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

CHANGES IN VERSION 1.3.3 (2014-08-21)
--------------------------------------

NEW FEATURES

    o Added the ability to retrieve annotation for genes/exons from UCSC or
    RefSeq through connection to UCSC Genome Browser public SQL database. The
    GC-content for each region is retrieved through BSgenome packages.
    o Added details regarding the number of genes returned by each algorithm
    when conducting combined analysis.

BUG FIXES

    o Fixed minor bug with warning level logging.
    o Fixed problem occured with the change of biomaRt attributes for newer
    organisms.

CHANGES IN VERSION 1.3.4 (2014-09-03)
--------------------------------------

NEW FEATURES

    o Added support for hg38

BUG FIXES

    o Fixed more problems occured with the change of biomaRt attributes for 
    newer organisms.
    o Fixed bug causing report crash when no genes are passing FDR threshold in
    paired comparisons.

CHANGES IN VERSION 1.3.5 (2014-09-30)
--------------------------------------

NEW FEATURES

    o Re-analysis based on saved gene models is now faster.
    o Added the ability to save time-consuming part of analyses also when 
    count.type="gene".

BUG FIXES

    o Fixed problem with RMySQL dependency when using annotation from UCSC.
    Solved with the usage of RSQLite, however, the process is a bit longer.
    
CHANGES IN VERSION 1.5.1 (2014-10-31)
--------------------------------------

NEW FEATURES

    o Support for pig genome (Sus scrofa, susScr3 in UCSC)
    
BUG FIXES

    o None 
    
CHANGES IN VERSION 1.5.15 (2014-12-22)
--------------------------------------

NEW FEATURES

    o Minor code improvements
    
BUG FIXES

    o Introduced a (hopefully robust) fix for constant changes in Ensembl
    schema for human GRC37 (hg19). It increases annotation retrieval time
    though
    o Fixed problem when input counts are a data.frame and count.type in exon,
    introduced during package upgrades. Thanks to Ben Elsworth, Garvan
    Institute of Medical Research, Austria.
    o Replaced "==" with all.equal while checking if the sum of weights is one
    when meta.p="weight". Of course this is the correct way to compare. Thanks 
    to Ben Elsworth, Garvan Institute of Medical Research, Syndey, Australia.
    o Fixed problem related to a bug in the current version of edgeR GLM and 
    the usage of ... in glmFit.

CHANGES IN VERSION 1.5.2 (2014-12-30)
--------------------------------------

NEW FEATURES

    o Added the argument exclude.list, to provide the possibility of excluding
    samples from any analysis, e.g. in the case where after a preliminary 
    metaseqr run, some samples are not of adequate quality. It is useful when
    a previous analysis is restored, so as not to repeat the construction of
    a gene model from exons for example.
    
BUG FIXES

    o None

CHANGES IN VERSION 1.5.21 (2015-01-09)
--------------------------------------

NEW FEATURES

    o None
    
BUG FIXES

    o Fixed small bug regarding annotation retrieval when directly using the
    get.annotation function for certain genomes (e.g. pig). Thanks to Rathi
    Ryan from Synthetic Genomics, Inc.

CHANGES IN VERSION 1.7.0 (2015-03-05)
--------------------------------------

NEW FEATURES

    o Added support for both forward and reverse RNA-Seq library preparation
    protocol. Thanks to Ben Elsworth, Garvan Institute of Medical Research, 
    Syndey, Australia.
    o Added Reads per Gene Model length (rpgm) measurement, where gene model
    length is either the sum of exon lengths or the gene length (depending on
    count.type argument).
    
BUG FIXES

    o Fixed a problem caused by a bug in baySeq 2.0.50 code which caused an
    analysis based in baySeq to crash.

CHANGES IN VERSION 1.7.12 (2015-05-15)
--------------------------------------

NEW FEATURES

    o None
    
BUG FIXES

    o Fixed a crashing problem when weight="pandora".
    o Fixed deprecation issues.

CHANGES IN VERSION 1.9.0 (2015-05-27)
--------------------------------------

NEW FEATURES

    o Added ability to export JSON for a few graphs to
    be used with Highcharts library for interactive 
    visualization.

BUG FIXES

    o None.

CHANGES IN VERSION 1.9.21 (2015-10-08)
--------------------------------------

NEW FEATURES

    o Added one more output list member of the main pipeline (metaseqr)
    containing all the processed data in a way that can be easily used
    for further downstream analysis in R. Contains also the metaseqr pipeline
    call and the parameters.

BUG FIXES

    o Fixed broken dependency with removed CRAN package MADAM which was
    used for the Fisher p-value combination. The fix was done by copying
    the two required functions from the last MADAM archived version (1.2).
    o Fixed a bug in make.sample.list which rendered the function unusable
    (credits to Marina Adamou-Tzani).
    o Fixed a very special-case small bug in the report generation only a single
    gene passes the multiple testing correction cutoff (thans to Martin Reczko,
    BSRC 'Alexander Fleming').
    o Fixed problem with Fisher p-value combination method (returning all NA due
    to the inexistence of names in the p-value vecror).
    o Fixed bug with flags of biotype filtered genes.

CHANGES IN VERSION 1.9.3 (2015-04-04)
--------------------------------------

NEW FEATURES

    o None

BUG FIXES

    o Fixed BED file reading by fixing the deprecated option in import.bed
    (asRangedData) from rtracklayer

CHANGES IN VERSION 1.11.2 (2016-07-26)
--------------------------------------

NEW FEATURES

    o Basic support for Quant-Seq experiments

BUG FIXES

    o None

CHANGES IN VERSION 1.11.4 (2017-04-04)
--------------------------------------

NEW FEATURES

    o None

BUG FIXES

    o Fixed importing of external gene file for non-supporting
    organism when count.type is "exon" or "utr"

CHANGES IN VERSION 1.17.4 (2017-10-06)
--------------------------------------

NEW FEATURES

    o New option: utr.flank for counting reads in 3' UTR flank regions when
    analyzing Quant-Seq data.
    o New gene filter: genes where x samples present less than y counts are
    excluded from statistical testing. x is determined as a fraction of 
    available samples.

BUG FIXES

    o Fixed bug in problematic backwards compatibility of strandedness in
    targets files which caused strandedness to be ignored (thans to Martin 
    Reczko, BSRC 'Alexander Fleming').

CHANGES IN VERSION 1.19.14 (2018-04-12)
--------------------------------------

NEW FEATURES

    o New option for count.type: when "transcript", the DE analysis is
    performed at the transcript level. Only works for Ensembl annotation.

BUG FIXES

    o Fixed a leftover which prevented completing the analysis when count.type
    is "exon".
