Last updated: 2020-04-08

Checks: 7 0

Knit directory: Comparative_APA/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20190902)

The command set.seed(20190902) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 2f5d4d5

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/chimp_log/
    Ignored:    code/human_log/
    Ignored:    data/.DS_Store
    Ignored:    data/TrialFiltersMeta.txt.sb-9845453e-R58Y0Q/
    Ignored:    data/mediation_prot/
    Ignored:    data/metadata_HCpanel.txt.sb-a5794dd2-i594qs/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  ._.DS_Store
    Untracked:  Chimp/
    Untracked:  Human/
    Untracked:  analysis/CrossChimpThreePrime.Rmd
    Untracked:  analysis/DiffTransProtvsExpression.Rmd
    Untracked:  analysis/DiffUsedUTR.Rmd
    Untracked:  analysis/GvizPlots.Rmd
    Untracked:  analysis/HandC.TvN
    Untracked:  analysis/PhenotypeOverlap10.Rmd
    Untracked:  analysis/annotationBias.Rmd
    Untracked:  analysis/assessReadQual.Rmd
    Untracked:  analysis/diffExpressionPantro6.Rmd
    Untracked:  code/._AlignmentScores.sh
    Untracked:  code/._BothFCMM.sh
    Untracked:  code/._BothFCMMPrim.sh
    Untracked:  code/._BothFCnewOInclusive.sh
    Untracked:  code/._ChimpStarMM2.sh
    Untracked:  code/._ClassifyLeafviz.sh
    Untracked:  code/._ClosestorthoEx.sh
    Untracked:  code/._Config_chimp.yaml
    Untracked:  code/._Config_chimp_full.yaml
    Untracked:  code/._Config_human.yaml
    Untracked:  code/._ConvertJunc2Bed.sh
    Untracked:  code/._CountNucleotides.py
    Untracked:  code/._CrossMapChimpRNA.sh
    Untracked:  code/._CrossMapThreeprime.sh
    Untracked:  code/._DiffSplice.sh
    Untracked:  code/._DiffSplicePlots.sh
    Untracked:  code/._DiffSplicePlots_gencode.sh
    Untracked:  code/._DiffSplice_gencode.sh
    Untracked:  code/._DiffSplice_removebad.sh
    Untracked:  code/._Filter255MM.sh
    Untracked:  code/._FilterPrimSec.sh
    Untracked:  code/._FindIntronForDomPAS.sh
    Untracked:  code/._FindIntronForDomPAS_DF.sh
    Untracked:  code/._GetMAPQscore.py
    Untracked:  code/._GetSecondaryMap.py
    Untracked:  code/._Lift5perPAS.sh
    Untracked:  code/._LiftFinalChimpJunc2Human.sh
    Untracked:  code/._LiftOrthoPAS2chimp.sh
    Untracked:  code/._MapBadSamples.sh
    Untracked:  code/._MismatchNumbers.sh
    Untracked:  code/._PAS_ATTAAA.sh
    Untracked:  code/._PAS_ATTAAA_df.sh
    Untracked:  code/._PAS_seqExpanded.sh
    Untracked:  code/._PASsequences.sh
    Untracked:  code/._PASsequences_DF.sh
    Untracked:  code/._PlotNuclearUsagebySpecies.R
    Untracked:  code/._PlotNuclearUsagebySpecies_DF.R
    Untracked:  code/._QuantMergedClusters.sh
    Untracked:  code/._RNATranscriptDTplot.sh
    Untracked:  code/._ReverseLiftFilter.R
    Untracked:  code/._RunFixLeafCluster.sh
    Untracked:  code/._RunNegMCMediation.sh
    Untracked:  code/._RunNegMCMediationDF.sh
    Untracked:  code/._RunPosMCMediationDF.err
    Untracked:  code/._RunPosMCMediationDF.sh
    Untracked:  code/._SAF2Bed.py
    Untracked:  code/._Snakefile
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._SnakefilePASfilt
    Untracked:  code/._SortIndexBadSamples.sh
    Untracked:  code/._StarMM2.sh
    Untracked:  code/._TestFC.sh
    Untracked:  code/._assignPeak2Intronicregion
    Untracked:  code/._assignPeak2Intronicregion.sh
    Untracked:  code/._bed215upbed.py
    Untracked:  code/._bed2Bedbothstrand.py
    Untracked:  code/._bed2SAF_gen.py
    Untracked:  code/._buildIndecpantro5
    Untracked:  code/._buildIndecpantro5.sh
    Untracked:  code/._buildLeafviz.sh
    Untracked:  code/._buildLeafviz_leadAnno.sh
    Untracked:  code/._buildStarIndex.sh
    Untracked:  code/._chimpChromprder.sh
    Untracked:  code/._chimpMultiCov.sh
    Untracked:  code/._chimpMultiCov255.sh
    Untracked:  code/._chimpMultiCovInclusive.sh
    Untracked:  code/._chooseSignalSite.py
    Untracked:  code/._cleanbed2saf.py
    Untracked:  code/._cluster.json
    Untracked:  code/._cluster2bed.py
    Untracked:  code/._clusterLiftReverse.sh
    Untracked:  code/._clusterLiftReverse_removebad.sh
    Untracked:  code/._clusterLiftprimary.sh
    Untracked:  code/._clusterLiftprimary_removebad.sh
    Untracked:  code/._converBam2Junc.sh
    Untracked:  code/._converBam2Junc_removeBad.sh
    Untracked:  code/._extraSnakefiltpas
    Untracked:  code/._extractPhyloReg.py
    Untracked:  code/._extractPhyloRegGene.py
    Untracked:  code/._extractPhylopGeneral.ph
    Untracked:  code/._extractPhylopGeneral.py
    Untracked:  code/._extractPhylopReg200down.py
    Untracked:  code/._extractPhylopReg200up.py
    Untracked:  code/._filter5percPAS.py
    Untracked:  code/._filterNumChroms.py
