NEWS
ballgown 2.1.1
- bug fix in texpr, eexpr, iexpr, and gexpr methods; they no longer crash with single-replicate objects
- Small documentation clarifications
ballgown 1.99.6
- bug fix in constructor: objects are now constructed correctly when only one sample is included in the object.
ballgown 1.99.5
- clarification of docs/warning messages when "time" variable has too few timepoints to fit natural splines
- bug fix in subset function: factor levels that don't appear in subset pData are now dropped
ballgown 1.99.4
- bug fix in plotting of single-transcript genes
ballgown 1.99.3
- unit test update due to changes in findOverlaps
ballgown 1.99.2
- bug fix: "ballgown" function now handles case when input feature names include quotes (').
ballgown 1.99.1
- Bioconductor 3.0 release. Version 0.99.7 is released as version 1.0.0.
ballgown 0.99.7
- new methods for accessing gene and transcript names and IDs
- development package (on GitHub) now has Travis CI integration, so the package's is built/tested with every new push and a status image is visible on the package README
ballgown 0.99.6
- ballgownrsem can now handle gzipped input files
- small fixes to eliminate warnings/errors on R CMD CHECK
ballgown 0.99.5
- "subset" function now behaves appropriately if sampleNames contain "dot" characters
ballgown 0.99.4
- Tablemaker source code moved out of Ballgown repository (both GitHub and BioC svn repos)
ballgown 0.99.3
- 'exprfilter' function added
ballgown 0.99.2
- 'ballgownrsem' function added (now compatible with RSEM output)
- RSEM slot added to ballgown S4 class
- bug fixes in 'subset' function
- library size adjustment in 'stattest' is now CSS normalization (using *log* FPKM) by default and is more customizable
ballgown 0.99.1
ballgown 0.99.0
- "meas" argument added to constructor function
- unit tests added
- vignette updated
- several bug fixes in plotting functions and statistical testing function
Alpha release, 30 March 2014:
- package announced