[ol8_developer_EPEL] R-qtl-1.48.1-3.el8.aarch64

Name:	R-qtl
Version:	1.48.1
Release:	3.el8
Architecture:	aarch64
Group:	Unspecified
Size:	7469683
License:	GPLv3
RPM:	R-qtl-1.48.1-3.el8.aarch64.rpm
Source RPM:	R-qtl-1.48.1-3.el8.src.rpm
Build Date:	Wed Aug 18 2021
Build Host:	host-100-100-224-33.blddevtest1iad.osdevelopmeniad.oraclevcn.com
Vendor:	Oracle America
URL:	https://rqtl.org/
Summary:	Tools for analyzing QTL experiments
Description:	R-qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. Our goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing. A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. We have implemented the main HMM algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses. The current version of R-qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). One may also fit higher-order QTL models by multiple imputation and Haley-Knott regression.

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- usr
  - lib
    
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    25
    
    37beb2edad83b495f009770361b853014b4df4
  - lib64
    
    R
    
    library
    
    qtl
    
    BUGS.txt
    
    CITATION
    
    DESCRIPTION
    
    INDEX
    
    INSTALL_ME.txt
    
    MQM-TODO.txt
    
    Meta
    
    Rd.rds
    
    data.rds
    
    features.rds
    
    hsearch.rds
    
    links.rds
    
    nsInfo.rds
    
    package.rds
    
    vignette.rds
    
    NAMESPACE
    
    NEWS.md
    
    R
    
    qtl
    
    qtl.rdb
    
    qtl.rdx
    
    data
    
    badorder.RData
    
    bristle3.RData
    
    bristleX.RData
    
    fake.4way.RData
    
    fake.bc.RData
    
    fake.f2.RData
    
    hyper.RData
    
    listeria.RData
    
    locations.RData
    
    map10.RData
    
    mapthis.RData
    
    multitrait.RData
    
    doc
    
    Sources
    
    MQM
    
    MQM-tour.R
    
    MQM-tour.Rnw
    
    MQM-tour.tex
    
    SweaveIt.R
    
    SweaveIt.Rout
    
    mqm
    
    advantages_Rd.txt
    
    advantages_latex.txt
    
    description.txt
    
    limitations.txt
    
    parallelisation_references.txt
    
    significance_references.txt
    
    standard_example.txt
    
    standard_references.txt
    
    standard_seealso.txt
    
    sweaveit.bat
    
    sweaveit.sh
    
    geneticmaps.Rnw
    
    new_multiqtl.Rnw
    
    new_summary_scanone.Rnw
    
    new_summary_scantwo.Rnw
    
    rqtltour.tex
    
    rqtltour2.tex
    
    bcsft.R
    
    bcsft.Rnw
    
    bcsft.pdf
    
    geneticmaps.R
    
    geneticmaps.pdf
    
    index.html
    
    new_multiqtl.R
    
    new_multiqtl.pdf
    
    new_summary_scanone.R
    
    new_summary_scanone.pdf
    
    new_summary_scantwo.R
    
    new_summary_scantwo.pdf
    
    rqtltour.R
    
    rqtltour.pdf
    
    rqtltour2.R
    
    rqtltour2.pdf
    
    help
    
    +.scanone.html
    
    +.scanoneperm.html
    
    +.scantwo.html
    
    +.scantwoperm.html
    
    -.scanone.html
    
    -.scanoneperm.html
    
    -.scantwo.html
    
    -.scantwoperm.html
    
    AnIndex
    
    MQM.html
    
    [.cross.html
    
    [.map.html
    
    [.scanoneperm.html
    
    [.scantwoperm.html
    
    a.starting.point.html
    
    add.cim.covar.html
    
    add.threshold.html
    
    addcovarint.html
    
    addint.html
    
    addloctocross.html
    
    addmarker.html
    
    addmarkerstointervalmap.html
    
    addpair.html
    
    addqtl.html
    
    addtoqtl.html
    
    aliases.rds
    
    allchrsplits.html
    
    argmax.geno.html
    
    arithscan.html
    
    arithscanperm.html
    
