Files in PriceLab/TrenaProjectAD
AD gene expression and variant data
.gitignore
DESCRIPTION
NAMESPACE
R/TrenaProjectAD.R
README.md
explore/WGS-Harmonization/createCovariatesTable.R
explore/WGS-Harmonization/extractVariants.R
explore/WGS-Harmonization/metadata-all/MSBB_assay_wholeGenomeSeq_metadata.csv
explore/WGS-Harmonization/metadata-all/MSBB_biospecimen_metadata.csv
explore/WGS-Harmonization/metadata-all/MSBB_individual_metadata.csv
explore/WGS-Harmonization/metadata-all/MayoRNAseq_assay_wholeGenomeSeq_metadata.csv
explore/WGS-Harmonization/metadata-all/MayoRNAseq_biospecimen_metadata.csv
explore/WGS-Harmonization/metadata-all/MayoRNAseq_individual_metadata.csv
explore/WGS-Harmonization/metadata-all/ROSMAP_biospecimen_metadata.csv
explore/WGS-Harmonization/metadata-all/ROSMAP_clinical.csv
explore/WGS-Harmonization/metadata-all/ROSMAP_clinical_codebook.pdf
explore/WGS-Harmonization/pilra-region.vcf
explore/WGS-Harmonization/tbl.covariates.rna.vcf.RData
explore/WGS-Harmonization/vcfSampleNames.R
explore/ampad-1898-samples/vcf/createPathAgingTableForMax.R
explore/ampad-1898-samples/vcf/downloadVcfs.R
explore/ampad-1898-samples/vcf/makefile
explore/ampad-1898-samples/vcf/mayoPathAgingSamplesAnnotated.tsv
explore/ampad-1898-samples/vcf/notes.txt
explore/ampad-1898-samples/vcf/synapse-debug.txt
explore/ampad-1898-samples/vcf/vcf.1894.sample.names.RData
explore/ampad.eQTLS/#ldlr.R#
explore/ampad.eQTLS/ldlr-eqtls.RData
explore/ampad.eQTLS/ldlr-geno.RData
explore/ampad.eQTLS/ldlr.R
explore/ampad.eQTLS/mayo.cer.ldlr.csv
explore/ampad.eQTLS/mayo.tcx.ldlr.csv
explore/ampad.eQTLS/rosmap.dlpfc.ldlr.csv
explore/ampad.eQTLS/tbl.geno.eqtl.ldlr.RData
explore/gwasLociImport/williams-natureNeuroscience2020.RData
explore/gwasLociImport/williams-natureNeuroscience2020.tsv
explore/ldlr/defineRegulatoryRegions-ldlr.R
explore/ldlr/tbl.oc.ldlr.atac.eqtl.merged.RData
explore/mayo-epigenetics/atac/Genes_toCheck_100_inFig3.txt
explore/mayo-epigenetics/atac/dbaConsensusRegionsScored.74273x30.RData
explore/mayo-epigenetics/atac/diffbind-earlyExploration.R
explore/mayo-epigenetics/atac/displayPeak.R
explore/mayo-epigenetics/atac/earlyResultMayoWholeGenome.RData
explore/mayo-epigenetics/atac/mayoAllPeaks.1052789x4.RData
explore/mayo-epigenetics/atac/mayoAllPeaks.merged.96064x4.RData
explore/mayo-epigenetics/atac/mayoDemo-all.R
explore/mayo-epigenetics/atac/mayoSamples-all.csv
explore/mayo-epigenetics/atac/mayoSamples-chr19.csv
explore/mayo-epigenetics/atac/readAllPeaks.R
explore/mayo-epigenetics/progressReport-june-2021/.#bin1-haploreg-raw.txt
explore/mayo-epigenetics/progressReport-june-2021/27jun2021-motifbreakR-30eqtl-associated.RData
explore/mayo-epigenetics/progressReport-june-2021/apoe/apoe-tms.R
explore/mayo-epigenetics/progressReport-june-2021/apoe/firstLook.R
explore/mayo-epigenetics/progressReport-june-2021/apoe/jaspar2018-hocomocoCore.meme
