NEWS

---

compcodeR 1.37.3

• Removed support for baySeq since it has been deprecated
• Added runComparisonShiny function

compcodeR 1.35.1

• Add a function for SVA + limma differential expression analysis

compcodeR 1.31.1

• Implement simulations according to the phylogenetic poisson log normal model
• Implement length-varying simulations
• New PhyloCompData object for phylogenetic informed simulation data
• Add possible length normalization to DESeq2 and limma analyses
• Add phylolm analyses

compcodeR 1.23.1

• Moved vignette to Rmd

compcodeR 1.17.1

• Removed support for SAMseq since samr has been removed from CRAN

compcodeR 1.5.3

• Updated baySeq code to match package version 2.2.0

compcodeR 1.5.2

• Updated NBPseq code to match package version 0.3.0

compcodeR 1.5.1

• Added the number of significant genes, then number of true positives, true negatives, false positives and false negatives as evaluation criteria.
• Bug fixes

compcodeR 1.3.4

• Fixed documentation

compcodeR 1.3.3

• Removed support for HTSDiff since it has been removed from CRAN

compcodeR 1.3.2

• Fixed a bug that prevented data sets with more than 17,343 genes to be simulated (thanks to Simon Greenaway)

compcodeR 1.3.1

• Updated vignette
• Added citation file

compcodeR 1.2.0

• Release version with Bioconductor 3.0

compcodeR 1.1.4

• Added MCC (Matthew's correlation coefficient) as evaluation measure

compcodeR 1.1.3

• Fixed summarizeSyntheticDataSet to work also for non-simulated data

compcodeR 1.1.2

• Added reference information for TCC (thanks to Koji Kadota)

compcodeR 1.1.1

• Bug fix in EBSeq quantile normalization (thanks to Rory Kirchner)

compcodeR 0.99.3

• Bug fixes

compcodeR 0.99.2

• Extended the examples
• Bug fixes

compcodeR 0.99.1

• inclusion of an additional comparison metric, relating the gene score to the signal strength for genes expressed in only one condition
• improved documentation of the compData class

compcodeR 0.99.0

• identical to 0.2.0, renamed for Bioconductor submission

compcodeR 0.2.0

• introduction of a new S4 class (compData) and associated functions
• more examples, checks and error messages
• more options for providing user-specified values in the data simulation
• changed the range of the color palette in the Spearman correlation plots to [-1,1]

compcodeR 0.1.0

• first version