Changelog 0.0

bcbioRNASeq 0.0.1 (2017-03-22)

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

bcbioRNASeq 0.0.2 (2017-03-28)

  • Added plotting functions.

bcbioRNASeq 0.0.3 (2017-03-31)

  • Reworked functions to utilize bcbio list object.

bcbioRNASeq 0.0.4 (2017-04-04)

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

bcbioRNASeq 0.0.5 (2017-04-06)

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

bcbioRNASeq 0.0.6 (2017-04-07)

  • Reworked handling of plots and tables during knits.

bcbioRNASeq 0.0.7 (2017-04-10)

  • NAMESPACE simplification using basejump package.

bcbioRNASeq 0.0.8 (2017-04-12)

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

bcbioRNASeq 0.0.9 (2017-04-13)

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

bcbioRNASeq 0.0.10 (2017-04-19)

  • Renamed import_* functions to read_*.

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 0.0.12 (2017-05-01)

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

bcbioRNASeq 0.0.13 (2017-05-08)

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 0.0.15 (2017-05-15)

  • Reworked and re-organized internal functions.

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 0.0.17 (2017-05-21)

  • Reduced number of exports and improved documentation.

bcbioRNASeq 0.0.18 (2017-05-24)

  • Simplified count pooling functions.

bcbioRNASeq 0.0.19 (2017-06-07)

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

bcbioRNASeq 0.0.20 (2017-06-09)

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

bcbioRNASeq 0.0.21 (2017-06-16)

  • Prepared draft of F1000 workflow document.

bcbioRNASeq 0.0.22 (2017-06-21)

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 0.0.24 (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 0.0.25 (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 0.0.26 (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 0.0.27 (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 0.0.28 (2017-10-17)

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