explore/mayo-epigenetics/progressReport-june-2021/bin1-gh+atac-roi-trenaAndFimo.RData
explore/mayo-epigenetics/progressReport-june-2021/bin1-haploreg-cooked-01.txt
explore/mayo-epigenetics/progressReport-june-2021/bin1-haploreg-raw.txt
explore/mayo-epigenetics/progressReport-june-2021/bin1.R
explore/mayo-epigenetics/progressReport-june-2021/bin1.trena.fimo.230kroi.RData
explore/mayo-epigenetics/progressReport-june-2021/calcs-26jun.RData
explore/mayo-epigenetics/progressReport-june-2021/firstSurvey.R
explore/mayo-epigenetics/progressReport-june-2021/haploReg-output-allLeadVariants-raw.txt
explore/mayo-epigenetics/progressReport-june-2021/hapoloreg-oneAtac-raw.txt
explore/mayo-epigenetics/progressReport-june-2021/jaspar2018.meme
explore/mayo-epigenetics/progressReport-june-2021/leadVariants.txt
explore/mayo-epigenetics/progressReport-june-2021/rs4439906.tsv
explore/mayo-epigenetics/progressReport-june-2021/tbl.bin1.haplotype.snps.RData
explore/mayo-epigenetics/progressReport-june-2021/tbl.eqtls.all38genes.RData
explore/mayo-epigenetics/progressReport-june-2021/tmsCore.R
explore/mayo-epigenetics/progressReport-june-2021/tmsRunner.R
explore/picalm/haploreg-r2gt0.4-results.txt
explore/picalm/quickLook-picalm.R
explore/ptk2b/create.tbl.tms.R
explore/ptk2b/defineRegulatoryRegions-ptk2b.R
explore/ptk2b/justMayoMatrices.R
explore/ptk2b/ptk2b-eqtl-study.R
explore/ptk2b/ptk2b.R
explore/ptk2b/run.trenas.R
explore/ptk2b/scatterplots.R
explore/ptk2b/tms-ptk2b.R
explore/ptk2b/wtModel.R
explore/rbpPredicting/Predictor.R
explore/rbpPredicting/jasparHocomoco.meme
explore/rbpPredicting/makefile
explore/rbpPredicting/testPredictor.R
explore/rs4575098/AD-eqtls-near-rs4575098-threshold-1e-4.RData
explore/rs4575098/AD-eqtls-near-rs4575098-threshold-1e-5.RData
explore/rs4575098/AD-eqtls-near-rs4575098-threshold-1e-6.RData
explore/rs4575098/determineRegionForModel.R
explore/rs4575098/ndufs2/AD-eqtls-near-rs4575098-threshold-1e-4.RData
explore/rs4575098/ndufs2/AD-eqtls-near-rs4575098-threshold-1e-5.RData
explore/rs4575098/ndufs2/AD-eqtls-near-rs4575098-threshold-1e-6.RData
explore/rs4575098/ndufs2/allVariantsWithin1M.of.rs4575098.RData
explore/rs4575098/ndufs2/ndufs2-viz.R
explore/rs4575098/ndufs2/runTMS.R
explore/rs4575098/ndufs2/tbl.fimo.NDUFS2.RData
explore/rs4575098/ndufs2/trena.NDUFS2.RData
explore/rs4575098/rs4575098.R
explore/rs4575098/tmsCore.R
explore/rs4575098/tmsRunner.R
explore/trenaPaper/models.RData
explore/trenaPaper/trem2.R
inst/demo/tvAD.R
inst/extdata/covariates/.Rhistory
inst/extdata/covariates/AMP-AD_MayoBB_UFL-Mayo-ISB_IlluminaHiSeq2000_TCX_Covariates_Flowcell_1.csv
inst/extdata/covariates/covariates.RData
inst/extdata/expression/.Rhistory
inst/extdata/expression/Scaled_Winsorized_MayoRNAseq_TCX-ENSG.RData
inst/extdata/expression/cerebellum.15167x263.RData
inst/extdata/expression/gtex.v8/Brain_Amygdala.RData
