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Changelog

Source: NEWS.md

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.