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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various changes to improve indexing in racExSet
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add doc for hla2set example
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various changes to improve indexing in racExSet
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internal for phasing
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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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ok
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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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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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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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ok
hbTestResults class introduced
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fix check on psid, be sure that mapped probeId lives in featureNames
fixed formula handling
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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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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.
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GGtools
minor
ok
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new approach to snp locations via GGdata dynamic exports
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passing check
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kill warnings
put the gene location in
fixed up gene-set based gwSnpScreen
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GGtools
various cleanup
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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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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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various to take snpMatrix 1.7 API
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various
masterSnps added
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GGtools
needed to address snpMatrix api changes in filtering of snpdepth() for genesets
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