addAei |
Add allele specific expression data to list |
addAntisense |
Add antisense transcript information to list |
addCisEqtl |
Add cis eQTL data to list |
addDnase |
Add data from Maurano et. al. Nat Genet. 2015 regarding allele specific DNAse hypersensitivty. |
addEnst |
Add transcript information to list |
addExpression |
Add RNAsequencing expression data list |
addGo |
Add gene ontology to list |
addGrasp |
Add GWAS data from GRASP to list |
addGwasCatalog |
Add GWAS data from NHGRI-EBI GWAS Catalog to list |
addLoc |
Add gene location information to list |
addPtv |
Add results from protein truncating variant algorithm made available by GTEx |
addPubmed |
Adds number of titles from Pubmed to list |
addSqtlAltrans |
Add results from Altrans splicingQTL algorithm to list |
addSqtlSeek |
Add results from SqtlSeek splicingQTL algorithm to list |
addTransEqtl |
Add trans eQTL data to list |
buildFromEnsgs |
Build empty list using ENSG gene ids. |
buildFromNames |
Build empty list using gene names. |
buildFromRegion |
Build empty list using genomic region. |
exampleMgl |
exampleMgl |
exMgl |
exMgl |
fixNames |
Fix genes with missing names |
fixSnpIds |
Convert chr_pos to rs id |
listElements |
Returns names of elements that are filled in |
listSeparate |
Returns an individual element for each gene |
makeAeiPlot |
Plot GTEx AEI ratios |
makeCoXpGene |
Tests pairwise co-expression for normalized expression data |
makeCoXpTranscript |
Tests pairwise co-expression between user defined transcripts in specified tissues |
makeDnaseSig |
Filter Dnase (Maurano) Results |
makeGo |
Returns a list with Gene Ontology data |
makeGoSearch |
Returns gene names with a given GO term |
makeMultiEqtl |
Returns SNPs identified as cis-eQTLs for more than one gene |
makeOverlap |
Returns SNPs that appear in two user-defined groups for a given gene |
makeOverlapTable |
Returns information for SNPs that appear in two user-defined groups for a given gene |
makePhenotypes |
Make list of GWAS-based traits |
makePhenotypeSearch |
Returns gene names with a given phenotype |
makeSnps |
Make SNP list |
makeSnpSearch |
Returns gene names with a given SNP |
makeSummary |
Returns a summary table of the number of eQTL and GWAS SNPs for each gene |
missNames |
Idenify genes with missing names |