v1.1.3

v1.1.3 - July 8^th 2026

• harmonize.batches(): added algorithm (ComBat/limma), ComBat.mode, and block; limma helps on sparse designs where ComBat hits a singular matrix
• harmonize.batches(): drop uncorrectable proteins with a warning, error on an empty result, and fix the algorithm/block defaults
• load.counts2 automatically converts the counts into log2 transformed.
• diff.analyses, diff.analyses.limma and diff.analyses.prolfqua now return, for each group, the standard deviation (sd.<group>) and standard error of the mean (sem.<group>) of the log2 expression values, plus lfcSE, the standard error of the log2(FoldChange). The new columns are appended at the end of the results table. lfcSE is NA when stat.test = "wilcoxon"
• updated manual and vignette accordingly to take into account for these exceptions and modifications

Full Changelog: 1.1.2...1.1.3