GGtools: software and data for analyses in genetics of gene expression

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software and data for analyses in genetics of gene expression and/or DNA methylation

Author
VJ Carey <stvjc@channing.harvard.edu>
Date of publication
None
Maintainer
VJ Carey <stvjc@channing.harvard.edu>
License
Artistic-2.0
Version
5.10.0

View on Bioconductor

Man pages

All.cis
functions that compute score tests for all SNP cis to genes,...
appraise
appraisal for eQTL prediction models
b1
mcwBestCis instances, integrative analysis output containers...
best.cis.eQTLs
collect genewise best scoring eQTL
best.trans.eQTLs
collect strongest trans SNP-gene associations in a buffer of...
bindmaf
bind testing metadata to a best.cis.eQTLs result
cgff2dt
translate the GFF3 from a ciseqByCluster/processgff output...
cisAssoc
test for variant-expression associations in cis, using VCF
CisConfig-class
Class '"CisConfig"'
ciseqByCluster
end-to-end cluster-based cis-eQTL search, and allied...
cisRun-class
Class '"cisRun"'
collectBest
given a collection of All.cis outputs (cisRun instances)...
concatCis
combine a list of cisRun instances to a single instance
EqAppr-class
Class '"EqAppr"'
eqBox
descriptive plot of expression against genotype for cisAssoc...
eqsens_dt
support for sensitivity analyses related to eQTL enumerations
eqtlTests
compute association statistics between all probes and SNP in...
eqtlTestsManager-class
Class '"eqtlTestsManager"'
eqtlTests.me
use MatrixEQTL computations and statistics as a back end to...
ex
ExpressionSet instance for illustrating integrative smlSet...
getCisMap
create, using Bioconductor annotation resources, a structure...
gffprocess
transform a collection of gff3 into a single tabix-indexed...
GGtools-package
software and data for analyses in genetics of gene expression
gwSnpTests
execute a series of tests for association between genotype...
hmm878
labeled GRanges with ChromHMM chromatin states for GM12878
pifdr
utility for computing plug-in FDR
qqhex
obtain qqplot coordinates for the specific case of comparing...
richNull
bind metadata concerning SNP allele frequency and other...
sampsInVCF
enumerate samples available in a VCF file
scoresCis
visualize a gene model with cis-eQTL association scores (-log...
sensanal
Summarize information from a collection of eQTL searches for...
sensiCisInput-class
Class '"sensiCisInput"'
sensiCisOutput-class
Class '"sensiCisOutput"'
simpleTiling
create a GRanges with a tiling of the human genome
snplocsDefault
name the default SNPlocs.Hsapiens.dbSNP.* package
strMultPop
serialization of a table from Stranger's multipopulation eQTL...
TransConfig-class
Class '"TransConfig"'
transeqByCluster
convenience functions for trans-eQTL testing
transManager-class
Class '"transManager"'
transScores
obtain the top trans associations for each SNP in an smlSet
transTab
tabulate results of transScores run
vcf2sm
generate a SnpMatrix instance on the basis of a VCF (4.0)...

