R/library/qtl/sampledata/listeria_rot.csv
R/library/qtl/html/plotLodProfile.html
R/library/qtl/doc/Sources/geneticmaps.Rnw
R/library/qtl/html/summary.scantwo.html
R/library/qtl/html/drop.markers.html
R/library/qtl/doc/Sources/new_summary_scanone.Rnw
R/library/qtl/html/mqmscan.html
R/library/qtl/contrib/bin/scripts/create-diff.sh
R/library/qtl/html/effectplot.html
R/library/qtl/INSTALL_ME.txt
R/library/qtl/html/mqmplotsingletrait.html
R/library/qtl/html/subset.scantwo.html
R/library/qtl/html/chrlen.html
R/library/qtl/html/replacemap.scantwo.html
R/library/qtl/html/write.cross.html
R/library/qtl/html/bayesint.html
R/library/qtl/html/plot.qtl.html
R/library/qtl/data/locations.RData
R/library/qtl/doc/rqtltour.pdf
R/library/qtl/html/compareorder.html
R/library/qtl/html/mqmplotcofactors.html
R/library/qtl/data/hyper.RData
R/library/qtl/html/scantwopermhk.html
R/library/qtl/html/simPhyloQTL.html
R/library/qtl/html/scanPhyloQTL.html
R/library/qtl/contrib/bin/FindRLibs.cmake
R/library/qtl/R/qtl
R/library/qtl/contrib/bin/rtest/test_mqm_hyper_prob.R
R/library/qtl/LICENSE.txt
R/library/qtl/html/refineqtl.html
R/library/qtl/html/locations.html
R/library/qtl/html/stepwiseqtl.html
R/library/qtl/html/makeqtl.html
R/library/qtl/html/pull.map.html
R/library/qtl/html/phenames.html
R/library/qtl/doc/rqtltour.R
R/library/qtl/contrib/biolib/README
R/library/qtl/html/summary.map.html
R/library/qtl/contrib/bin/test/t12/cofactors.txt
R/library/qtl/html/pull.genoprob.html
R/library/qtl/html/scanoneboot.html
R/library/qtl/README.md
R/library/qtl/html/a.starting.point.html
R/library/qtl/contrib/bin/mqmmain.cpp
R/library/qtl/html/chrnames.html
R/library/qtl/html/summary.ripple.html
R/library/qtl/html/argmax.geno.html
R/library/qtl/html/summary.scanoneboot.html
R/library/qtl/html/fitstahl.html
R/library/qtl/contrib/bin/test/chrid.dat
R/library/qtl/html/summary.qtl.html
R/library/qtl/html/plot.missing.html
R/library/qtl/contrib/bin/test/t22/cofactors.txt
R/library/qtl/contrib/bin/test/std/settings2.txt
R/library/qtl/html/markernames.html
R/library/qtl/contrib/bin/test/std/genotypes1.txt
R/library/qtl/html/formMarkerCovar.html
R/library/qtl/contrib/bin/test/pheno.dat
R/library/qtl/html/mqmplotclusteredheatmap.html
R/library/qtl/contrib/bin/test/regression/t23out.txt
R/library/qtl/contrib/bin/test/regression/t12out.txt
R/library/qtl/html/convert.scanone.html
R/library/qtl/html/droponemarker.html
R/library/qtl/html/bristle3.html
R/library/qtl/doc/index.html
R/library/qtl/contrib/bin/test/chridhyper.txt
R/library/qtl/doc/Sources/MQM/mqm/significance_references.txt
R/library/qtl/html/subset.map.html
R/library/qtl/html/transformPheno.html
R/library/qtl/sampledata/listeria_qc_cro.txt
R/library/qtl/html/cim.html
R/library/qtl/html/totmar.html
R/library/qtl/html/nchr.html
R/library/qtl/contrib/bin/test/geno.dat
R/library/qtl/html/countXO.html
R/library/qtl/html/condense.scantwo.html
R/library/qtl/doc/new_summary_scanone.R
