NEWS

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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