    Untracked:  code/._filterPASforMP.py
    Untracked:  code/._filterPostLift.py
    Untracked:  code/._filterPrimaryread.py
    Untracked:  code/._filterSecondaryread.py
    Untracked:  code/._fixExonFC.py
    Untracked:  code/._fixFCheadforExp.py
    Untracked:  code/._fixLeafCluster.py
    Untracked:  code/._fixLiftedJunc.py
    Untracked:  code/._fixUTRexonanno.py
    Untracked:  code/._formathg38Anno.py
    Untracked:  code/._formatpantro6Anno.py
    Untracked:  code/._getRNAseqMapStats.sh
    Untracked:  code/._hg19MapStats.sh
    Untracked:  code/._humanChromorder.sh
    Untracked:  code/._humanMultiCov.sh
    Untracked:  code/._humanMultiCov255.sh
    Untracked:  code/._humanMultiCov_inclusive.sh
    Untracked:  code/._intersectLiftedPAS.sh
    Untracked:  code/._liftJunctionFiles.sh
    Untracked:  code/._liftPAS19to38.sh
    Untracked:  code/._liftedchimpJunc2human.sh
    Untracked:  code/._makeNuclearDapaplots.sh
    Untracked:  code/._makeNuclearDapaplots_DF.sh
    Untracked:  code/._makeSamplyGroupsHuman_TvN.py
    Untracked:  code/._mapRNAseqhg19.sh
    Untracked:  code/._mapRNAseqhg19_newPipeline.sh
    Untracked:  code/._maphg19.sh
    Untracked:  code/._maphg19_subjunc.sh
    Untracked:  code/._mediation_test.R
    Untracked:  code/._mergeChimp3prime_inhg38.sh
    Untracked:  code/._mergeandBWRNAseq.sh
    Untracked:  code/._mergedBam2BW.sh
    Untracked:  code/._nameClusters.py
    Untracked:  code/._negativeMediation_montecarlo.R
    Untracked:  code/._negativeMediation_montecarloDF.R
    Untracked:  code/._numMultimap.py
    Untracked:  code/._overlapMMandOrthoexon.sh
    Untracked:  code/._overlapPASandOrthoexon.sh
    Untracked:  code/._overlapapaQTLPAS.sh
    Untracked:  code/._parseHg38.py
    Untracked:  code/._postiveMediation_montecarlo_DF.R
    Untracked:  code/._prepareCleanLiftedFC_5perc4LC.py
    Untracked:  code/._prepareLeafvizAnno.sh
    Untracked:  code/._preparePAS4lift.py
    Untracked:  code/._primaryLift.sh
    Untracked:  code/._processhg38exons.py
    Untracked:  code/._quantJunc.sh
    Untracked:  code/._quantJunc_TEST.sh
    Untracked:  code/._quantJunc_removeBad.sh
    Untracked:  code/._quantLiftedPASPrimary.sh
    Untracked:  code/._quantMerged_seperatly.sh
    Untracked:  code/._recLiftchim2human.sh
    Untracked:  code/._revLiftPAShg38to19.sh
    Untracked:  code/._reverseLift.sh
    Untracked:  code/._runCheckReverseLift.sh
    Untracked:  code/._runChimpDiffIso.sh
    Untracked:  code/._runCountNucleotides.sh
    Untracked:  code/._runFilterNumChroms.sh
    Untracked:  code/._runHumanDiffIso.sh
    Untracked:  code/._runNuclearDiffIso_DF.sh
    Untracked:  code/._runNuclearDifffIso.sh
    Untracked:  code/._runTotalDiffIso.sh
    Untracked:  code/._run_chimpverifybam.sh
    Untracked:  code/._run_verifyBam.sh
    Untracked:  code/._snakemake.batch
    Untracked:  code/._snakemakePAS.batch
    Untracked:  code/._snakemakePASchimp.batch
    Untracked:  code/._snakemakePAShuman.batch
    Untracked:  code/._snakemake_chimp.batch
    Untracked:  code/._snakemake_human.batch
    Untracked:  code/._snakemakefiltPAS.batch
    Untracked:  code/._snakemakefiltPAS_chimp
    Untracked:  code/._snakemakefiltPAS_chimp.sh
    Untracked:  code/._snakemakefiltPAS_human.sh
    Untracked:  code/._spliceSite2Fasta.py
    Untracked:  code/._submit-snakemake-chimp.sh
    Untracked:  code/._submit-snakemake-human.sh
    Untracked:  code/._submit-snakemakePAS-chimp.sh
    Untracked:  code/._submit-snakemakePAS-human.sh
    Untracked:  code/._submit-snakemakefiltPAS-chimp.sh
    Untracked:  code/._submit-snakemakefiltPAS-human.sh
    Untracked:  code/._subset_diffisopheno_Nuclear_HvC.py
    Untracked:  code/._subset_diffisopheno_Nuclear_HvC_DF.py
    Untracked:  code/._subset_diffisopheno_Total_HvC.py
    Untracked:  code/._threeprimeOrthoFC.sh
    Untracked:  code/._transcriptDTplotsNuclear.sh
    Untracked:  code/._verifyBam4973.sh
    Untracked:  code/._verifyBam4973inHuman.sh
    Untracked:  code/._wrap_chimpverifybam.sh
    Untracked:  code/._wrap_verifyBam.sh
    Untracked:  code/._writeMergecode.py
    Untracked:  code/.snakemake/
    Untracked:  code/ALLPAS_sequenceDF.err
    Untracked:  code/ALLPAS_sequenceDF.out
    Untracked:  code/AlignmentScores.err
    Untracked:  code/AlignmentScores.out
    Untracked:  code/AlignmentScores.sh
    Untracked:  code/BothFCMM.err
    Untracked:  code/BothFCMM.out
    Untracked:  code/BothFCMM.sh
    Untracked:  code/BothFCMMPrim.err
    Untracked:  code/BothFCMMPrim.out
    Untracked:  code/BothFCMMPrim.sh
    Untracked:  code/BothFCnewOInclusive.sh
    Untracked:  code/BothFCnewOInclusive.sh.err
    Untracked:  code/BothFCnewOInclusive.sh.out