R/library/qtl/contrib/bin/test/std/phenotypes1.txt
R/library/qtl/html/calc.genoprob.html
R/library/qtl/html/ripple.html
R/library/qtl/doc/bcsft.R
R/library/qtl/html/read.cross.html
R/library/qtl/html/plot.scanoneperm.html
R/library/qtl/html/replacemap.scanone.html
R/library/qtl/contrib/bin/rtest/test_augmentation.R
R/library/qtl/html/addqtl.html
R/library/qtl/html/geno.image.html
R/library/qtl/html/find.markerpos.html
R/library/qtl/html/c.scanoneperm.html
R/library/qtl/html/plot.scantwo.html
R/library/qtl/html/mqmplotcircle.html
R/library/qtl/html/nmissing.html
R/library/qtl/html/mqmautocofactors.html
R/library/qtl/html/scanqtl.html
R/library/qtl/help/AnIndex
R/library/qtl/html/simulateMissingData.html
R/library/qtl/help/qtl.rdb
R/library/qtl/html/fake.f2.html
R/library/qtl/html/max.scantwo.html
R/library/qtl/html/mqmprocesspermutation.html
R/library/qtl/html/mqmplotheatmap.html
R/library/qtl/html/mqmsetcofactors.html
R/library/qtl/help/qtl.rdx
R/library/qtl/html/plot.scanoneboot.html
R/library/qtl/html/typingGap.html
R/library/qtl/html/mqmaugment.html
R/library/qtl/html/nphe.html
R/library/qtl/contrib/bin/test/regression/t11out.txt
R/library/qtl/html/geno.table.html
R/library/qtl/html/calc.penalties.html
R/library/qtl/MQM-TODO.txt
R/library/qtl/html/addpair.html
R/library/qtl/html/addloctocross.html
R/library/qtl/doc/Sources/MQM/mqm/advantages_Rd.txt
R/library/qtl/sampledata/listeria_qc_map.txt
R/library/qtl/html/c.scantwo.html
R/library/qtl/html/mqmscanall.html
R/library/qtl/doc/Sources/new_multiqtl.Rnw
R/library/qtl/contrib/bin/test/regression/t22out.txt
R/library/qtl/html/bristleX.html
R/library/qtl/html/c.scantwoperm.html
R/library/qtl/INDEX
R/library/qtl/html/interpPositions.html
R/library/qtl/html/map10.html
R/library/qtl/html/nmar.html
R/library/qtl/contrib/bin/test/settingshyper.txt
R/library/qtl/doc/geneticmaps.R
R/library/qtl/html/summary.cross.html
R/library/qtl/data/fake.bc.RData
R/library/qtl/html/drop.nullmarkers.html
R/library/qtl/html/max.scanPhyloQTL.html
R/library/qtl/html/arithscan.html
R/library/qtl/html/find.flanking.html
R/library/qtl/html/plot.geno.html
R/library/qtl/data/fake.f2.RData
R/library/qtl/data/badorder.RData
R/library/qtl/contrib/biolib/CMakeLists.txt
R/library/qtl/contrib/bin/test/markerpos.txt
R/library/qtl/contrib/bin/test/std/phenotypes2.txt
R/library/qtl/html/summary.fitqtl.html
R/library/qtl/html/inferredpartitions.html
R/library/qtl/NAMESPACE
R/library/qtl/html/inferFounderHap.html
R/library/qtl/html/00Index.html
R/library/qtl/html/R.css
R/library/qtl/html/sim.geno.html
R/library/qtl/html/clean.cross.html
R/library/qtl/contrib/scripts/repl_inputs.rb
R/library/qtl/data/mapthis.RData
R/library/qtl/html/addtoqtl.html
R/library/qtl/doc/new_summary_scantwo.R
R/library/qtl/doc/Sources/MQM/mqm/standard_example.txt
R/library/qtl/html/convert.map.html
R/library/qtl/html/drop.dupmarkers.html
R/library/qtl/html/mqmfind.marker.html
R/library/qtl/doc/bcsft.pdf
R/library/qtl/html/badorder.html
