CHANGES IN VERSION 0.9.0 (2013-11-21)
-------------------------------------

NEW FEATURES


    o First release

CHANGES IN VERSION 0.9.1 (2013-11-27)
--------------------------------------

NEW FEATURES

    o Permutation methods for combining p-values from multiple statistics
    o More interactive and compact report

BUG FIXES

    o A bug in exon filters resulting in removing genes/transcripts with only 
    one exon
    o A serious bug in exon filters causing wrong genes to be filtered out under
    circumstances

CHANGES IN VERSION 0.91.0 (2014-01-03)
--------------------------------------

NEW FEATURES

  o Functions to create simulated datasets
  o Functions to create false discovery and ROC curves


BUG FIXES

    o A bug in p-value vector naming causing unordered p-values for limma and
    baySeq when combining methods
    o Smaller bug fixes

CHANGES IN VERSION 0.92.0 (2014-01-25)
--------------------------------------

NEW FEATURES

    o Functions to estimate weights for combining p-values based on simulated
    datasets from real data

BUG FIXES

    o Smaller bug fixes

CHANGES IN VERSION 0.93.0 (2014-02-12)
--------------------------------------

NEW FEATURES

    o Support for Arabidopsis thaliana
    o Additional validation functions

BUG FIXES

    o Bugs affecting multilevel factorial analysis (single factor, more than two
    conditions)
    o Smaller bug fixes

CHANGES IN VERSION 0.99.0 (2014-02-21)
--------------------------------------

NEW FEATURES

    o Support for Pan troglodytes
    o Improved the simulator to i) simulate length bias and ii) better length
    selection

BUG FIXES

    o Code changes to comply with Bioconductor's guidelines

CHANGES IN VERSION 0.99.1 (2014-03-12)
--------------------------------------

NEW FEATURES

    o Ability to export counts table (raw and normalized) when reading from BAM
    files or just normalized otherwise
    o Valid examples for many functions

BUG FIXES

  o More code and codestyle changes to comply with Bioconductor's guidelines

CHANGES IN VERSION 0.99.2 (2014-03-14)
--------------------------------------

NEW FEATURES

    o Ability to display only the top x% of significant genes to avoid 
    excessively big reports

BUG FIXES

    o More code and codestyle changes to comply with Bioconductor's guidelines

CHANGES IN VERSION 0.99.3 (2014-03-17)
--------------------------------------

NEW FEATURES

    o Function to check and warn if a main metaseqr argument is invalid (may
    prevent crashes during run)

BUG FIXES

    o Small bug fix in read2count function

CHANGES IN VERSION 0.99.4 (2014-03-18)
--------------------------------------

BUG FIXES

    o Removed all <<- assignments
    o Changed the Depends of DESCRIPTION file to import less packages in the 
    main environment
    o Added qvalue package to Depends as there was a problem with NBPSeq

CHANGES IN VERSION 0.99.5 (2014-03-31)
--------------------------------------

NEW FEATURES

    o Changed directory structure of the report to look more organized and pro
    o Added the ability to save and retrieve the gene model counts list (counts
    for each exon) in an .RData file to be reused in another analysis later, as
    summarizing genes is one of the most time-consuming parts.

BUG FIXES

    o Minor problems with the report

CHANGES IN VERSION 0.99.6 (2014-04-09)
--------------------------------------

NEW FEATURES

    o Example on how to estimate statistical test weights in the vignette

BUG FIXES

    o Bug when exporting flags when gene or exon filters are NULL

CHANGES IN VERSION 1.0.0 (2014-04-11)
--------------------------------------


NEW FEATURES

    o Function to calculate the F1-score (or harmonic mean of precision and
    recall)
    o Mature and tested enough to go from 0.x.y version to 1.0.0

CHANGES IN VERSION 1.3.2 (2014-05-05)
--------------------------------------

NEW FEATURES

    o Function to merge exons belonging to different isoforms to a set of
    "virtual" exons to help construct a single gene model with unique exons
    o Simplified the usage of read2count()

BUG FIXES

    o Major bug in "exon" mode that inflated the number of reads for certain 
    genes with many isoforms
    o Minor bug in argument checking, not allowing to not save the gene model in
    "exon" mode