    Untracked:  code/ChimpStarMM2.err
    Untracked:  code/ChimpStarMM2.out
    Untracked:  code/ChimpStarMM2.sh
    Untracked:  code/ClassifyLeafviz.sh
    Untracked:  code/ClosestorthoEx.err
    Untracked:  code/ClosestorthoEx.out
    Untracked:  code/ClosestorthoEx.sh
    Untracked:  code/Config_chimp.yaml
    Untracked:  code/Config_chimp_full.yaml
    Untracked:  code/Config_human.yaml
    Untracked:  code/ConvertJunc2Bed.err
    Untracked:  code/ConvertJunc2Bed.out
    Untracked:  code/ConvertJunc2Bed.sh
    Untracked:  code/CountNucleotides.py
    Untracked:  code/CrossMapChimpRNA.sh
    Untracked:  code/CrossMapThreeprime.sh
    Untracked:  code/CrossmapChimp3prime.err
    Untracked:  code/CrossmapChimp3prime.out
    Untracked:  code/CrossmapChimpRNA.err
    Untracked:  code/CrossmapChimpRNA.out
    Untracked:  code/DiffSplice.err
    Untracked:  code/DiffSplice.out
    Untracked:  code/DiffSplice.sh
    Untracked:  code/DiffSplicePlots.err
    Untracked:  code/DiffSplicePlots.out
    Untracked:  code/DiffSplicePlots.sh
    Untracked:  code/DiffSplicePlots_gencode.sh
    Untracked:  code/DiffSplice_gencode.sh
    Untracked:  code/DiffSplice_removebad.err
    Untracked:  code/DiffSplice_removebad.out
    Untracked:  code/DiffSplice_removebad.sh
    Untracked:  code/Filter255.err
    Untracked:  code/Filter255.out
    Untracked:  code/Filter255MM.sh
    Untracked:  code/FilterPrimSec.err
    Untracked:  code/FilterPrimSec.out
    Untracked:  code/FilterPrimSec.sh
    Untracked:  code/FilterReverseLift.err
    Untracked:  code/FilterReverseLift.out
    Untracked:  code/FindIntronForDomPAS.err
    Untracked:  code/FindIntronForDomPAS.out
    Untracked:  code/FindIntronForDomPAS.sh
    Untracked:  code/FindIntronForDomPAS_DF.sh
    Untracked:  code/GencodeDiffSplice.err
    Untracked:  code/GencodeDiffSplice.out
    Untracked:  code/GetMAPQscore.py
    Untracked:  code/GetSecondaryMap.py
    Untracked:  code/HchromOrder.err
    Untracked:  code/HchromOrder.out
    Untracked:  code/IntersectMMandOrtho.err
    Untracked:  code/IntersectMMandOrtho.out
    Untracked:  code/IntersectPASandOrtho.err
    Untracked:  code/IntersectPASandOrtho.out
    Untracked:  code/JunctionLift.err
    Untracked:  code/JunctionLift.out
    Untracked:  code/JunctionLiftFinalChimp.err
    Untracked:  code/JunctionLiftFinalChimp.out
    Untracked:  code/Lift5perPAS.sh
    Untracked:  code/Lift5perPASbed.err
    Untracked:  code/Lift5perPASbed.out
    Untracked:  code/LiftClustersFirst.err
    Untracked:  code/LiftClustersFirst.out
    Untracked:  code/LiftClustersFirst_remove.err
    Untracked:  code/LiftClustersFirst_remove.out
    Untracked:  code/LiftClustersSecond.err
    Untracked:  code/LiftClustersSecond.out
    Untracked:  code/LiftClustersSecond_remove.err
    Untracked:  code/LiftClustersSecond_remove.out
    Untracked:  code/LiftFinalChimpJunc2Human.sh
    Untracked:  code/LiftOrthoPAS2chimp.sh
    Untracked:  code/LiftorthoPAS.err
    Untracked:  code/LiftorthoPASt.out
    Untracked:  code/Log.out
    Untracked:  code/MapBadSamples.err
    Untracked:  code/MapBadSamples.out
    Untracked:  code/MapBadSamples.sh
    Untracked:  code/MapStats.err
    Untracked:  code/MapStats.out
    Untracked:  code/MaxEntCode/
    Untracked:  code/MergeClusters.err
    Untracked:  code/MergeClusters.out
    Untracked:  code/MergeClusters.sh
    Untracked:  code/MismatchNumbers.err
    Untracked:  code/MismatchNumbers.out
    Untracked:  code/MismatchNumbers.sh
    Untracked:  code/PAS_ATTAAA.err
    Untracked:  code/PAS_ATTAAA.out
    Untracked:  code/PAS_ATTAAA.sh
    Untracked:  code/PAS_ATTAAADF.err
    Untracked:  code/PAS_ATTAAADF.out
    Untracked:  code/PAS_ATTAAA_df.sh
    Untracked:  code/PAS_seqExpanded.sh
    Untracked:  code/PAS_sequence.err
    Untracked:  code/PAS_sequence.out
    Untracked:  code/PAS_sequenceDF.err
    Untracked:  code/PAS_sequenceDF.out
    Untracked:  code/PASexpanded_sequenceDF.err
    Untracked:  code/PASexpanded_sequenceDF.out
    Untracked:  code/PASsequences.sh
    Untracked:  code/PASsequences_DF.sh
    Untracked:  code/PlotNuclearUsagebySpecies.R
    Untracked:  code/PlotNuclearUsagebySpecies_DF.R
    Untracked:  code/QuantMergeClusters
    Untracked:  code/QuantMergeClusters.err
    Untracked:  code/QuantMergeClusters.out
    Untracked:  code/QuantMergedClusters.sh
    Untracked:  code/RNATranscriptDTplot.err
    Untracked:  code/RNATranscriptDTplot.out
    Untracked:  code/RNATranscriptDTplot.sh
    Untracked:  code/Rev_liftoverPAShg19to38.err
    Untracked:  code/Rev_liftoverPAShg19to38.out
    Untracked:  code/ReverseLiftFilter.R
    Untracked:  code/RunFixCluster.err
    Untracked:  code/RunFixCluster.out