    badorder.html
    
    bayesint.html
    
    bristle3.html
    
    bristleX.html
    
    c.cross.html
    
    c.scanone.html
    
    c.scanoneperm.html
    
    c.scantwo.html
    
    c.scantwoperm.html
    
    calc.errorlod.html
    
    calc.genoprob.html
    
    calc.penalties.html
    
    calc.plod.html
    
    cbind.scanone.html
    
    cbind.scanoneperm.html
    
    cbind.scantwo.html
    
    cbind.scantwoperm.html
    
    checkAlleles.html
    
    checkStepwiseqtlStart.html
    
    checkcovar.html
    
    checkformula.html
    
    chrlen.html
    
    chrnames.html
    
    cim.html
    
    clean.cross.html
    
    clean.html
    
    clean.scantwo.html
    
    cleanGeno.html
    
    comparecrosses.html
    
    comparegeno.html
    
    compareorder.html
    
    condense.html
    
    condense.scantwo.html
    
    convert.html
    
    convert.map.html
    
    convert.scanone.html
    
    convert.scantwo.html
    
    convert2bcsft.html
    
    convert2riself.html
    
    convert2risib.html
    
    convert2sa.html
    
    countXO.html
    
    countqtlterms.html
    
    create.map.html
    
    deparseQTLformula.html
    
    drop.dupmarkers.html
    
    drop.markers.html
    
    drop.nullmarkers.html
    
    dropfromqtl.html
    
    droponemarker.html
    
    effectplot.html
    
    effectscan.html
    
    est.map.html
    
    est.rf.html
    
    fake.4way.html
    
    fake.bc.html
    
    fake.f2.html
    
    fill.geno.html
    
    find.flanking.html
    
    find.marker.html
    
    find.markerindex.html
    
    find.markerpos.html
    
    find.pheno.html
    
    find.pseudomarker.html
    
    find.pseudomarkerpos.html
    
    findDupMarkers.html
    
    find_large_intervals.html
    
    findmarkerindex.html
    
    fitqtl.html
    
    fitqtlengine.html
    
    fitstahl.html
    
    flip.order.html
    
    flipcross.html
    
    formLinkageGroups.html
    
    formMarkerCovar.html
    
    genAllPartitions.html
    
    geno.crosstab.html
    
    geno.image.html
    
    geno.table.html
    
    getgenonames.html
    
    getid.html
    
    getsex.html
    
    groupclusteredheatmap.html
    
    hyper.html
    
    imf.cf.html
    
    imf.h.html
    
    imf.k.html
    
    imf.m.html
    
    imf.stahl.html
    
    inferFounderHap.html
    
    inferredpartitions.html
    
    interpPositions.html
    
    jittermap.html
    
    listeria.html
    
    locateXO.html
    
    locatemarker.html
    
    locations.html
    
    lodint.html
    
    makeqtl.html
    
    map10.html
    
    map2table.html
    
    mapthis.html
    
    markerlrt.html
    
    markernames.html
    
    matchchr.html
    
    max.scanPhyloQTL.html
    
    max.scanone.html
    
    max.scantwo.html
    
    max.scantwocondensed.html
    
    mf.cf.html
    
    mf.h.html
    
    mf.k.html
    
    mf.m.html
    
    mf.stahl.html
    
    movemarker.html
    
    mqm_version.html
    
    mqmaugment.html
    
    mqmautocofactors.html
    
    mqmextractmarkers.html
    
    mqmfind.marker.html
    
    mqmgetmodel.html
    
    mqmpermutation.html
    
    mqmplot.circle.html
    
    mqmplot.cistrans.html
    
    mqmplot.clusteredheatmap.html
    
    mqmplot.cofactors.html
    
    mqmplot.directedqtl.html
    
    mqmplot.heatmap.html
    
    mqmplot.multitrait.html
    
    mqmplot.permutations.html
    
    mqmplot.singletrait.html
    
    mqmplotcircle.html
    
    mqmplotcistrans.html
    
    mqmplotclusteredheatmap.html
    
    mqmplotcofactors.html
    
