NEWS

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consensusDE 1.5.1 (2019-12-03)

• strand_mode argument replaces ignore_strand in buildSummarized.
• fragments default in buildSummarized changed to FALSE
• update vignette

consensusDE 1.3.4 (2019-09-16)

• table_means function of multi_de_pairs updated to be n=1 aware
• add warning when less than two biological replicates

consensusDE 1.3.3 (2019-06-27)

• norm_method paramter in multi_de_pairs to allow only EDASeq normalisation

consensusDE 1.3.2 (2019-06-21)

• make character output for annotation
• remove prior normalisation for RUVr

consensusDE 1.3.1 (2019-06-18)

• 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 1.3.0 onwards is BioC 3.9

consensusDE 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)

consensusDE 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

consensusDE 1.0.5 (2019-12-16)

• fixing first column name when writing tables for edgeR, Voom and DEseq
• fixed RUV model coefficients carrying through

consensusDE 1.0.4 (2019-12-12)

• fixed ranking bug for combined data
• adding min_p to merged tables

consensusDE 1.0.3 (2019-12-10)

• fixed ensembl_annotate option for multi_de_pairs
• added BiocGenerics as depends

consensusDE 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

consensusDE 1.0.1 (2019-12-07)

• Fixed bugs - build gtf from path

consensusDE 1.0.0 (2018-11-01)

• Submitted to Bioconductor