    Untracked:  code/RunFixLeafCluster.sh
    Untracked:  code/RunNegMCMediation.err
    Untracked:  code/RunNegMCMediation.sh
    Untracked:  code/RunNegMCMediationDF.err
    Untracked:  code/RunNegMCMediationDF.out
    Untracked:  code/RunNegMCMediationDF.sh
    Untracked:  code/RunNegMCMediationr.out
    Untracked:  code/RunPosMCMediation.err
    Untracked:  code/RunPosMCMediation.sh
    Untracked:  code/RunPosMCMediationDF.err
    Untracked:  code/RunPosMCMediationDF.out
    Untracked:  code/RunPosMCMediationDF.sh
    Untracked:  code/RunPosMCMediationr.out
    Untracked:  code/SAF215upbed_gen.py
    Untracked:  code/SAF2Bed.py
    Untracked:  code/Snakefile
    Untracked:  code/SnakefilePAS
    Untracked:  code/SnakefilePASfilt
    Untracked:  code/SortIndexBadSamples.err
    Untracked:  code/SortIndexBadSamples.out
    Untracked:  code/SortIndexBadSamples.sh
    Untracked:  code/StarMM2.err
    Untracked:  code/StarMM2.out
    Untracked:  code/StarMM2.sh
    Untracked:  code/TestFC.err
    Untracked:  code/TestFC.out
    Untracked:  code/TestFC.sh
    Untracked:  code/TotalTranscriptDTplot.err
    Untracked:  code/TotalTranscriptDTplot.out
    Untracked:  code/Upstream10Bases_general.py
    Untracked:  code/allPASSeq_df.sh
    Untracked:  code/apaQTLsnake.err
    Untracked:  code/apaQTLsnake.out
    Untracked:  code/apaQTLsnakePAS.err
    Untracked:  code/apaQTLsnakePAS.out
    Untracked:  code/apaQTLsnakePAShuman.err
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assignPeak2Intronicregion.sh
    Untracked:  code/bam2junc.err
    Untracked:  code/bam2junc.out
    Untracked:  code/bam2junc_remove.err
    Untracked:  code/bam2junc_remove.out
    Untracked:  code/bed215upbed.py
    Untracked:  code/bed2Bedbothstrand.py
    Untracked:  code/bed2SAF_gen.py
    Untracked:  code/bed2saf.py
    Untracked:  code/bg_to_cov.py
    Untracked:  code/buildIndecpantro5
    Untracked:  code/buildIndecpantro5.sh
    Untracked:  code/buildLeafviz.err
    Untracked:  code/buildLeafviz.out
    Untracked:  code/buildLeafviz.sh
    Untracked:  code/buildLeafviz_leadAnno.sh
    Untracked:  code/buildLeafviz_leafanno.err
    Untracked:  code/buildLeafviz_leafanno.out
    Untracked:  code/buildStarIndex.sh
    Untracked:  code/callPeaksYL.py
    Untracked:  code/chimpChromprder.sh
    Untracked:  code/chimpMultiCov.err
    Untracked:  code/chimpMultiCov.out
    Untracked:  code/chimpMultiCov.sh
    Untracked:  code/chimpMultiCov255.sh
    Untracked:  code/chimpMultiCovInclusive.err
    Untracked:  code/chimpMultiCovInclusive.out
    Untracked:  code/chimpMultiCovInclusive.sh
    Untracked:  code/chooseAnno2Bed.py
    Untracked:  code/chooseAnno2SAF.py
    Untracked:  code/chooseSignalSite.py
    Untracked:  code/chromOrder.err
    Untracked:  code/chromOrder.out
    Untracked:  code/classifyLeafviz.err
    Untracked:  code/classifyLeafviz.out
    Untracked:  code/cleanbed2saf.py
    Untracked:  code/cluster.json
    Untracked:  code/cluster2bed.py
    Untracked:  code/clusterLiftReverse.sh
    Untracked:  code/clusterLiftReverse_removebad.sh
    Untracked:  code/clusterLiftprimary.sh
    Untracked:  code/clusterLiftprimary_removebad.sh
    Untracked:  code/clusterPAS.json
    Untracked:  code/clusterfiltPAS.json
    Untracked:  code/comands2Mege.sh
    Untracked:  code/converBam2Junc.sh
    Untracked:  code/converBam2Junc_removeBad.sh
    Untracked:  code/convertNumeric.py
    Untracked:  code/environment.yaml
    Untracked:  code/extraSnakefiltpas
    Untracked:  code/extractPhyloReg.py
    Untracked:  code/extractPhyloRegGene.py
    Untracked:  code/extractPhylopGeneral.py
    Untracked:  code/extractPhylopReg200down.py
    Untracked:  code/extractPhylopReg200up.py
    Untracked:  code/filter5perc.R
    Untracked:  code/filter5percPAS.py
    Untracked:  code/filter5percPheno.py
    Untracked:  code/filterBamforMP.pysam2_gen.py
    Untracked:  code/filterJuncChroms.err
    Untracked:  code/filterJuncChroms.out
    Untracked:  code/filterMissprimingInNuc10_gen.py
    Untracked:  code/filterNumChroms.py
    Untracked:  code/filterPASforMP.py
    Untracked:  code/filterPostLift.py
    Untracked:  code/filterPrimaryread.py
    Untracked:  code/filterSAFforMP_gen.py
    Untracked:  code/filterSecondaryread.py
    Untracked:  code/filterSortBedbyCleanedBed_gen.R
    Untracked:  code/filterpeaks.py
    Untracked:  code/fixExonFC.py
    Untracked:  code/fixFChead.py
    Untracked:  code/fixFChead_bothfrac.py
    Untracked:  code/fixFCheadforExp.py
    Untracked:  code/fixLeafCluster.py
    Untracked:  code/fixLiftedJunc.py
    Untracked:  code/fixUTRexonanno.py
    Untracked:  code/formathg38Anno.py