inst/extdata/expression/gtex.v8/Brain_Anterior_cingulate_cortex_BA24.RData
inst/extdata/expression/gtex.v8/Brain_Caudate_basal_ganglia.RData
inst/extdata/expression/gtex.v8/Brain_Cerebellar_Hemisphere.RData
inst/extdata/expression/gtex.v8/Brain_Cerebellum.RData
inst/extdata/expression/gtex.v8/Brain_Cortex.RData
inst/extdata/expression/gtex.v8/Brain_Cortex.gtexV8.24821x205.RData
inst/extdata/expression/gtex.v8/Brain_Frontal_Cortex_BA9.RData
inst/extdata/expression/gtex.v8/Brain_Hippocampus.RData
inst/extdata/expression/gtex.v8/Brain_Hypothalamus.RData
inst/extdata/expression/gtex.v8/Brain_Nucleus_accumbens_basal_ganglia.RData
inst/extdata/expression/gtex.v8/Brain_Putamen_basal_ganglia.RData
inst/extdata/expression/gtex.v8/Brain_Spinal_cord_cervical_c-1.RData
inst/extdata/expression/gtex.v8/Brain_Substantia_nigra.RData
inst/extdata/expression/rosmap.14235x632.RData
inst/extdata/expression/temporalCortex.15167x264.RData
inst/extdata/genomeAnnotation/manifest.yaml
inst/extdata/genomeAnnotation/tbl.hiC.psychEncode.RData
inst/extdata/genomicRegions/boca-hg38-consensus-ATAC.RData
inst/extdata/genomicRegions/mayoAllPeaks.merged.96064x4.RData
inst/extdata/gwasLoci/#fixupAssociatedVariantsTable.R#
inst/extdata/gwasLoci/.#fixupAssociatedVariantsTable.R
inst/extdata/gwasLoci/fixUpTable.R
inst/extdata/gwasLoci/fixupAssociatedVariantsTable.R
inst/extdata/gwasLoci/hg19ToHg38.over.chain
inst/extdata/gwasLoci/notes.txt
inst/extdata/gwasLoci/posthuma-2020.xlsx
inst/extdata/gwasLoci/posthuma-38-loci.csv
inst/extdata/gwasLoci/supTable8-fineMap-990-genes.txt
inst/extdata/gwasLoci/supplementaryTable8-fineMap-3823-variants.tsv
inst/extdata/gwasLoci/tbl.posthuma-38-geneAssociations-curated-3828x12.RData
inst/extdata/gwasLoci/tbl.posthuma-38-geneAssociations-curated-3828x13.RData
inst/extdata/gwasLoci/tbl.posthuma-38-loci-curated.RData
inst/extdata/gwasLoci/testTables.R
inst/extdata/gwasLoci/williams-natureNeuroscience2020.RData
inst/extdata/regulatoryModels/tbl.model.RData
inst/extdata/variants/GWAS.snps.RData
inst/scripts/buildGeneInfoTable/.Rhistory
inst/scripts/buildGeneInfoTable/buildGeneInfoTable.R
inst/scripts/extractSnpsFromVCFs/extractByDiagnosis.R
inst/scripts/extractSnpsFromVCFs/inpp5d.AD.vcf.RData
inst/scripts/motifbreakR/oneSnp.R
inst/scripts/motifbreakR/results.chr:88884592:A:C.RData
inst/scripts/motifbreakR/snp.bed
inst/unitTests/test_TrenaProjectAD.R
makefile
man/TrenaProject-class.Rd
man/TrenaProjectAD-class.Rd
misc/multiScore/boca/tbl.boca.RData
misc/sgm/trem2.R
prep/bigFimo/from-khaleesi/tbl.fimo.B4GALT3.RData
prep/bigFimo/from-khaleesi/tbl.fimo.FCER1G.RData
prep/bigFimo/from-khaleesi/tbl.fimo.HSPA6.RData
prep/bigFimo/from-khaleesi/tbl.fimo.KLHDC9.RData
prep/bigFimo/from-khaleesi/tbl.fimo.NDUFS2.RData
prep/bigFimo/from-khaleesi/tbl.fimo.NIT1.RData
prep/bigFimo/from-khaleesi/tbl.fimo.PPOX.RData
prep/bigFimo/from-khaleesi/tbl.fimo.TSTD1.RData
