Changes in version 1.2.1 (2019-07-12) + norm_method paramter in multi_de_pairs to allow only EDASeq normalisation + make character output for annotation + remove prior normalisation for RUVr + fix buildSummarized bug in detection of minimum paired numbers + fix buildSummarized htseq with out of order rownames + add parameter to buildSummarized for technical_reps + technical_reps merges reads from technical replicates + change merged column name from p_max to p_intersect + change LogFC of merged results to mean(LogFC) of all methods + change AveExpr of merged results to mean(AveExpr) of all methods + addition of merged column name p_union (Union) + addition of merged column name LogFC_sd (Standard Deviation of FC) + updating plotting functions to add weight for LogFC_sd + add numbers for each category to legend of plots + disabled cooksCutoff for DESeq2 for comparability of all p-value rankings + add option gtf_annotate multi_de_pairs for annotation of gene symbols from gtf and combine with tx_db + update vignette Version 1.2.0 (BioC 3.9 update) Changes in version 1.0.7 (2019-03-01) + export RUV corrected summarized file before model fit + option to summarize read by transcript, exon or cds added to buildSummarized + added chromosome coordinates to annotation of merged results + include gtf or txdb as meta-data in summarized object + added option, htseq_dir, to import HTSEQ count files to buildSummarized + fixed sample_table format check (refactorise) Changes in version 1.0.6 (2019-12-31) + add legend and label option to multi_de_plots + fixing bug for paired mode model matrix in multi_de_pairs without RUV + update vignette Changes in version 1.0.5 (2019-12-16) + fixing first column name when writing tables for edgeR, Voom and DEseq + fixed RUV model coefficients carrying through Changes in version 1.0.4 (2019-12-12) + fixed ranking bug for combined data + adding min_p to merged tables Changes in version 1.0.3 (2019-12-10) + fixed ensembl_annotate option for multi_de_pairs + added BiocGenerics as depends Changes in version 1.0.2 (2019-12-09) + filter error update to buildSummarized + add error reporting with incorrect pairs or group numbers + add option to force_build to buildSummarized + fix color bug in diag_plots + fix annotation documentation for multi_de_pairs + update filter option to permit from summarized experiment + update vignette Changes in version 1.0.1 (2019-12-07) + Fixed bugs - build gtf from path Changes in version 1.0.0 (2018-11-01) + Submitted to Bioconductor