    Untracked:  code/generateStarIndex.err
    Untracked:  code/generateStarIndex.out
    Untracked:  code/generateStarIndexHuman.err
    Untracked:  code/generateStarIndexHuman.out
    Untracked:  code/getAlloverlap.py
    Untracked:  code/getRNAseqMapStats.sh
    Untracked:  code/hg19MapStats.err
    Untracked:  code/hg19MapStats.out
    Untracked:  code/hg19MapStats.sh
    Untracked:  code/humanChromorder.sh
    Untracked:  code/humanFiles
    Untracked:  code/humanMultiCov.err
    Untracked:  code/humanMultiCov.out
    Untracked:  code/humanMultiCov.sh
    Untracked:  code/humanMultiCov255.err
    Untracked:  code/humanMultiCov255.out
    Untracked:  code/humanMultiCov255.sh
    Untracked:  code/humanMultiCovInclusive.err
    Untracked:  code/humanMultiCovInclusive.out
    Untracked:  code/humanMultiCov_inclusive.sh
    Untracked:  code/intersectAnno.err
    Untracked:  code/intersectAnno.out
    Untracked:  code/intersectAnnoExt.err
    Untracked:  code/intersectAnnoExt.out
    Untracked:  code/intersectLiftedPAS.sh
    Untracked:  code/leafcutter_merge_regtools_redo.py
    Untracked:  code/liftJunctionFiles.sh
    Untracked:  code/liftPAS19to38.sh
    Untracked:  code/liftoverPAShg19to38.err
    Untracked:  code/liftoverPAShg19to38.out
    Untracked:  code/log/
    Untracked:  code/make5percPeakbed.py
    Untracked:  code/makeFileID.py
    Untracked:  code/makeNuclearDapaplots.sh
    Untracked:  code/makeNuclearDapaplots_DF.sh
    Untracked:  code/makeNuclearPlots.err
    Untracked:  code/makeNuclearPlots.out
    Untracked:  code/makeNuclearPlotsDF.err
    Untracked:  code/makeNuclearPlotsDF.out
    Untracked:  code/makePheno.py
    Untracked:  code/makeSamplyGroupsChimp_TvN.py
    Untracked:  code/makeSamplyGroupsHuman_TvN.py
    Untracked:  code/mapRNAseqhg19.sh
    Untracked:  code/mapRNAseqhg19_newPipeline.sh
    Untracked:  code/maphg19.err
    Untracked:  code/maphg19.out
    Untracked:  code/maphg19.sh
    Untracked:  code/maphg19_new.err
    Untracked:  code/maphg19_new.out
    Untracked:  code/maphg19_sub.err
    Untracked:  code/maphg19_sub.out
    Untracked:  code/maphg19_subjunc.sh
    Untracked:  code/mediation_test.R
    Untracked:  code/merge.err
    Untracked:  code/mergeChimp3prime_inhg38.sh
    Untracked:  code/merge_leafcutter_clusters_redo.py
    Untracked:  code/mergeandBWRNAseq.sh
    Untracked:  code/mergeandsort_ChimpinHuman.err
    Untracked:  code/mergeandsort_ChimpinHuman.out
    Untracked:  code/mergedBam2BW.sh
    Untracked:  code/mergedbam2bw.err
    Untracked:  code/mergedbam2bw.out
    Untracked:  code/mergedbamRNAand2bw.err
    Untracked:  code/mergedbamRNAand2bw.out
    Untracked:  code/nameClusters.py
    Untracked:  code/namePeaks.py
    Untracked:  code/negativeMediation_montecarlo.R
    Untracked:  code/negativeMediation_montecarloDF.R
    Untracked:  code/nuclearTranscriptDTplot.err
    Untracked:  code/nuclearTranscriptDTplot.out
    Untracked:  code/numMultimap.py
    Untracked:  code/overlapMMandOrthoexon.sh
    Untracked:  code/overlapPAS.err
    Untracked:  code/overlapPAS.out
    Untracked:  code/overlapPASandOrthoexon.sh
    Untracked:  code/overlapapaQTLPAS.sh
    Untracked:  code/overlapapaQTLPAS_extended.sh
    Untracked:  code/overlapapaQTLPAS_samples.sh
    Untracked:  code/parseHg38.py
    Untracked:  code/peak2PAS.py
    Untracked:  code/pheno2countonly.R
    Untracked:  code/postiveMediation_montecarlo.R
    Untracked:  code/postiveMediation_montecarlo_DF.R
    Untracked:  code/prepareAnnoLeafviz.err
    Untracked:  code/prepareAnnoLeafviz.out
    Untracked:  code/prepareCleanLiftedFC_5perc4LC.py
    Untracked:  code/prepareLeafvizAnno.sh
    Untracked:  code/preparePAS4lift.py
    Untracked:  code/prepare_phenotype_table.py
    Untracked:  code/primaryLift.err
    Untracked:  code/primaryLift.out
    Untracked:  code/primaryLift.sh
    Untracked:  code/processhg38exons.py
    Untracked:  code/quantJunc.sh
    Untracked:  code/quantJunc_TEST.sh
    Untracked:  code/quantJunc_removeBad.sh
    Untracked:  code/quantLiftedPAS.err
    Untracked:  code/quantLiftedPAS.out
    Untracked:  code/quantLiftedPAS.sh
    Untracked:  code/quantLiftedPASPrimary.err
    Untracked:  code/quantLiftedPASPrimary.out
    Untracked:  code/quantLiftedPASPrimary.sh
    Untracked:  code/quatJunc.err
    Untracked:  code/quatJunc.out
    Untracked:  code/recChimpback2Human.err
    Untracked:  code/recChimpback2Human.out
    Untracked:  code/recLiftchim2human.sh
    Untracked:  code/revLift.err
    Untracked:  code/revLift.out
    Untracked:  code/revLiftPAShg38to19.sh
    Untracked:  code/reverseLift.sh
    Untracked:  code/runCheckReverseLift.sh
    Untracked:  code/runChimpDiffIso.sh