    mqmplotdirectedqtl.html
    
    mqmplotheatmap.html
    
    mqmplotmultitrait.html
    
    mqmplotpermutations.html
    
    mqmplotsingletrait.html
    
    mqmprocesspermutation.html
    
    mqmscan.html
    
    mqmscanall.html
    
    mqmscanfdr.html
    
    mqmsetcofactors.html
    
    mqmtestnormal.html
    
    multitrait.html
    
    nchr.html
    
    nind.html
    
    nmar.html
    
    nmissing.html
    
    nphe.html
    
    nqrank.html
    
    nqtl.html
    
    ntyped.html
    
    nullmarkers.html
    
    orderMarkers.html
    
    parseformula.html
    
    paths.rds
    
    phenames.html
    
    pickMarkerSubset.html
    
    plot.comparegeno.html
    
    plot.cross.html
    
    plot.errorlod.html
    
    plot.geno.html
    
    plot.info.html
    
    plot.map.html
    
    plot.missing.html
    
    plot.pheno.html
    
    plot.pxg.html
    
    plot.qtl.html
    
    plot.rf.html
    
    plot.rfmatrix.html
    
    plot.scanPhyloQTL.html
    
    plot.scanone.html
    
    plot.scanoneboot.html
    
    plot.scanoneperm.html
    
    plot.scantwo.html
    
    plot.scantwoperm.html
    
    plotErrorlod.html
    
    plotGeno.html
    
    plotInfo.html
    
    plotLodProfile.html
    
    plotMap.html
    
    plotMissing.html
    
    plotModel.html
    
    plotPXG.html
    
    plotPheno.html
    
    plotRF.html
    
    polyplot.html
    
    print.addcovarint.html
    
    print.addint.html
    
    print.compactqtl.html
    
    print.cross.html
    
    print.map.html
    
    print.qtl.html
    
    print.scanoneboot.html
    
    print.scantwo.html
    
    print.summary.addpair.html
    
    print.summary.compactqtl.html
    
    print.summary.comparegeno.html
    
    print.summary.cross.html
    
    print.summary.fitqtl.html
    
    print.summary.map.html
    
    print.summary.qtl.html
    
    print.summary.ripple.html
    
    print.summary.scanone.html
    
    print.summary.scanoneperm.html
    
    print.summary.scantwo.html
    
    print.summary.scantwo.old.html
    
    print.summary.scantwoperm.html
    
    pull.argmaxgeno.html
    
    pull.draws.html
    
    pull.geno.html
    
    pull.genoprob.html
    
    pull.map.html
    
    pull.markers.html
    
    pull.pheno.html
    
    pull.rf.html
    
    qtl-internal.html
    
    qtl-package.html
    
    qtl.rdb
    
    qtl.rdx
    
    qtlversion.html
    
    rbind.scanoneperm.html
    
    rbind.scantwoperm.html
    
    read.cross.html
    
    readMWril.html
    
    reduce2grid.html
    
    refineqtl.html
    
    reorderqtl.html
    
    replace.map.html
    
    replacemap.cross.html
    
    replacemap.html
    
    replacemap.scanone.html
    
    replacemap.scantwo.html
    
    replaceqtl.html
    
    rescalemap.html
    
    reviseXdata.html
    
    reviseqtlnuminformula.html
    
    ripple.html
    
    scanPhyloQTL.html
    
    scanall.html
    
    scanone.html
    
    scanoneboot.html
    
    scanonevar.html
    
    scanonevar.meanperm.html
    
    scanonevar.varperm.html
    
    scanqtl.html
    
    scantwo.html
    
    scantwopermhk.html
    
    shiftmap.html
    
    sim.cross.html
    
    sim.geno.html
    
    sim.map.html
    
    simFounderSnps.html
    
    simPhyloQTL.html
    
    simulateMissingData.html
    
    simulatemissingdata.html
    
    stepwiseqtl.html
    
    strip.partials.html
    
    subrousummaryscantwo.html
    
    subset.cross.html
    
    subset.map.html
    
    subset.scanone.html
    
    subset.scanoneperm.html
    
    subset.scantwo.html
    