R/library/qtl/html/summary.scanoneperm.html
R/library/qtl/html/fake.4way.html
R/library/qtl/contrib/bin/test/std/genotypes2m.txt
R/library/qtl/html/summary.scanone.html
R/library/qtl/html/orderMarkers.html
R/library/qtl/html/cbind.scantwoperm.html
R/library/qtl/html/pull.pheno.html
R/library/qtl/help/aliases.rds
R/library/qtl/doc/geneticmaps.pdf
R/library/qtl/sampledata/listeria_raw.txt
R/library/qtl/contrib/bin/test/std/settings1.txt
R/library/qtl/html/listeria.html
R/library/qtl/html/lodint.html
R/library/qtl/html/geno.crosstab.html
R/library/qtl/html/plot.errorlod.html
R/library/qtl/contrib/bin/test/regression/t31out.txt
R/library/qtl/sampledata/listeria.csv
R/library/qtl/html/calc.errorlod.html
R/library/qtl/html/plot.rfmatrix.html
R/library/qtl/contrib/bin/test/regression/t24out.txt
R/library/qtl/contrib/bin/test/std/genotypes3m.txt
R/library/qtl/contrib/bin/test/genohyper.txt
R/library/qtl/html/scanonevar.html
R/library/qtl/html/allchrsplits.html
R/library/qtl/html/plot.pxg.html
R/library/qtl/BUGS.txt
R/library/qtl/contrib/bin/regressiontests.bat
R/library/qtl/contrib/bin/scripts/regression_tests_windows.bat
R/library/qtl/html/replaceqtl.html
R/library/qtl/html/effectscan.html
R/library/qtl/html/mqmpermutation.html
R/library/qtl/html/mqmextractmarkers.html
R/library/qtl/html/movemarker.html
R/library/qtl/html/scanone.html
R/library/qtl/html/simFounderSnps.html
R/library/qtl/help/paths.rds
R/library/qtl/sampledata/listeria.qtx
R/library/qtl/data/map10.RData
R/library/qtl/MD5
R/library/qtl/contrib/bin/test/std/settings3.txt
R/library/qtl/html/mqmscanfdr.html
R/library/qtl/html/getid.html
R/library/qtl/html/fake.bc.html
R/library/qtl/Meta/hsearch.rds
R/library/qtl/html/comparecrosses.html
R/library/qtl/html/plot.rf.html
R/library/qtl/html/nqtl.html
R/library/qtl/html/addcovarint.html
R/library/qtl/html/nind.html
R/library/qtl/Meta/links.rds
R/library/qtl/contrib/bin/test/std/genotypes3.txt
R/library/qtl/html/subset.scanoneperm.html
R/library/qtl/html/tryallpositions.html
R/library/qtl/html/mqmplotcistrans.html
R/library/qtl/html/scanonevar.varperm.html
R/library/qtl/contrib/bin/scripts/r.sh
R/library/qtl/html/pull.draws.html
R/library/qtl/html/summary.scanPhyloQTL.html
R/library/qtl/html/c.cross.html
R/library/qtl/contrib/scripts/update_header.rb
R/library/qtl/doc/Sources/MQM/mqm/parallelisation_references.txt
R/library/qtl/doc/Sources/MQM/mqm/limitations.txt
R/library/qtl/html/reorderqtl.html
R/library/qtl/Meta/data.rds
R/library/qtl/sampledata/listeria_phe.csv
R/library/qtl/html/checkAlleles.html
R/library/qtl/doc/rqtltour2.R
R/library/qtl/html/mqmgetmodel.html
R/library/qtl/html/pickMarkerSubset.html
R/library/qtl/html/plot.scantwoperm.html
R/library/qtl/contrib/bin/test/cofactors.txt
R/library/qtl/doc/Sources/MQM/MQM-tour.Rnw
R/library/qtl/contrib/scripts/cleanup.sh
R/library/qtl/html/findDupMarkers.html
R/library/qtl/contrib/bin/CMakeLists.txt
R/library/qtl/html/hyper.html