    Untracked:  code/runChimpDiffIsoDF.sh
    Untracked:  code/runCountNucleotides.err
    Untracked:  code/runCountNucleotides.out
    Untracked:  code/runCountNucleotides.sh
    Untracked:  code/runCountNucleotidesPantro6.err
    Untracked:  code/runCountNucleotidesPantro6.out
    Untracked:  code/runCountNucleotides_pantro6.sh
    Untracked:  code/runFilterNumChroms.sh
    Untracked:  code/runHumanDiffIso.sh
    Untracked:  code/runHumanDiffIsoDF.sh
    Untracked:  code/runNuclearDiffIso_DF.sh
    Untracked:  code/runNuclearDifffIso.sh
    Untracked:  code/runTotalDiffIso.sh
    Untracked:  code/run_Chimpleafcutter_ds.err
    Untracked:  code/run_Chimpleafcutter_ds.out
    Untracked:  code/run_Chimpverifybam.err
    Untracked:  code/run_Chimpverifybam.out
    Untracked:  code/run_Humanleafcutter_dF.err
    Untracked:  code/run_Humanleafcutter_dF.out
    Untracked:  code/run_Humanleafcutter_ds.err
    Untracked:  code/run_Humanleafcutter_ds.out
    Untracked:  code/run_Nuclearleafcutter_ds.err
    Untracked:  code/run_Nuclearleafcutter_ds.out
    Untracked:  code/run_Nuclearleafcutter_dsDF.err
    Untracked:  code/run_Nuclearleafcutter_dsDF.out
    Untracked:  code/run_Totalleafcutter_ds.err
    Untracked:  code/run_Totalleafcutter_ds.out
    Untracked:  code/run_chimpverifybam.sh
    Untracked:  code/run_verifyBam.sh
    Untracked:  code/run_verifybam.err
    Untracked:  code/run_verifybam.out
    Untracked:  code/slurm-62824013.out
    Untracked:  code/slurm-62825841.out
    Untracked:  code/slurm-62826116.out
    Untracked:  code/slurm-64108209.out
    Untracked:  code/slurm-64108521.out
    Untracked:  code/slurm-64108557.out
    Untracked:  code/snakePASChimp.err
    Untracked:  code/snakePASChimp.out
    Untracked:  code/snakePAShuman.out
    Untracked:  code/snakemake.batch
    Untracked:  code/snakemakeChimp.err
    Untracked:  code/snakemakeChimp.out
    Untracked:  code/snakemakeHuman.err
    Untracked:  code/snakemakeHuman.out
    Untracked:  code/snakemakePAS.batch
    Untracked:  code/snakemakePASFiltChimp.err
    Untracked:  code/snakemakePASFiltChimp.out
    Untracked:  code/snakemakePASFiltHuman.err
    Untracked:  code/snakemakePASFiltHuman.out
    Untracked:  code/snakemakePASchimp.batch
    Untracked:  code/snakemakePAShuman.batch
    Untracked:  code/snakemake_chimp.batch
    Untracked:  code/snakemake_human.batch
    Untracked:  code/snakemakefiltPAS.batch
    Untracked:  code/snakemakefiltPAS_chimp.sh
    Untracked:  code/snakemakefiltPAS_human.sh
    Untracked:  code/spliceSite2Fasta.py
    Untracked:  code/submit-snakemake-chimp.sh
    Untracked:  code/submit-snakemake-human.sh
    Untracked:  code/submit-snakemakePAS-chimp.sh
    Untracked:  code/submit-snakemakePAS-human.sh
    Untracked:  code/submit-snakemakefiltPAS-chimp.sh
    Untracked:  code/submit-snakemakefiltPAS-human.sh
    Untracked:  code/subset_diffisopheno.py
    Untracked:  code/subset_diffisopheno_Chimp_tvN.py
    Untracked:  code/subset_diffisopheno_Chimp_tvN_DF.py
    Untracked:  code/subset_diffisopheno_Huma_tvN.py
    Untracked:  code/subset_diffisopheno_Huma_tvN_DF.py
    Untracked:  code/subset_diffisopheno_Nuclear_HvC.py
    Untracked:  code/subset_diffisopheno_Nuclear_HvC_DF.py
    Untracked:  code/subset_diffisopheno_Total_HvC.py
    Untracked:  code/test
    Untracked:  code/test.txt
    Untracked:  code/threeprimeOrthoFC.out
    Untracked:  code/threeprimeOrthoFC.sh
    Untracked:  code/threeprimeOrthoFCcd.err
    Untracked:  code/transcriptDTplotsNuclear.sh
    Untracked:  code/transcriptDTplotsTotal.sh
    Untracked:  code/verifyBam4973.sh
    Untracked:  code/verifyBam4973inHuman.sh
    Untracked:  code/verifybam4973.err
    Untracked:  code/verifybam4973.out
    Untracked:  code/verifybam4973HumanMap.err
    Untracked:  code/verifybam4973HumanMap.out
    Untracked:  code/wrap_Chimpverifybam.err
    Untracked:  code/wrap_Chimpverifybam.out
    Untracked:  code/wrap_chimpverifybam.sh
    Untracked:  code/wrap_verifyBam.sh
    Untracked:  code/wrap_verifybam.err
    Untracked:  code/wrap_verifybam.out
    Untracked:  code/writeMergecode.py
    Untracked:  data/._.DS_Store
    Untracked:  data/._HC_filenames.txt
    Untracked:  data/._HC_filenames.txt.sb-4426323c-IKIs0S
    Untracked:  data/._HC_filenames.xlsx
    Untracked:  data/._MapPantro6_meta.txt
    Untracked:  data/._MapPantro6_meta.txt.sb-a5794dd2-Cskmlm
    Untracked:  data/._MapPantro6_meta.xlsx
    Untracked:  data/._OppositeSpeciesMap.txt
    Untracked:  data/._OppositeSpeciesMap.txt.sb-a5794dd2-mayWJf
    Untracked:  data/._OppositeSpeciesMap.xlsx
    Untracked:  data/._RNASEQ_metadata.txt
    Untracked:  data/._RNASEQ_metadata.txt.sb-4426323c-TE4ns3
