NEWS

changes in version 2.1.1
    * bug fix in texpr, eexpr, iexpr, and gexpr methods; they no longer crash with single-replicate objects
    * Small documentation clarifications

Version 1.99.6 released in Bioconductor 3.1 as Version 2.1.0.

changes in version 1.99.6
    * bug fix in constructor: objects are now constructed correctly when only one sample is included in the object.

changes in version 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

changes in version 1.99.4
    * bug fix in plotting of single-transcript genes

changes in version 1.99.3
    * unit test update due to changes in findOverlaps

changes in version 1.99.2
    * bug fix: "ballgown" function now handles case when input feature names include quotes (').

changes in version 1.99.1
    * Bioconductor 3.0 release. Version 0.99.7 is released as version 1.0.0.

changes in version 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

changes in version 0.99.6
    * ballgownrsem can now handle gzipped input files
    * small fixes to eliminate warnings/errors on R CMD CHECK

changes in version 0.99.5
    * "subset" function now behaves appropriately if sampleNames contain  "dot" characters

changes in version 0.99.4
    * Tablemaker source code moved out of Ballgown repository (both GitHub and BioC svn repos)

changes in version 0.99.3
    * `exprfilter` function added

changes in version 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

Version 0.99.1 was released on Bioconductor on 28 July 2014

changes in version 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