NEWS

---

mosdef 1.6.0

• Slight edits to have better behaved de_volcano() and go_volcano() functions, with filters/looks depending on the adjusted p-values, and a better management of the color values to be used when plotting the different subsets

mosdef 1.4.0

• gene_plot() defaults now to NULL in the intgroup parameter, which translates into using the first colData item

mosdef 1.2.0

• New functionality added for general scope tasks, such as feature annotation and summaries on the expression tables
• The gene_plot() function now is (again) able to handle the specification of more than one grouping variable

mosdef 1.0.0

• mosdef is on Bioconductor!

mosdef 0.99.4

• Added persistent location to the script that generates the data objects

mosdef 0.99.3

• Working on the size and time constraints for the vignette/package to build and check on the BBS

mosdef 0.99.2

• Better specification of data objects format and location in the installed folder

mosdef 0.99.1

• This version contains the newly implemented changes as a response to the Bioconductor review. In brief, this includes:

  • renaming the functions (and parameters) to a more consistent style
  • reduction of the dependencies and runtime of checks/tests
  • more details on the exported data objects, and on the outputs (detailed in the vignette)
  • better structure for the vignette with cross-references among sections
  • modularization of some functions to avoid repetitive code
  • implementation of an API which is already framework-agnostic, to later accommodate e.g. edgeR/limma. Mainly, this implies the renaming of the dds to a more generic de_container, whereas the res_de parameter stays constant.

  For a full list of all changes implemented, please refer to the PR on the mosdef repository https://github.com/imbeimainz/mosdef/pull/11/

mosdef 0.99.0

• Ready for submission to Bioconductor!

mosdef 0.4.0

• Using longtests to reduce checking time, as per Bioc guidelines

mosdef 0.3.0

• Reordered the functions thematically into a better file naming structure
• Renaming of functions to better mirror their aim - e.g. topGOtable() -> run_topGO(), while also homogenizing the case

mosdef 0.2.0

• Vignette contains worked out examples for the whole package
• Added the de_table_painter() function

mosdef 0.1.0

• Changed the examples to macrophage, fixed minor bugs and added some parameters to the buttonifier function

mosdef 0.0.2

• Added new features (go_volcano, input_checks, de_volcano). Styled up the package and maybe more

mosdef 0.0.1

• Added the main functionality

mosdef 0.0.0.9000

• Added a NEWS.md file to track changes to the package.