Changes in version 2.5.12                        

Minor Changes

  - Fixed sva batch correction function

                       Changes in version 2.5.11                        

Major Changes

  - Allowed AIC function to take multiple covariates as input

                       Changes in version 2.5.10                        

Major Changes

  - Added a new kBET tab for measuring batch effect presence

                        Changes in version 2.5.9                        

Major Changes

  - Added AIC under batch correction tab

                        Changes in version 2.5.8                        

Major Changes

  - Added svaseq as a batch correction method

                        Changes in version 2.5.7                        

Minor Changes

  - Added a data onject with subject IDs and BMI info to match the
    original study with the curatedTBData info and provide missing BMI
    info

                        Changes in version 2.5.6                        

Major Changes

  - Added Kruskal-Wallis test as a differential expression analysis
    method

                        Changes in version 2.5.5                        

Major Changes

  - Added ANOVA as a differential expression analysis method

                        Changes in version 2.5.4                        

Major Changes

  - Redesigned tab flow; upload tab reduced, batch correction tab
    created, and lambda stat and neg binomial distribution check moved
    to appropriate tabs

Minor Changes

  - Updated lambda statistic to provide a recommendation and to check
    for balanced experimental design
  - Abbreviated Normalization usage description

Bug Fix

  - Updated "counts" language to "assay" for uploaded data

                        Changes in version 2.5.3                        

Major Changes

  - Added lambda statistic

Bug Fix

  - Corrected log to be log(x+1) and changed CPM(x+1) to CPM(x)

                        Changes in version 2.5.2                        

Major Changes

  - Added edgeR as a normalization method
  - Added edgeR as a differential expression analysis method

                        Changes in version 2.5.1                        

Major Changes

  - Added TB data example

Minor Changes

  - Changed sapply to vapply in nb check

                        Changes in version 2.2.5                        

Minor Changes

  - Added sva batch correction method (for unknown variation correction)

                        Changes in version 2.2.4                        

Major Changes

  - Updated variation ratio analysis to be log transformed
  - Added umap exploratory option

                        Changes in version 2.2.3                        

Major Changes

  - Added limma as a batch correction
  - Added umap plot option
  - Added ellipses to pca plot

Minor Changes

  - Set p-val plot x scale to always be 0 to 1
  - Removed Intercept from p-val violin plots

                        Changes in version 2.2.2                        

Minor Changes

  - Updated SE object upload to allow assays of any name (no longer
    require one assay to be called "counts")

                        Changes in version 2.2.1                        

Minor Changes

  - Added pval information to the DESeq2 binomial evaluation

                        Changes in version 2.1.6                        

Bug Fixes

  - Corrected code for proper division of less than or 20+ samples

#Version 2.1.5

bug Fixes

  - Coerce variable of interest to a factor

                        Changes in version 2.1.4                        

Major Changes

  - Added negative binomial check for 20+ samples to DESeq2

                        Changes in version 2.1.3                        

Major Changes

  - Added negative binomial check for less than 20 samples to DESeq2

                        Changes in version 2.1.2                        

Major Changes

  - Added Variation Ratio Statistic to the explained variation tab

Minor Changes

  - Removed extra "Samples" column from example data
  - Uploaded bladder example data batch variable as a factor

                        Changes in version 2.1.1                        

Bug Fixes

  - Updated imports to include shinyjs
  - Updated imports to remove dendextend which is no longer utilized
  - Corrected typos in Intro vignette

                        Changes in version 2.0.0                        

Bug Fixes

  - Fixed various errors for the Bioconductor build

Major Changes

  - Created interactive Shiny interface
  - Allow user upload of data
  - Allow user download of Batch corrected and/or normalized data
  - Added Example Data Functionality

Minor Changes

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

Changes made to dendrogram

  - Added dendrogram_color_palette.R for coloring dendrogram
  - Updated dendrogram.R allowing batch & category to plot together