    Untracked:  data/._RNASEQ_metadata.txt.sb-51f67ae1-HXp7Gq
    Untracked:  data/._RNASEQ_metadata_2Removed.txt
    Untracked:  data/._RNASEQ_metadata_2Removed.txt.sb-4426323c-a4lBwx
    Untracked:  data/._RNASEQ_metadata_2Removed.xlsx
    Untracked:  data/._RNASEQ_metadata_stranded.txt
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-a5794dd2-D659m2
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-a5794dd2-ImNMoY
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-e4bf31f0-ZGnGgl
    Untracked:  data/._RNASEQ_metadata_stranded.xlsx
    Untracked:  data/._TrialFiltersMeta.txt
    Untracked:  data/._TrialFiltersMeta.txt.sb-9845453e-R58Y0Q
    Untracked:  data/._metadata_HCpanel.txt
    Untracked:  data/._metadata_HCpanel.txt.sb-a3d92a2d-b9cYoF
    Untracked:  data/._metadata_HCpanel.txt.sb-a5794dd2-i594qs
    Untracked:  data/._metadata_HCpanel.txt.sb-f4823d1e-qihGek
    Untracked:  data/._metadata_HCpanel.xlsx
    Untracked:  data/._metadata_HCpanel_frompantro5.xlsx
    Untracked:  data/._~$RNASEQ_metadata.xlsx
    Untracked:  data/._~$metadata_HCpanel.xlsx
    Untracked:  data/._.xlsx
    Untracked:  data/BaseComp/
    Untracked:  data/CleanLiftedPeaks_FC_primary/
    Untracked:  data/CompapaQTLpas/
    Untracked:  data/DNDS/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffExpression/
    Untracked:  data/DiffIso_Nuclear/
    Untracked:  data/DiffIso_Nuclear_DF/
    Untracked:  data/DiffIso_Total/
    Untracked:  data/DiffSplice/
    Untracked:  data/DiffSplice_liftedJunc/
    Untracked:  data/DiffSplice_removeBad/
    Untracked:  data/DominantPAS/
    Untracked:  data/DominantPAS_DF/
    Untracked:  data/EvalPantro5/
    Untracked:  data/HC_filenames.txt
    Untracked:  data/HC_filenames.xlsx
    Untracked:  data/Khan_prot/
    Untracked:  data/Li_eqtls/
    Untracked:  data/MapPantro6_meta.txt
    Untracked:  data/MapPantro6_meta.xlsx
    Untracked:  data/MapStats/
    Untracked:  data/NormalizedClusters/
    Untracked:  data/NuclearHvC/
    Untracked:  data/NuclearHvC_DF/
    Untracked:  data/OppositeSpeciesMap.txt
    Untracked:  data/OppositeSpeciesMap.xlsx
    Untracked:  data/OrthoExonBed/
    Untracked:  data/OverlapBenchmark/
    Untracked:  data/OverlappingPAS/
    Untracked:  data/PAS/
    Untracked:  data/PAS_SAF/
    Untracked:  data/PAS_doubleFilter/
    Untracked:  data/Peaks_5perc/
    Untracked:  data/Pheno_5perc/
    Untracked:  data/Pheno_5perc_DF_nuclear/
    Untracked:  data/Pheno_5perc_nuclear/
    Untracked:  data/Pheno_5perc_nuclear_old/
    Untracked:  data/Pheno_5perc_total/
    Untracked:  data/PhyloP/
    Untracked:  data/Pol2Chip/
    Untracked:  data/RNASEQ_metadata.txt
    Untracked:  data/RNASEQ_metadata_2Removed.txt
    Untracked:  data/RNASEQ_metadata_2Removed.xlsx
    Untracked:  data/RNASEQ_metadata_stranded.txt
    Untracked:  data/RNASEQ_metadata_stranded.txt.sb-e4bf31f0-ZGnGgl/
    Untracked:  data/RNASEQ_metadata_stranded.xlsx
    Untracked:  data/SignalSites/
    Untracked:  data/SignalSites_doublefilter/
    Untracked:  data/SpliceSite/
    Untracked:  data/TestAnnoBiasOE/
    Untracked:  data/TestMM2/
    Untracked:  data/TestMM2_AS/
    Untracked:  data/TestMM2_PrimaryRead/
    Untracked:  data/TestMM2_SeondaryRead/
    Untracked:  data/TestMM2_mismatch/
    Untracked:  data/TestMM2_quality/
    Untracked:  data/TestWithinMergePAS/
    Untracked:  data/Test_FC_methods/
    Untracked:  data/Threeprime2Ortho/
    Untracked:  data/TotalFractionPAS/
    Untracked:  data/TotalHvC/
    Untracked:  data/TrialFiltersMeta.txt
    Untracked:  data/TwoBadSampleAnalysis/
    Untracked:  data/Wang_ribo/
    Untracked:  data/apaQTLGenes/
    Untracked:  data/bioGRID/
    Untracked:  data/chainFiles/
    Untracked:  data/cleanPeaks_anno/
    Untracked:  data/cleanPeaks_byspecies/
    Untracked:  data/cleanPeaks_lifted/
    Untracked:  data/files4viz_nuclear/
    Untracked:  data/files4viz_nuclear_DF/
    Untracked:  data/gviz/
    Untracked:  data/leafviz/
    Untracked:  data/liftover_files/
    Untracked:  data/mediation/
    Untracked:  data/mediation_DF/
    Untracked:  data/metadata_HCpanel.txt
    Untracked:  data/metadata_HCpanel.xlsx
    Untracked:  data/metadata_HCpanel_frompantro5.txt
    Untracked:  data/metadata_HCpanel_frompantro5.xlsx
    Untracked:  data/multimap/
    Untracked:  data/orthoUTR/
    Untracked:  data/primaryLift/
    Untracked:  data/reverseLift/
    Untracked:  data/testQuant/
    Untracked:  data/~$RNASEQ_metadata.xlsx
    Untracked:  data/~$metadata_HCpanel.xlsx
    Untracked:  data/.xlsx
    Untracked:  output/._.DS_Store
    Untracked:  output/dtPlots/
    Untracked:  projectNotes.Rmd
    Untracked:  proteinModelSet.Rmd

