NEWS.md

In GabrielHoffman/zenith: Gene set analysis following differential expression using linear (mixed) modeling with dream

zenith 1.5.3

• March 8, 2024
• add coef to zenithPR_gsa()

# zenith 1.5.2 - Feb 2, 2024 - resolve issue with renameing gene sets when multiple coefs are used

zenith 1.5.1

• throw error when zenith is run on multiple coefs

zenith 1.3.1

• user can specify organism

zenith 1.1.2

• April 20, 2023
• fix warnings for limma

zenith 1.1.1

• fix warnings

zenith 1.0.2

• add zenithPR_gsa()

zenith 1.0.1

• fixes to Bioconductor

zenith 0.99.13

• fix bug in degrees of freedom for zenith() null

zenith 0.99.12

• update dependencies

zenith 0.99.10

• replace recodeToList() since this functionality already exists

zenith 0.99.9

• Update to address issues from https://github.com/Bioconductor/Contributions/issues/2630#issuecomment-1171369001

zenith 0.99.8

• plotZenithResults() as default

zenith 0.99.7

• update plotZenithResults_gg()

zenith 0.99.6

• add plotZenithResults_gg()

zenith 0.99.2

• fix documentation
• add zenith_gsa()

zenith 0.99.0

• submit to BioC

zenith 1.0.7

• update docs

zenith 1.0.6

• in zenith() set inter.gene.cor=0.01 to be default to be consistent with limma::camera

zenith 1.0.5

• bug fix in zenith() when progressbar=FALSE

zenith 1.0.3

• fix issue with corInGeneSet() when some residuals are NA

zenith 1.0.2

• flag to disable correlation in zenith()

zenith 1.0.1

• improve documentation
• get_GeneOntology() uses getGenesets(...,hierarchical=TRUE)

zenith 1.0.0

• Improve documetation
• fix bug with residuals

zenith 0.99.10

• Upgrade t- MSigDB 7.2

zenith 0.99.10

• Update documentation

zenith 0.99.9

• zenith report error when squaredStats is TRUE

zenith 0.99.8

• Much faster loading of cached gene sets
• enforce:
• variancePartition (>= 1.19.16)
• EnrichmentBrowser (>= 2.19.13)

zenith 0.99.7

• Enforce subsetting of residuals from MArrayLM

zenith 0.99.6

• zenith() now returns effect size and standard error
• if squaredStats==TRUE, return PValue = p.greater

zenith 0.99.5

• Fix small error caused by fit$method

zenith 0.99.4

• zenith uses t statistical for fixed effect models and z.std for mixed effects

zenith 0.99.3

• zenith now works when dream uses random effects
• more accurate time in progress bar

GabrielHoffman/zenith documentation built on March 10, 2024, 11:43 p.m.