Package: Pi
Type: Package
Title: Leveraging Genetic Evidence to Prioritise Drug Targets at the
        Gene and Pathway Level
Version: 2.8.0
Date: 2021-11-30
Author: Hai Fang, the ULTRA-DD Consortium, Julian C Knight
Maintainer: Hai Fang <hfang.shanghai@gmail.com>
Depends: igraph, dnet, ggplot2, graphics
Imports: Matrix, GenomicRanges, GenomeInfoDb, supraHex, scales,
        grDevices, ggrepel, ROCR, randomForest, glmnet, lattice, caret,
        plot3D, stats, methods, MASS, IRanges, BiocGenerics, dplyr,
        tidyr, ggnetwork, osfr, RCircos, purrr, readr, tibble
Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png,
        GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr,
        rtracklayer, ggbio, Gviz, data.tree, jsonlite
Description: Priority index or Pi is developed as a genomic-led target prioritisation system. It integrates functional genomic predictors, knowledge of network connectivity and immune ontologies to prioritise potential drug targets at the gene and pathway level.
URL: http://pi314.r-forge.r-project.org
BugReports: https://github.com/hfang-bristol/Pi/issues
Collate: 'ClassMethod-Pi.r' 'xRWR.r' 'xPier.r' 'xPierGenes.r'
        'xPierSNPs.r' 'xPierPathways.r' 'xPierManhattan.r'
        'xPierSubnet.r' 'xPierMatrix.r' 'xPierEvidence.r'
        'xPredictROCR.r' 'xPredictCompare.r' 'xContour.r'
        'xMLrandomforest.r' 'xPierSNPsAdv.r' 'xGSsimulator.r'
        'xMLdotplot.r' 'xMLdensity.r' 'xMLzoom.r' 'xPierGSEA.r'
        'xGSEAdotplot.r' 'xGSEAbarplot.r' 'xPierTrack.r'
        'xPierTrackAdv.r' 'xGSEAconciser.r' 'xPierAnno.r' 'xMLglmnet.r'
        'xMLfeatureplot.r' 'xMLparameters.r' 'xMLcaret.r'
        'xMLcompare.r' 'xPierCross.r' 'xVisEvidence.r' 'xPierROCR.r'
        'xMLrename.r' 'xVisEvidenceAdv.r' 'xCorrelation.r' 'xPierCor.r'
        'xPierGRs.r' 'xPierABF.r' 'xPierSNPsAdvABF.r'
        'xPierABFheatmap.r' 'xPierMRS.r' 'xHeatmap.r'
        'xCheckParallel.r' 'xDefineNet.r' 'xSNPscores.r'
        'xSNP2nGenes.r' 'xSNP2eGenes.r' 'xSNP2cGenes.r'
        'xSparseMatrix.r' 'xSM2DF.r' 'xDefineEQTL.r' 'xDefineHIC.r'
        'xEnricherGenes.r' 'xDefineOntology.r' 'xEnricher.r'
        'xDAGanno.r' 'xColormap.r' 'xSubneterGenes.r'
        'xSymbol2GeneID.r' 'xSNPlocations.r' 'xGR.r' 'xLiftOver.r'
        'xGGnetwork.r' 'xPieplot.r' 'xGR2xGeneScores.r' 'xGRscores.r'
        'xGR2xGenes.r' 'xGR2nGenes.r' 'xGRsort.r' 'xMEabf.r'
        'xRDataLoader.r' 'xAggregate.r' 'xGeneID2Symbol.r' 'xCircos.r'
        'xVisNet.r' 'xEnrichViewer.r' 'xVisKernels.r' 'xEnrichForest.r'
        'xCombineNet.r' 'xLayout.r' 'xConverter.r'
License: GPL-3
VignetteBuilder: knitr
biocViews: Software, Genetics, GraphAndNetwork, Pathways,
        GeneExpression, GeneTarget, GenomeWideAssociation,
        LinkageDisequilibrium, Network, HiC
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_15
git_last_commit: 019a211
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-27 00:25:21 UTC; biocbuild
Built: R 4.2.0; ; 2022-04-27 09:53:20 UTC; windows