Files in this package

GGtools/DESCRIPTION
GGtools/NAMESPACE
GGtools/NEWS
GGtools/R
GGtools/R/AllClasses.R
GGtools/R/AllGenerics.R
GGtools/R/Eqappr.R
GGtools/R/alleq.R
GGtools/R/basicappraise.R
GGtools/R/best.trans.eQTLs.R
GGtools/R/bindmaf.R
GGtools/R/binqq.R
GGtools/R/cisConfig.R
GGtools/R/cisEqTools.R
GGtools/R/cisa.R
GGtools/R/eqME.R
GGtools/R/eqtlEstimates.R
GGtools/R/eqtlTests.R
GGtools/R/fdr.all.cis.R
GGtools/R/getFDR.R
GGtools/R/gffprocess.R
GGtools/R/gwSnpTests.R
GGtools/R/harvest.R
GGtools/R/managers.R
GGtools/R/meta.R
GGtools/R/meta.all.R
GGtools/R/meta.transScores.R
GGtools/R/modutils.R
GGtools/R/pifdr.R
GGtools/R/pureSensSoft.R
GGtools/R/relocate.R
GGtools/R/scan.R
GGtools/R/scoredist.R
GGtools/R/seqinfo.R
GGtools/R/snplocsDefault.R
GGtools/R/snpsCisToGenes.R
GGtools/R/summInfra.R
GGtools/R/thinclass.R
GGtools/R/topFeats.R
GGtools/R/topSnps.R
GGtools/R/transutils.R
GGtools/R/vcfutils.R
GGtools/README
GGtools/TODO.txt
GGtools/build
GGtools/build/vignette.rds
GGtools/data
GGtools/data/b1.rda
GGtools/data/b2.rda
GGtools/data/datalist
GGtools/data/eset.rda
GGtools/data/hg19.si.df.rda
GGtools/data/hmm878.rda
GGtools/data/lgeu.rda
GGtools/data/strMultPop.rda
GGtools/inst
GGtools/inst/CITATION
GGtools/inst/cloud
GGtools/inst/cloud/ciseqByCluster.R
GGtools/inst/cloud/newtest.R
GGtools/inst/doc
GGtools/inst/doc/GGtools.R
GGtools/inst/doc/GGtools.Rnw
GGtools/inst/doc/GGtools.pdf
GGtools/inst/extpacksupp
GGtools/inst/extpacksupp/DESCRIPTION.proto
GGtools/inst/extpacksupp/zzz.R
GGtools/inst/hapmap
GGtools/inst/hapmap/relationships_w_pops_051208.txt
GGtools/inst/hapmap/smallc20CEU.txt.gz
GGtools/inst/hapmap/src.rel.txt
GGtools/inst/oldRsrc
GGtools/inst/oldRsrc/X2chunk.R
GGtools/inst/oldRsrc/allS4.R
GGtools/inst/oldRsrc/bestCis.R
GGtools/inst/oldRsrc/bindScores.R
GGtools/inst/oldRsrc/cisFDR.R
GGtools/inst/oldRsrc/cisSnpTests.R
GGtools/inst/oldRsrc/cisgetter.R
GGtools/inst/oldRsrc/clipPCs.R
GGtools/inst/oldRsrc/comb.R
GGtools/inst/oldRsrc/egtset.R
GGtools/inst/oldRsrc/eqtlEstimates.R
GGtools/inst/oldRsrc/exome_minp.R
GGtools/inst/oldRsrc/externalize.R
GGtools/inst/oldRsrc/feqtltests.R
GGtools/inst/oldRsrc/filterCode.R
GGtools/inst/oldRsrc/fullsynth.R
GGtools/inst/oldRsrc/geneRanges.R
GGtools/inst/oldRsrc/geneTrack.R
GGtools/inst/oldRsrc/getTransScores.R
GGtools/inst/oldRsrc/gwSnpScreen.R
GGtools/inst/oldRsrc/interleave2cis.R
GGtools/inst/oldRsrc/machutils.R
GGtools/inst/oldRsrc/minp.R
GGtools/inst/oldRsrc/multff.R
GGtools/inst/oldRsrc/newEQTL.R
GGtools/inst/oldRsrc/pcc.R
GGtools/inst/oldRsrc/permEx.R
GGtools/inst/oldRsrc/probeloc.R
GGtools/inst/oldRsrc/regressOut.R
GGtools/inst/oldRsrc/scoresInRanges.R
GGtools/inst/oldRsrc/shiftRight.R
GGtools/inst/oldRsrc/snp130locs.R
GGtools/inst/oldRsrc/sumDirectors.R
GGtools/inst/oldRsrc/zzz.R
GGtools/inst/oldman
GGtools/inst/oldman/GGtools-package.Rd
GGtools/inst/oldman/X2chunk.Rd
GGtools/inst/oldman/best.cis.eQTLs.Rd
GGtools/inst/oldman/calfig.Rd
GGtools/inst/oldman/cisProxScores-class.Rd
GGtools/inst/oldman/cisProxScores.Rd
GGtools/inst/oldman/clipPCs.Rd
GGtools/inst/oldman/degnerASE01.Rd
GGtools/inst/oldman/dropMonomorphies.Rd
GGtools/inst/oldman/eqtlEstimatesManager-class.Rd
GGtools/inst/oldman/eqtlFDRtab-class.Rd
GGtools/inst/oldman/eqtlTests.Rd
