Changes in version 1.5.3 - March 8, 2024 - add coef to zenithPR_gsa() Changes in version 1.5.2 - Feb 2, 2024 - resolve issue with renameing gene sets when multiple coefs are used Changes in version 1.5.1 - throw error when zenith is run on multiple coefs Changes in version 1.3.1 - user can specify organism Changes in version 1.1.2 - April 20, 2023 - fix warnings for limma Changes in version 1.1.1 - fix warnings Changes in version 1.0.7 - update docs Changes in version 1.0.6 - in zenith() set inter.gene.cor=0.01 to be default to be consistent with limma::camera Changes in version 1.0.5 - bug fix in zenith() when progressbar=FALSE Changes in version 1.0.3 - fix issue with corInGeneSet() when some residuals are NA Changes in version 1.0.2 - add zenithPR_gsa() - flag to disable correlation in zenith() Changes in version 1.0.1 - fixes to Bioconductor - improve documentation - get_GeneOntology() uses getGenesets(...,hierarchical=TRUE) Changes in version 1.0.0 - Improve documetation - fix bug with residuals Changes in version 0.99.13 - fix bug in degrees of freedom for zenith() null Changes in version 0.99.12 - update dependencies Changes in version 0.99.10 - replace recodeToList() since this functionality already exists - Upgrade t- MSigDB 7.2 - Update documentation Changes in version 0.99.9 - Update to address issues from https://github.com/Bioconductor/Contributions/issues/2630#issuecomment-1171369001 - zenith report error when squaredStats is TRUE Changes in version 0.99.8 - plotZenithResults() as default - Much faster loading of cached gene sets - enforce: - variancePartition (>= 1.19.16) - EnrichmentBrowser (>= 2.19.13) Changes in version 0.99.7 - update plotZenithResults_gg() - Enforce subsetting of residuals from MArrayLM Changes in version 0.99.6 - add plotZenithResults_gg() - zenith() now returns effect size and standard error - if squaredStats==TRUE, return PValue = p.greater Changes in version 0.99.5 - Fix small error caused by fit$method Changes in version 0.99.4 - zenith uses t statistical for fixed effect models and z.std for mixed effects Changes in version 0.99.3 - zenith now works when dream uses random effects - more accurate time in progress bar Changes in version 0.99.2 - fix documentation - add zenith_gsa() Changes in version 0.99.0 - submit to BioC