NEWS

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ribiosNGS 1.5.1 (2026-01-30)

• Updated ribiosNGS to fit the latest biokit output structure.
• ggpubr is now only suggested, not imported.
• Updated SLURM integration to work with latest HPC updates.

ribiosNGS 1.0-14 (2015-12-03)

• Added truncatedDgeTable and writeTruncatedDgeTables.

ribiosNGS 1.0-13 (2015-08-11)

• Replace NA with zero counts if needed.

ribiosNGS 1.0-12 (2015-06-12)

• RiboSeq: fixed a bug in matching the two matrices by row names.

ribiosNGS 1.0-11 (2015-02-16)

• Substantial update of S4 classes and functions.
• Added annotate method.

ribiosNGS 1.0-7 (2014-11-03)

• Added EdgeResult object.
• Exported functions needed for MPS.

ribiosNGS 1.0-6 (2014-10-31)

• Started using roxygen2 for documentation.
• edgeR workflow wrapped into edgeBuild, edgeTest, and edgeRun.
• Removed edge.DGE function (no longer used).

ribiosNGS 1.0-5 (2013-01-22)

• pairs.Rscript moved to /SOFT/bi/apps/ribios/scripts/pairs.

ribiosNGS 1.0-4 (2012-09-10)

• Bug fix: read.table in merge.Rscript does not recognize single quote as quote character.

ribiosNGS 1.0-3 (2012-06-19)

• Modified merge.Rscript: suffixes do not cause error, -outfile can be missing (stdout as default), -noheader/-header is a mandatory parameter.

ribiosNGS 1.0-2 (2011-12-20)

• Added documentation and testing data for edgeR.DGE.

ribiosNGS 0.99.0 (2026-02-14)

Bioconductor submission

• Prepared package for Bioconductor submission.
• Set version to 0.99.0 as required for new Bioconductor submissions.
• Updated DESCRIPTION: expanded Description field, added biocViews, updated minimum R version to >= 4.4.0, added VignetteBuilder.
• Added @return documentation tags to all exported functions.
• Added introductory vignette with worked example.
• Converted \dontrun{} to \donttest{} where appropriate.
• Ensured par() settings are saved and restored via on.exit().
• Added GitHub Actions CI workflow for R CMD check.