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GGtools
fixup dQuote issue
force updated GGBase
various extensions allowing GeneSet on lhs of formulae
introduced formula interface to control for confounders in phenoData
kill warnings

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GGtools
ok
working through invokePhase
depend on rpart
demo output file
various to support parsing Phase output

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GGtools
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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GGtools
various changes to improve indexing in racExSet

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GGtools
add doc for hla2set example

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GGtools
various changes to improve indexing in racExSet

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GGtools
internal for phasing

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GGtools
new personal haplotyping function (after running phase)
phase processing
trackSet support

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GGtools
minor update to depends on GGBase
support for phenoVar as
dependent variable
shut down the bioinfo supplement (eval=FALSE)

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GGtools
ok

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GGtools
interface to mapLD
mapLD interface added

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GGtools
Removed usage (or reference) to pstricks tex style in BioC vignettes.

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GGtools
various doc improvements to pass check cleanly on 2.8
pass on windows
ok
passing check on gladstone

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GGtools
improve annotation slot for 2021

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GGtools
Update GGtools in response to changes in rtracklayer. trackSet method
becomes coercion method from cwSnpScreenResult to RangedData. No
longer depends on rtracklayer; explicitly import IRanges.

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GGtools
ok

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GGtools
NEWS file, some additional GGexsite text
some added text
versions consistent?
helper
a helper Makevars version
going to configurable GGEXsite
ggexplorer.org stable for now
various items as we port GGEXsite
moving along
needed quotes
new configurable GGexplorer infrastructure

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GGtools
ok
hbTestResults class introduced

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GGtools
fix check on psid, be sure that mapped probeId lives in featureNames
fixed formula handling

[/GGtools] permanent link

GGtools
improvements to coalesce with encoDnaseI

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GGtools
improved class connecting to GGBase
move out old Rnw
fixups depend on GGBase
fixups to depend on GGBase
fixups to rely on GGBase

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GGtools
hbTests

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GGtools
ok

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GGtools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

[/GGtools] permanent link

GGtools
minor
ok

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GGtools
new approach to snp locations via GGdata dynamic exports

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GGtools
passing check

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GGtools
kill warnings
put the gene location in
fixed up gene-set based gwSnpScreen

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GGtools
various cleanup

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GGtools
various alterations to get multiGw screen in
improvements to coalesce with encoDnaseI

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GGtools
ok
various corrections related to annotating plots and supporting track export

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GGtools
Removed unneeded geneplotter dependency.

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GGtools
twSnpScreen added for transcriptome-wide snp screen
added pos method for snpMeta

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GGtools
various changes to facilitate gene sets and rendering improvements

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GGtools
improve topSnps

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GGtools
new support function
improved supp2SQLite
make sure it orders chromsomes suitably

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GGtools
pass chk
minor import change

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GGtools
various to take snpMatrix 1.7 API

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GGtools
various
masterSnps added

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GGtools
needed to address snpMatrix api changes in filtering of snpdepth() for genesets

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