R/library/qtl/html/rescalemap.html
R/library/qtl/html/fitqtl.html
R/library/qtl/html/mapthis.html
R/library/qtl/contrib/bin/scripts/profiler.sh
R/library/qtl/contrib/bin/test/t23/cofactors.txt
R/library/qtl/contrib/bin/test/regression/t21out.txt
R/library/qtl/html/plot.scanPhyloQTL.html
R/library/qtl/contrib/bin/README
R/library/qtl/html/addmarker.html
R/library/qtl/html/locateXO.html
R/library/qtl/html/replace.map.html
R/library/qtl/contrib/bin/test/t33/cofactors.txt
R/library/qtl/html/mqmtestnormal.html
R/library/qtl/doc/bcsft.Rnw
R/library/qtl/contrib/bin/test/std/markers3.txt
R/library/qtl/html/c.scanone.html
R/library/qtl/html/dropfromqtl.html
R/library/qtl/html/est.rf.html
R/library/qtl/TODO.txt
R/library/qtl/contrib/bin/test/filledgenohyper.txt
R/library/qtl/html/subset.cross.html
R/library/qtl/html/pull.rf.html
R/library/qtl/contrib/bin/test/t11/cofactors.txt
R/library/qtl/doc/new_multiqtl.R
R/library/qtl/contrib/scripts/install_rqtl.sh
R/library/qtl/sampledata/phe.txt
R/library/qtl/contrib/bin/test/regression/t32out.txt
R/library/qtl/html/nqrank.html
R/library/qtl/contrib/scripts/run_all_tests.sh
R/library/qtl/html/find.pheno.html
R/library/qtl/html/cleanGeno.html
R/library/qtl/contrib/bin/scripts/regression_tests.sh
R/library/qtl/html/mqmplotdirectedqtl.html
R/library/qtl/sampledata/listeria_gen_rot.csv
R/library/qtl/html/formLinkageGroups.html
R/library/qtl/doc/Sources/new_summary_scantwo.Rnw
R/library/qtl/html/addint.html
R/library/qtl/sampledata/listeria_gen.csv
R/library/qtl/html/multitrait.html
R/library/qtl/html/map2table.html
R/library/qtl/html/clean.scantwo.html
R/library/qtl/contrib/bin/test/regression/t11out-test0.txt
R/library/qtl/html/markerlrt.html
R/library/qtl/sampledata/map.txt
R/library/qtl/html/scanonevar.meanperm.html
R/library/qtl/contrib/bin/mqmdebugout.cpp
R/library/qtl/html/plot.cross.html
R/library/qtl/Meta/vignette.rds
R/library/qtl/contrib/bin/test/settings.dat
R/library/qtl/data/bristle3.RData
R/library/qtl/Meta/package.rds
R/library/qtl/contrib/bin/rtest/test_scanone_mr.R
R/library/qtl/doc/Sources/rqtltour.tex
R/library/qtl/html/pull.markers.html
R/library/qtl/html/convert.scantwo.html
R/library/qtl/html/add.cim.covar.html
R/library/qtl/doc/Sources/MQM/mqm/advantages_latex.txt
R/library/qtl/html/plot.scanone.html
R/library/qtl/html/switchAlleles.html
R/library/qtl/doc/Sources/rqtltour2.tex
R/library/qtl/doc/Sources/MQM/sweaveit.bat
R/library/qtl/html/subset.scanone.html
R/library/qtl/R/qtl.rdb
R/library/qtl/contrib/bin/test/std/markers1.txt
R/library/qtl/R/qtl.rdx
R/library/qtl/doc/new_summary_scanone.pdf
R/library/qtl/html/ntyped.html
R/library/qtl/contrib/bin/test/phenohyper.txt
R/library/qtl/html/nullmarkers.html
R/library/qtl/data/fake.4way.RData
R/library/qtl/html/strip.partials.html
R/library/qtl/sampledata/listeria_maps.txt
R/library/qtl/html/find.marker.html
R/library/qtl/html/subset.scantwoperm.html
R/library/qtl/html/readMWril.html
R/library/qtl/sampledata/listeria_map.txt
