NEWS
BatchQC 2.7.2
Minor Changes
- Changed maintainer from Jessica Anderson to Yaoan Leng
Minor Changes
- Added lambda example to Intro vignette
BatchQC 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
BatchQC 2.5.21
Major Changes
- Added Harman method in batch correction
BatchQC 2.5.20
Minor Changes
- Updated AIC to provide an overall metric
BatchQC 2.5.19
Minor Changes
- Added color to the generated kBET plots
BatchQC 2.5.18
Minor Changes
- Added summary statistics and p-values for explained variation boxplots
BatchQC 2.5.17
Major Changes
- Added edgeR negative binomial tests
Minor Changes
- Updated non-parametric (large sample) thresholds and adjusted p-value info
BatchQC 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
BatchQC 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
BatchQC 2.5.14
Minor Changes
- Added voom as a normalization method
Bug Fixes
- Corrected limma correction to allow 1 covariate
BatchQC 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
BatchQC 2.5.12
Minor Changes
- Fixed sva batch correction function
- Added covar to UMAP
BatchQC 2.5.11
Major Changes
- Allowed AIC function to take multiple covariates as input
BatchQC 2.5.10
Major Changes
- Added a new kBET tab for measuring batch effect presence
BatchQC 2.5.9
Major Changes
- Added AIC under batch correction tab
BatchQC 2.5.8
Major Changes
- Added svaseq as a batch correction method
BatchQC 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
BatchQC 2.5.6
Major Changes
- Added Kruskal-Wallis test as a differential expression analysis method
BatchQC 2.5.5
Major Changes
- Added ANOVA as a differential expression analysis method
BatchQC 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
BatchQC 2.5.3
Major Changes
Bug Fix
- Corrected log to be log(x+1) and changed CPM(x+1) to CPM(x)
BatchQC 2.5.2
Major Changes
- Added edgeR as a normalization method
- Added edgeR as a differential expression analysis method
BatchQC 2.5.1
Major Changes
Minor Changes
- Changed sapply to vapply in nb check
BatchQC 2.2.5
Minor Changes
- Added sva batch correction method (for unknown variation correction)
BatchQC 2.2.4
Major Changes
- Updated variation ratio analysis to be log transformed
- Added umap exploratory option
BatchQC 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
BatchQC 2.2.2
Minor Changes
- Updated SE object upload to allow assays of any name (no longer require one
assay to be called "counts")
BatchQC 2.2.1
Minor Changes
- Added pval information to the DESeq2 binomial evaluation
BatchQC 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
BatchQC 2.1.4
Major Changes
- Added negative binomial check for 20+ samples to DESeq2
BatchQC 2.1.3
Major Changes
- Added negative binomial check for less than 20 samples to DESeq2
BatchQC 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
BatchQC 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
BatchQC 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