- Added sva batch correction method (for unknown variation correction)
- Updated variation ratio analysis to be log transformed
- Added umap exploratory option
- Added limma as a batch correction
- Added umap plot option
- Added ellipses to pca plot
- Set p-val plot x scale to always be 0 to 1
- Removed Intercept from p-val violin plots
- Updated SE object upload to allow assays of any name (no longer require one assay to be called "counts")
- Added pval information to the DESeq2 binomial evaluation
- Corrected code for proper division of less than or 20+ samples
#Version 2.1.5
- Coerce variable of interest to a factor
- Added negative binomial check for 20+ samples to DESeq2
- Added negative binomial check for less than 20 samples to DESeq2
- Added Variation Ratio Statistic to the explained variation tab
- Removed extra "Samples" column from example data
- Uploaded bladder example data batch variable as a factor
- Updated imports to include shinyjs
- Updated imports to remove dendextend which is no longer utilized
- Corrected typos in Intro vignette
- Fixed various errors for the Bioconductor build
- Created interactive Shiny interface
- Allow user upload of data
- Allow user download of Batch corrected and/or normalized data
- Added Example Data Functionality
- Added a
NEWS.mdfile to track changes to the package.
- Added
dendrogram_color_palette.Rfor coloring dendrogram - Updated
dendrogram.Rallowing batch & category to plot together