (2017-04-07)

• Reworked handling of plots and tables during knits.

bcbioRNASeq 0.0.5 (2017-04-06)

• Initial commit of differential expression and gene set enrichment functions.

bcbioRNASeq 0.0.4 (2017-04-04)

• Added bcbio object integrity checks.
• Improved detection and handling of lane split samples.

bcbioRNASeq 0.0.3 (2017-03-31)

• Reworked functions to utilize bcbio list object.

bcbioRNASeq 0.0.2 (2017-03-28)

• Added plotting functions.

bcbioRNASeq 0.0.1 (2017-03-22)

• Start of package development.
• Initial draft release supporting automatic loading of bcbio run data.

[clusterProfiler]: [covr]: https://github.com/jimhester/covr [dplyr]: http://dplyr.tidyverse.org [edgeR]: https://doi.org/doi:10.18129/B9.bioc.edgeR [Ensembl]: http://www.ensembl.org [ensembldb]: https://doi.org/doi:10.18129/B9.bioc.ensembldb [F1000]: https://f1000.com [HBC]: http://bioinformatics.sph.harvard.edu [lintr]: https://github.com/jimhester/lintr [macOS]: https://www.apple.com/macos [Markdown]: https://daringfireball.net/projects/markdown/syntax [RDAVIDWebService]: https://doi.org/doi:10.18129/B9.bioc.RDAVIDWebService [R Markdown]: http://rmarkdown.rstudio.com [Stem Cell Commons]: http://stemcellcommons.org [testthat]: https://github.com/hadley/testthat [tidyeval]: http://dplyr.tidyverse.org/articles/programming.html [tidyverse]: https://www.tidyverse.org/ [tximport]: https://doi.org/doi:10.18129/B9.bioc.tximport [Travis-CI]: https://travis-ci.org [viridis]: https://cran.r-project.org/web/packages/viridis/index.html