bcbioRNASeq 0.0.26

  • 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

  • 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

  • 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

  • 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

bcbioRNASeq 0.0.21

  • Prepared draft of F1000 workflow document.

bcbioRNASeq 0.0.20

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

bcbioRNASeq 0.0.19

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

bcbioRNASeq 0.0.18

  • Simplified count pooling functions.

bcbioRNASeq 0.0.17

  • Reduced number of exports and improved documentation.

bcbioRNASeq 0.0.16

  • 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

  • Reworked and re-organized internal functions.

bcbioRNASeq 0.0.14

  • 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

bcbioRNASeq 0.0.12

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

bcbioRNASeq 0.0.11

  • 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

  • Renamed import_* functions to read_*.

bcbioRNASeq 0.0.9

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

bcbioRNASeq 0.0.8

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

bcbioRNASeq 0.0.7

  • NAMESPACE simplification using basejump package.

bcbioRNASeq 0.0.6

  • Reworked handling of plots and tables during knits.

bcbioRNASeq 0.0.5

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

bcbioRNASeq 0.0.4

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

bcbioRNASeq 0.0.3

  • Reworked functions to utilize bcbio list object.

bcbioRNASeq 0.0.2

  • Added plotting functions.

bcbioRNASeq 0.0.1

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