GGtools/inst/oldman/eqtlTestsManager-class.Rd
GGtools/inst/oldman/ex6.Rd
GGtools/inst/oldman/exome_minp.Rd
GGtools/inst/oldman/externalize.Rd
GGtools/inst/oldman/geneIndcol.Rd
GGtools/inst/oldman/geneRanges.Rd
GGtools/inst/oldman/genewiseFDRtab.Rd
GGtools/inst/oldman/gwSnpTests.Rd
GGtools/inst/oldman/hla2set.Rd
GGtools/inst/oldman/hmceuB36.2021.Rd
GGtools/inst/oldman/imphm2_1KG_20.Rd
GGtools/inst/oldman/m20.Rd
GGtools/inst/oldman/makeCommonSNPs.Rd
GGtools/inst/oldman/manhPlot.Rd
GGtools/inst/oldman/mkCisTransDirector.Rd
GGtools/inst/oldman/mrefhap2sm.Rd
GGtools/inst/oldman/multiCisDirector-class.Rd
GGtools/inst/oldman/pcChooser.Rd
GGtools/inst/oldman/permEx.Rd
GGtools/inst/oldman/plot-methods.Rd
GGtools/inst/oldman/probeLocations.Rd
GGtools/inst/oldman/relocate.Rd
GGtools/inst/oldman/sm2ped.Rd
GGtools/inst/oldman/topSnps-methods.Rd
GGtools/inst/oldman/transManager-class.Rd
GGtools/inst/oldman/transScores.Rd
GGtools/inst/oldman/transTab.Rd
GGtools/inst/oldman/vcf2sm-methods.Rd
GGtools/inst/oldman/vcf2sm.Rd
GGtools/inst/parts
GGtools/inst/parts/20.rda
GGtools/inst/parts/21.rda
GGtools/inst/provenance
GGtools/inst/provenance/human
GGtools/inst/provenance/human/doallgzOct17b.R
GGtools/inst/provenance/human/getall.sh
GGtools/inst/provenance/human/notes.txt
GGtools/inst/provenance/mouse
GGtools/inst/provenance/mouse/notes.txt
GGtools/inst/pup
GGtools/inst/pup/combn238_chr6.pup
GGtools/inst/rdas
GGtools/inst/rdas/ceu_21.rda
GGtools/inst/rdas/ceu_22.rda
GGtools/inst/scripts
GGtools/inst/scripts/lkme.Rnw
GGtools/inst/scripts/lkme.pdf
GGtools/inst/vcf
GGtools/inst/vcf/CEU.exon.2010_09.genotypes.vcf.gz
GGtools/inst/vcf/CEU.exon.2010_09.genotypes.vcf.gz.tbi
GGtools/inst/vcf/c20exch.vcf.gz
GGtools/inst/vcf/c20exch.vcf.gz.tbi
GGtools/inst/vcf/provenance.txt
GGtools/inst/vcf/valid-4.0.vcf.gz
GGtools/man
GGtools/man/All.cis.Rd
GGtools/man/CisConfig-class.Rd
GGtools/man/EqAppr-class.Rd
GGtools/man/GGtools-package.Rd
GGtools/man/TransConfig-class.Rd
GGtools/man/appraise.Rd
GGtools/man/b1.Rd
GGtools/man/best.cis.eQTLs.Rd
GGtools/man/best.trans.eQTLs.Rd
GGtools/man/bindmaf.Rd
GGtools/man/cgff2dt.Rd
GGtools/man/cisAssoc.Rd
GGtools/man/cisRun-class.Rd
GGtools/man/ciseqByCluster.Rd
GGtools/man/collectBest.Rd
GGtools/man/concatCis.Rd
GGtools/man/eqBox.Rd
GGtools/man/eqsens_dt.Rd
GGtools/man/eqtlTests.Rd
GGtools/man/eqtlTests.me.Rd
GGtools/man/eqtlTestsManager-class.Rd
GGtools/man/ex.Rd
GGtools/man/getCisMap.Rd
GGtools/man/gffprocess.Rd
GGtools/man/gwSnpTests.Rd
GGtools/man/hmm878.Rd
GGtools/man/pifdr.Rd
GGtools/man/qqhex.Rd
GGtools/man/richNull.Rd
GGtools/man/sampsInVCF.Rd
GGtools/man/scoresCis.Rd
GGtools/man/sensanal.Rd
GGtools/man/sensiCisInput-class.Rd
GGtools/man/sensiCisOutput-class.Rd
GGtools/man/simpleTiling.Rd
GGtools/man/snplocsDefault.Rd
GGtools/man/strMultPop.Rd
GGtools/man/transManager-class.Rd
GGtools/man/transScores.Rd
GGtools/man/transTab.Rd
GGtools/man/transeqByCluster.Rd
GGtools/man/vcf2sm.Rd
GGtools/tests
GGtools/tests/cis.R
GGtools/tests/eqvgwst.R
GGtools/tests/f2.fdr.rda
GGtools/tests/f2.score.rda
GGtools/tests/test.meqtlTests.R
GGtools/tests/test.meta.trans.R
GGtools/tests/testCisMap.R
GGtools/tests/testTrans.R
GGtools/vignettes
GGtools/vignettes/GGtools.Rnw
GGtools/vignettes/cpne1Brow.pdf
GGtools/vignettes/ggtvig.bib