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