NEWS
NOISeq 2.22.1 (2018-02-01)
NOISeq 2.14.1 (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.
NOISeq 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)
NOISeq 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.
NOISeq 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.
NOISeq 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.
NOISeq 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.
NOISeq 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.