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 RMarkdown 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 RMarkdown 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)

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 RMarkdown 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)

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.