R/library/qtl/html/max.scanone.html
R/library/qtl/html/pull.geno.html
R/library/qtl/html/table2map.html
R/library/qtl/html/fill.geno.html
R/library/qtl/contrib/bin/test/regression/t33out.txt
R/library/qtl/html/cbind.scanoneperm.html
R/library/qtl/contrib/bin/test/regression/debugout_dnorm.txt
R/library/qtl/doc/Sources/MQM/mqm/standard_seealso.txt
R/library/qtl/data/bristleX.RData
R/library/qtl/html/reduce2grid.html
R/library/qtl/sampledata/listeria_phe_rot.csv
R/library/qtl/html/pull.argmaxgeno.html
R/library/qtl/html/arithscanperm.html
R/library/qtl/doc/new_multiqtl.pdf
R/library/qtl/contrib/scripts/check_rqtl.sh
R/library/qtl/html/mqmplotmultitrait.html
R/library/qtl/html/xaxisloc.scanone.html
R/library/qtl/html/top.errorlod.html
R/library/qtl/html/convert2sa.html
R/library/qtl/libs/x64/qtl.dll
R/library/qtl/contrib/bin/test/std/markers2.txt
R/library/qtl/html/convert2risib.html
R/library/qtl/html/qtl-internal.html
R/library/qtl/html/summary.scantwoperm.html
R/library/qtl/contrib/bin/rtest/regression/scanone_mr.rtest
R/library/qtl/html/summary.scantwo.old.html
R/library/qtl/contrib/bin/rtest/regression/mqm_listeria1.rtest
R/library/qtl/doc/Sources/MQM/SweaveIt.R
R/library/qtl/contrib/bin/test/markerposhyper.txt
R/library/qtl/html/findmarkerindex.html
R/library/qtl/doc/new_summary_scantwo.pdf
R/library/qtl/html/mqmplotpermutations.html
R/library/qtl/html/shiftmap.html
R/library/qtl/html/find.pseudomarker.html
R/library/qtl/doc/Sources/MQM/mqm/standard_references.txt
R/library/qtl/html/convert2riself.html
R/library/qtl/html/qtlversion.html
R/library/qtl/contrib/bin/test/regression/t25out.txt
R/library/qtl/contrib/bin/scripts/cleanup.sh
R/library/qtl/html/groupclusteredheatmap.html
R/library/qtl/contrib/bin/test/std/phenotypes3.txt
R/library/qtl/doc/Sources/MQM/mqm/description.txt
R/library/qtl/html/sim.cross.html
R/library/qtl/contrib/bin/wincompile.bat
R/library/qtl/html/comparegeno.html
R/library/qtl/html/plot.info.html
R/library/qtl/contrib/bin/test/std/genotypes2.txt
R/library/qtl/contrib/bin/test/regression/debugout_pbeta.txt
R/library/qtl/html/sim.map.html
R/library/qtl/doc/Sources/MQM/sweaveit.sh
R/library/qtl/html/MQM.html
R/library/qtl/DESCRIPTION
R/library/qtl/html/plot.map.html
R/library/qtl/data/listeria.RData
R/library/qtl/html/scantwo.html
R/library/qtl/contrib/bin/test/regression/t13out.txt
R/library/qtl/html/plotModel.html
R/library/qtl/sampledata/README.txt
R/library/qtl/contrib/bin/test/regression/t34out.txt
R/library/qtl/contrib/bin/rtest/test_mqm_listeria1.R
R/library/qtl/CITATION
R/library/qtl/Meta/nsInfo.rds
R/library/qtl/html/jittermap.html
R/library/qtl/html/est.map.html
R/library/qtl/html/switch.order.html
R/library/qtl/html/add.threshold.html
R/library/qtl/Meta/Rd.rds
R/library/qtl/doc/rqtltour2.pdf
R/library/qtl/html/flip.order.html
R/library/qtl/data/multitrait.RData
R/library/qtl/STATUS.txt
R/library/qtl/sampledata/gen.txt
R/library/qtl/html/plot.pheno.html