Unstaged changes:
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/speciesSpecific.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd 2f5d4d5 brimittleman 2020-04-08 change number and add 3; utr
html a7536f9 brimittleman 2020-04-03 Build site.
Rmd bf79d5e brimittleman 2020-04-03 update catalot
html 5525b39 brimittleman 2020-01-21 Build site.
Rmd 2e66af9 brimittleman 2020-01-21 add ss and PAS num DF 
library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.3.1  
✔ readr   1.3.1       ✔ forcats 0.3.0  
── Conflicts ────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(reshape2)

Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':

    smiths
library(workflowr)
This is workflowr version 1.6.0
Run ?workflowr for help getting started

Nuclear fraction

In this analysis I will look at thenumber of PAS per species at a gene level. I am only including PAS in chr1-22. These results use mean usage accross fraction.

PAS=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", stringsAsFactors = F, header = T)

I am looking at PAS at .05 or greater in either species.

PAS_sm=PAS %>% dplyr::select(gene, Chimp, Human) 

PAS_m= melt(PAS_sm, id.var="gene", variable.name="species", value.name="meanUsage") %>% filter(meanUsage >=0.1) %>% group_by(species, gene) %>% summarise(nPAS=n())

#pos = more human, neg = more chimp 
PAS_spread=PAS_m %>% spread(species, nPAS, fill=0) %>% mutate(DiffPAS=Human-Chimp)
summary(PAS_spread$DiffPAS)
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
-4.00000  0.00000  0.00000  0.05956  1.00000  5.00000 
#more human
nrow(PAS_spread[PAS_spread$DiffPAS>0,])
[1] 2599
#more chimp
nrow(PAS_spread[PAS_spread$DiffPAS<0,])
[1] 2210
#same
nrow(PAS_spread[PAS_spread$DiffPAS==0,])
[1] 4744
#all
nrow(PAS_spread)
[1] 9553
ggplot(PAS_spread, aes(x=DiffPAS)) + geom_bar(stat="count") +geom_vline(xintercept = mean(PAS_spread$DiffPAS),col="red") + labs(title="Difference in number of PAS at 10% Human vs Chimp", y="Genes", x="N Human PAS - N Chimp PAS")

Version Author Date
a7536f9 brimittleman 2020-04-03
5525b39 brimittleman 2020-01-21

Plot distribution of N pas by species:

Wilcoxan test to see if there is a difference in this distribution.

ChimpNPAS=PAS_m %>% filter(species=="Chimp")
HumanNPAS=PAS_m %>% filter(species=="Human")


wilcox.test(HumanNPAS$nPAS,ChimpNPAS$nPAS )

    Wilcoxon rank sum test with continuity correction

data:  HumanNPAS$nPAS and ChimpNPAS$nPAS
W = 46201000, p-value = 1.34e-15
alternative hypothesis: true location shift is not equal to 0
PAS_m$nPAS=as.factor(PAS_m$nPAS)
ggplot(PAS_m,aes(x=nPAS, by=species, fill=species)) + geom_histogram(stat="count",position = "dodge") +  scale_fill_brewer(palette = "Dark2") + labs(title="Distribution for number of PAS at 10% ", x="Number of PAS",y="Genes")
Warning: Ignoring unknown parameters: binwidth, bins, pad

Version Author Date
a7536f9 brimittleman 2020-04-03
5525b39 brimittleman 2020-01-21

Look at number without a filter:

PAS_m5= melt(PAS_sm, id.var="gene", variable.name="species", value.name="meanUsage") %>% filter(meanUsage >=0.05) %>% group_by(species, gene) %>% summarise(nPAS=n())
PAS_m5$nPAS=as.factor(PAS_m5$nPAS)
ggplot(PAS_m5,aes(x=nPAS, by=species, fill=species)) + geom_histogram(stat="count",position = "dodge") +  scale_fill_brewer(palette = "Dark2") + labs(title="Distribution for number of PAS at 5% Nuclear Fraction ", x="Number of PAS",y="Genes")
Warning: Ignoring unknown parameters: binwidth, bins, pad


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] workflowr_1.6.0 reshape2_1.4.3  forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1     tidyr_0.8.3    
 [9] tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5   haven_1.1.2        lattice_0.20-38   
 [4] colorspace_1.3-2   generics_0.0.2     htmltools_0.3.6   
 [7] yaml_2.2.0         rlang_0.4.0        later_0.7.5       
[10] pillar_1.3.1       glue_1.3.0         withr_2.1.2       
[13] RColorBrewer_1.1-2 modelr_0.1.2       readxl_1.1.0      
[16] plyr_1.8.4         munsell_0.5.0      gtable_0.2.0      
[19] cellranger_1.1.0   rvest_0.3.2        evaluate_0.12     
[22] labeling_0.3       knitr_1.20         httpuv_1.4.5      
[25] broom_0.5.1        Rcpp_1.0.2         promises_1.0.1    
[28] scales_1.0.0       backports_1.1.2    jsonlite_1.6      
[31] fs_1.3.1           hms_0.4.2          digest_0.6.18     
[34] stringi_1.2.4      grid_3.5.1         rprojroot_1.3-2   
[37] cli_1.1.0          tools_3.5.1        magrittr_1.5      
[40] lazyeval_0.2.1     crayon_1.3.4       whisker_0.3-2     
[43] pkgconfig_2.0.2    xml2_1.2.0         lubridate_1.7.4   
[46] assertthat_0.2.0   rmarkdown_1.10     httr_1.3.1        
[49] rstudioapi_0.10    R6_2.3.0           nlme_3.1-137      
[52] git2r_0.26.1       compiler_3.5.1