Version: 1.27
Text: library(hash) is going away in 2022, so we need to replace that
        functionality with native R 4.2 environments. Shouldn't impact
        users.

Version: 1.21
Text: changing some less than signs to less than or equal to, to ensure
        we get results.

Version: 1.21
Text: planning a refactor to handle other gene ID systems and example
        datasets. not done

Version: 1.15
Text: new legends in scatterplots.

Version: 1.15
Text: custom point colors in PCA plot function. uses
        sampleMeta$CustomColor and disables the built in legend.

Version: 1.15
Text: custom genes in plots. See ExtractProjection() very useful, not
        yet in vignette - it calculates a projection among your custom
        gene set.

Version: 1.15
Text: Add lfcThreshold to the DESeq routines, so the p-values are
        adjusted correctly. ( implemented 1.15.1 ) This changes the
        behavior of most of the system. Expect a different gene set.

Version: 1.15
Text: New option to INIT() called renormalize, allowing user to specify
        preferred matrix normalization schema rather than the default
        DESeq2::varianceStabilizingTransform (when renormalize=FALSE).

Version: 1.15
Text: uses p.adjust(method='BH') on GOSeq's results to shorten the GO
        term list. use the 'padj' column.

Version: 1.15
Text: New option to DESeq , vst with blind=TRUE/FALSE at user
        discretion.

Version: 1.15
Text: added CITATION FILE in 1.15.13

Version: 1.15
Text: tweaking vignette in 1.15.15 to debug bioconductor OSX
        build-server LaTeX versions. And 1.15.16, switching from
        biblatex to natbib.

Version: 1.11.5
Category: BUG FIXES
Text: updating dependencies caused a crash. Investigating. GO.db seems
        to no longer support double-brackets accessor. Refactored for
        GO.db 3.6.0's requirement of select()

Version: 1.11.2
Category: BUG FIXES
Text: updating dependencies caused a crash. Investigating. Biomart
        seems to no longer support "hsapiens_gene_ensembl"
        (sometimes/bug) Intermittent bug fixed in a later biomaRt
        edition.

Version: 1.11.2
Category: BUG FIXES
Text: R 3.5.0 support calls for a tweak in GOCatEngine.R

Version: 1.7.1
Category: BUG FIXES
Text: sampleMeta may load as factors, and uses strings later. To
        prevent possible sample-swapping, need to make all inputs as
        strings/notfactors. We can force this internally.

Version: 1.3.9
Category: BUG FIXES
Text: Dependency GOSeq 1.23.2 no longer supports gene ID system
        "refGene", so it has been changed to Entrez Gene IDs under the
        name "knownGene" instead. Merged gene tables now key off ENTREZ
        instead of REFSEQ. Now tested and built on R 3.3.0.

Version: 1.3.8
Category: FEATURE
Text: Adjusting the color thresholds for HMG diagram and Gamma scores
        to be properly scaled by dimensionality. Previous z-scoring
        method was occasionally making errors. Now a Gamma score of 1
        indicates the distance between centroids, which would otherwise
        naturally scale by the square root of the geneset dimension.

Version: 1.3.8
Category: FEATURE
Text: Updated Vignette

Version: 1.3.6
Category: FEATURE
Text: Simplified final output figure "HMG" and associated tables "HMG1"
        and "HMG2" calculate the distance to each centroid so the
        interpretation of results is simpler. Strong overlap to the HMA
        file.

Version: 1.3.6
Category: FEATURE
Text: Entries in the Vignette for this new 2 table output.

Version: 1.3.4
Category: BUG FIXES
Text: Dependency GenomicRanges no longer exports "assay()"

Version: 1.3.3
Category: Rebuilt for R 3.2.2
Text:

Version: 1.3.3
Category: BUG FIXES
Text: Biomart.org went down for "ensembl" late 2015. now we ask
        "www.ensembl.org" directly for their mart. Resolves some
        warnings, and fixes ID collection.

Version: 0.99.15
Category: BUG FIXES
Text: bugfix in gene ID systems passed to goseq.

Version: 0.99.12
Category: NEW FEATURES
Text: expanding user manuals to clarify how figures and clustering is
        performed.

Version: 0.99.11
Category: BUG FIXES
Text: bugfix in ProcessAll cardinality message.

Version: 0.99.11
Category: BUG FIXES
Text: Error catching around PCA.

Version: 0.99.11
Category: BUG FIXES
Text: Heatmap genelist now respects Annote_Filter file when LIMIT$HARD.

Version: 0.99.11
Category: BUG FIXES
Text: Cleaned up warnings when no rows for HMA.

Version: 0.99.11
Category: BUG FIXES
Text: Bugfix in PCA regarding non-negative definite covariance from
        princomp's eigen: replaced all instances with prcomp().

Version: 0.99.10
Category: BUG FIXES
Text: bugfix in G$LIMIT$baseMean and explanations of naming conventions
        in the vignette.

Version: 0.99.4
Category: SIGNIFICANT USER-VISIBLE CHANGES
Text: replacing DESeq with DESeq2 Fall2014

Version: 0.0.0
Category: NEW FEATURES
Text: Release package. Fall 2014.