Changes in version 0.2.3 (2026-05-07)                  

Minor fix

  - Fixed an error associated with a unit test.

                 Changes in version 0.2.2 (2025-11-11)                  

Bug fix

  - Fixed a bug associated with the recent missForest update.

                 Changes in version 0.2.1 (2023-07-17)                  

Documentation updates

  - In previous versions, the functionality of the uniq_pep parameter
    (see create_df help page) was incorrectly described. We corrected
    the description to match its functionality as follows: "Numerical.
    Proteins that are identified by this number or fewer number of
    unique peptides are filtered out (default is 2).Only applies when
    input_type = "MaxQuant".

Bug fixes

  - In previous versions, volcano_plot function plotted
    "-log~10~(P-value)" on the y-axis by default even when sig = "adjP"
    and only colored the dots by their significance based on "adjP". In
    this version, sig = "adjP" shows "-log~10~.adj. P-value" on the
    y-axis and colors the dots by their "adjP" significance.

                 Changes in version 0.2.0 (2023-01-17)                  

New data types allowed

  - A new argument (data_type) added to the create_df function to
    accommodate other types of LFQ data (raw intensity, iBAQ).

A new input type added

  - A new argument input_type added to the create_df function to allow
    users to input data from a standard quantitative matrix.

Workflow changes

  - To allow for missing data imputation prior to or after data
    normalization step (depending on the imputation method used), the
    following changes were made:
      - norm_df and imp_df arguments replaced with a generic df argument
        in the functions, find_dep, impute_na, normalize_data, and
        heatmap_de
      - A note was added to the tutorials to clarify that for some
        imputation methods, such as the kNN method, data normalization
        should be performed prior to imputation.

Default machine learning algorithms

  - naive_bayes added to the default algorithm_list argument in the
    train_models function.

                 Changes in version 0.1.1 (2022-11-01)                  

Bug fixes

  - Fixes a minor issue with create_df when removing potential
    contaminants. The number of potential contaminants removed is now
    shown in the console.
  - Fixes an issue with find_dep that previously used a fixed value for
    the adj_method argument.
  - Fixes an issue with the file_path argument for saving the
    "TopHits.txt" file produced by the find_dep function.

Other changes

  - Citation file updated with the biorxiv preprint details.
  - Readme file updated with information on the Shiny App.
  - Help pages updated.

                 Changes in version 0.1.0 (2022-07-20)                  

  - First official release!