CHANGES IN VERSION 1.11.1 ------------------------- * fixed unit test for plotting without replicates as DESeq2 no longer supports silentl treating as replicates since version 1.22 CHANGES IN VERSION 1.7.2 ------------------------- * added betaPrior = TRUE to nbinomWaldTest in order to keep the shrinkage of the log2 fold changes. (The shrinkage is now disabled by default in DESeq2) * Changed R dependency to R 3.4 * Added WholeGenome Bioc View CHANGES IN VERSION 1.7.1 ------------------------- * extended the importing section in the vignette a little bit * fixed the robust mean function so that now plotting also works without replicates * new function robust_mean that is used in plotting * when importing matrices, it is now checked that their column names correspond to the sample IDs given CHANGES IN VERSION 1.3.3 ------------------------- * updated CITATION file to point to the published paper CHANGES IN VERSION 1.3.2 ------------------------- * Bioc 3.4 devel version CHANGES IN VERSION 1.1.8 ------------------------- * summarizeCountsPerPosition has been improved and erroneously hard-coded options can now be actually set. This improved version was developed by Sebastian Gibb (http://sebastiangibb.de/). CHANGES IN VERSION 1.1.7 ------------------------- * added new function importData_soGGi to import .bam files in R directly CHANGES IN VERSION 1.1.6 ------------------------- * added CITATION file containing the information on the PeerJ preprint BUG FIXES * added require(mgcv) to the examplse from from plotProfiles to pass the check() from devtools * also added mgcv to suggests CHANGES IN VERSION 1.1.5 ------------------------- BUG FIXES * bug fixes by Hervé Pages CHANGES IN VERSION 1.1.4 ------------------------- BUG FIXES * bug fixes by Hervé Pages CHANGES IN VERSION 1.1.3 ------------------------- BUG FIXES * fixed a wrong preview of the sample annotation table in the vignette * fixed a wrong reference in the runTesting function help * made small changes to the export statement in the roxygen docs CHANGES IN VERSION 1.1.2 ------------------------- BUG FIXES * changed the bibliography to a standard rmarkdown one. This should fix the vignette compilation problem. CHANGES IN VERSION 1.1.1 ------------------------- BUG FIXES * fixed a literature query in the vignette that tried to resolve a DOI via knitcitations::citep() and would often lead to a compilation error on the Bioconductor servers. CHANGES IN VERSION 1.1.0 ------------------------- * initial Bioc devel release