version 2.16.0 (2016-02-11)
- NOISeqBIO has been modified when few replicates are available and the computation time has been drastically removed.  
- Gene clustering in NOISeqBIO when few replicates are available: It will be done when total number of samples is 9 or less (instead of 10 or less).
- Fixed a bug in "biotype detection" plot. It failed when none of the genes in the sample had values = 0.
- Corrected an error in the calculation of standard deviation of D statistic in NOISeqBIO.

version 2.14.0 (2015-08-05)
 - Fixed a bug in "MD" plot
 - Fixed a bug in NOISeq-sim (i.e. noiseq function for no replicates)

version 2.12.0 (2015-06-09)
 - New "biotype detection" plot for comparing two samples or conditions. Also a proportion test is performed to compare the abundance of a given biotype between two samples/condtions.
 - New functions to generate Principal Component Analysis plots from either NOISeq object or expression matrix.
 - New ARSyNseq function to correct batch effect or reduce noise from unknown sources when batch information is not available.
 - Quality Control PDF report now includes the new "biotype detection" plot and PCA.
 - The User's Guide has been improved and extended to include the new functionalities.
 - Bugs were fixed.

version 2.6.0 (2014-02-24)
 - Fixed bug in dat() function. Now data with two samples are allowed.
 - dat() function was also modified so parameter "norm" is accepted for "countsbio", "lengthbias" and "GCbias" plots.

version 2.4.0 (2013-11-20)
 - A bug in "RNA composition" plot was fixed.
 - The "CountsBio" barplot has been modified.
 - User's guide and Reference manual have been improved.
 - A bug in "Saturation" plot has been fixed.
 - Normalization function has been modified so the user may choose the possibility of not applying a length correction although the length is provided.
 - NOISeqBIO results now include the log fold change (log2FC).
 - MD plot is now available also for NOISeqBIO results and D is plotted in log-scale.
 - A bug in "explo.plot" function has been fixed.

version 2.2.0 (2013-10-14)
 - New function to generate a Quality Control Report in PDF format including all the exploratory plots.
 - Plot to evaluate RNA composition bias has been changed.
 - Some bugs have been fixed.

version 2.0.0 (2013-07-25)
 - Included the new version of NOISeq for biological replicates: NOISeqBIO
 - Improved the exploratory plots for the quality control of the data that now include diagnostic plots for bias detection
 - Included a function to filter out low count features
 - Fixed the readData function so it can read the chromosome information if the chromosomes are not in numeric format.
 - The NOISeq output includes now the biotype information, if provided to the readData function.
 - A new exploratory plot for differential expression results has been added to the DE.plot function, in which the distribution of differentially expressed features across chromosomes or biotypes is shown.



 








