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

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

AuthorVJ Carey <stvjc@channing.harvard.edu>
Date of publicationNone
MaintainerVJ Carey <stvjc@channing.harvard.edu>
LicenseArtistic-2.0
Version5.10.0

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

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