    subset.scantwoperm.html
    
    summary.addcovarint.html
    
    summary.addint.html
    
    summary.compactqtl.html
    
    summary.comparegeno.html
    
    summary.cross.html
    
    summary.fitqtl.html
    
    summary.map.html
    
    summary.qtl.html
    
    summary.ripple.html
    
    summary.scanPhyloQTL.html
    
    summary.scanone.html
    
    summary.scanoneboot.html
    
    summary.scanoneperm.html
    
    summary.scantwo.html
    
    summary.scantwo.old.html
    
    summary.scantwocondensed.html
    
    summary.scantwoperm.html
    
    summaryMap.html
    
    summaryScantwoOld.html
    
    switch.order.html
    
    switchAlleles.html
    
    table2map.html
    
    top.errorlod.html
    
    totmar.html
    
    transformPheno.html
    
    tryallpositions.html
    
    typingGap.html
    
    write.cross.html
    
    xaxisloc.scanone.html
    
    html
    
    00Index.html
    
    MQM.html
    
    R.css
    
    a.starting.point.html
    
    add.cim.covar.html
    
    add.threshold.html
    
    addcovarint.html
    
    addint.html
    
    addloctocross.html
    
    addmarker.html
    
    addpair.html
    
    addqtl.html
    
    addtoqtl.html
    
    allchrsplits.html
    
    argmax.geno.html
    
    arithscan.html
    
    arithscanperm.html
    
    badorder.html
    
    bayesint.html
    
    bristle3.html
    
    bristleX.html
    
    c.cross.html
    
    c.scanone.html
    
    c.scanoneperm.html
    
    c.scantwo.html
    
    c.scantwoperm.html
    
    calc.errorlod.html
    
    calc.genoprob.html
    
    calc.penalties.html
    
    cbind.scanoneperm.html
    
    cbind.scantwoperm.html
    
    checkAlleles.html
    
    chrlen.html
    
    chrnames.html
    
    cim.html
    
    clean.cross.html
    
    clean.scantwo.html
    
    cleanGeno.html
    
    comparecrosses.html
    
    comparegeno.html
    
    compareorder.html
    
    condense.scantwo.html
    
    convert.map.html
    
    convert.scanone.html
    
    convert.scantwo.html
    
    convert2riself.html
    
    convert2risib.html
    
    convert2sa.html
    
    countXO.html
    
    drop.dupmarkers.html
    
    drop.markers.html
    
    drop.nullmarkers.html
    
    dropfromqtl.html
    
    droponemarker.html
    
    effectplot.html
    
    effectscan.html
    
    est.map.html
    
    est.rf.html
    
    fake.4way.html
    
    fake.bc.html
    
    fake.f2.html
    
    fill.geno.html
    
    find.flanking.html
    
    find.marker.html
    
    find.markerpos.html
    
    find.pheno.html
    
    find.pseudomarker.html
    
    findDupMarkers.html
    
    find_large_intervals.html
    
    findmarkerindex.html
    
    fitqtl.html
    
    fitstahl.html
    
    flip.order.html
    
    formLinkageGroups.html
    
    formMarkerCovar.html
    
    geno.crosstab.html
    
    geno.image.html
    
    geno.table.html
    
    getid.html
    
    groupclusteredheatmap.html
    
    hyper.html
    
    inferFounderHap.html
    
    inferredpartitions.html
    
    interpPositions.html
    
    jittermap.html
    
    listeria.html
    
    locateXO.html
    
    locations.html
    
    lodint.html
    
    makeqtl.html
    
    map10.html
    
    map2table.html
    
    mapthis.html
    
    markerlrt.html
    
    markernames.html
    
    max.scanPhyloQTL.html
    
    max.scanone.html
    
    max.scantwo.html
    
    movemarker.html
    
    mqmaugment.html
    
    mqmautocofactors.html
    
    mqmextractmarkers.html
    
    mqmfind.marker.html
    
    mqmgetmodel.html
    
