Changes in version 2.7.2 Minor Changes - Changed maintainer from Jessica Anderson to Yaoan Leng Minor Changes - Added lambda example to Intro vignette Changes in version 2.5.22 Major Changes - Updated AIC GoF to run lognormal and voom for nondiscrete data - Added a boxplot of the distribution of aic values to aic_compute - Added AIC_median value - Updated compute_aic to return a dataframe (rather than multiple) and a boxplox Minor Changes - Added Harman description to shiny interface - Added checkbox for advanced options for Harman Changes in version 2.5.21 Major Changes - Added Harman method in batch correction Changes in version 2.5.20 Minor Changes - Updated AIC to provide an overall metric Changes in version 2.5.19 Minor Changes - Added color to the generated kBET plots Changes in version 2.5.18 Minor Changes - Added summary statistics and p-values for explained variation boxplots Changes in version 2.5.17 Major Changes - Added edgeR negative binomial tests Minor Changes - Updated non-parametric (large sample) thresholds and adjusted p-value info Changes in version 2.5.16 Minor Changes - Updated negative binomial test to allow users to set the low sample threshold - Created place holders in negative binomial function for edgeR usability - Increased umap point size Changes in version 2.5.15 Minor Changes - Added "log_option" to UMAP to allow seamless UMAP plotting for counts data Bug Fixes - Reworked dendrogram_alpha_numeric_check to use is.numeric() instead of as.numeric() to avoid warning due to coercion Changes in version 2.5.14 Minor Changes - Added voom as a normalization method Bug Fixes - Corrected limma correction to allow 1 covariate Changes in version 2.5.13 Major Changes - Updated Vignette to reflect updates to BatchQC (distribution checks, kBET, UMAP) - Updated vignette example data to be TB data Minor Changes - Updated UMAP example to include covar option - Changed location of kBET tab Changes in version 2.5.12 Minor Changes - Fixed sva batch correction function - Added covar to UMAP 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