    mqmpermutation.html
    
    mqmplotcircle.html
    
    mqmplotcistrans.html
    
    mqmplotclusteredheatmap.html
    
    mqmplotcofactors.html
    
    mqmplotdirectedqtl.html
    
    mqmplotheatmap.html
    
    mqmplotmultitrait.html
    
    mqmplotpermutations.html
    
    mqmplotsingletrait.html
    
    mqmprocesspermutation.html
    
    mqmscan.html
    
    mqmscanall.html
    
    mqmscanfdr.html
    
    mqmsetcofactors.html
    
    mqmtestnormal.html
    
    multitrait.html
    
    nchr.html
    
    nind.html
    
    nmar.html
    
    nmissing.html
    
    nphe.html
    
    nqrank.html
    
    nqtl.html
    
    ntyped.html
    
    nullmarkers.html
    
    orderMarkers.html
    
    phenames.html
    
    pickMarkerSubset.html
    
    plot.comparegeno.html
    
    plot.cross.html
    
    plot.errorlod.html
    
    plot.geno.html
    
    plot.info.html
    
    plot.map.html
    
    plot.missing.html
    
    plot.pheno.html
    
    plot.pxg.html
    
    plot.qtl.html
    
    plot.rf.html
    
    plot.rfmatrix.html
    
    plot.scanPhyloQTL.html
    
    plot.scanone.html
    
    plot.scanoneboot.html
    
    plot.scanoneperm.html
    
    plot.scantwo.html
    
    plot.scantwoperm.html
    
    plotLodProfile.html
    
    plotModel.html
    
    pull.argmaxgeno.html
    
    pull.draws.html
    
    pull.geno.html
    
    pull.genoprob.html
    
    pull.map.html
    
    pull.markers.html
    
    pull.pheno.html
    
    pull.rf.html
    
    qtl-internal.html
    
    qtlversion.html
    
    read.cross.html
    
    readMWril.html
    
    reduce2grid.html
    
    refineqtl.html
    
    reorderqtl.html
    
    replace.map.html
    
    replacemap.scanone.html
    
    replacemap.scantwo.html
    
    replaceqtl.html
    
    rescalemap.html
    
    ripple.html
    
    scanPhyloQTL.html
    
    scanone.html
    
    scanoneboot.html
    
    scanonevar.html
    
    scanonevar.meanperm.html
    
    scanonevar.varperm.html
    
    scanqtl.html
    
    scantwo.html
    
    scantwopermhk.html
    
    shiftmap.html
    
    sim.cross.html
    
    sim.geno.html
    
    sim.map.html
    
    simFounderSnps.html
    
    simPhyloQTL.html
    
    simulateMissingData.html
    
    stepwiseqtl.html
    
    strip.partials.html
    
    subset.cross.html
    
    subset.map.html
    
    subset.scanone.html
    
    subset.scanoneperm.html
    
    subset.scantwo.html
    
    subset.scantwoperm.html
    
    summary.comparegeno.html
    
    summary.cross.html
    
    summary.fitqtl.html
    
    summary.map.html
    
    summary.qtl.html
    
    summary.ripple.html
    
    summary.scanPhyloQTL.html
    
    summary.scanone.html
    
    summary.scanoneboot.html
    
    summary.scanoneperm.html
    
    summary.scantwo.html
    
    summary.scantwo.old.html
    
    summary.scantwoperm.html
    
    switch.order.html
    
    switchAlleles.html
    
    table2map.html
    
    top.errorlod.html
    
    totmar.html
    
    transformPheno.html
    
    tryallpositions.html
    
    typingGap.html
    
    write.cross.html
    
    xaxisloc.scanone.html
    
    libs
    
    qtl.so
    
    sampledata
    
    README.txt
    
    gen.txt
    
    listeria.csv
    
    listeria.qtx
    
    listeria_gen.csv
    
    listeria_gen_rot.csv
    
    listeria_map.txt
    
    listeria_maps.txt
    
    listeria_phe.csv
    
    listeria_phe_rot.csv
    
    listeria_qc_cro.txt
    
    listeria_qc_map.txt
    
    listeria_raw.txt
    
    listeria_rot.csv
    
    map.txt
    
    phe.txt