About

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.

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:    data/.DS_Store
    Ignored:    data/perm_QTL_trans_noMP_5percov/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  KalistoAbundance18486.txt
    Untracked:  analysis/4suDataIGV.Rmd
    Untracked:  analysis/DirectionapaQTL.Rmd
    Untracked:  analysis/EvaleQTLs.Rmd
    Untracked:  analysis/YL_QTL_test.Rmd
    Untracked:  analysis/ncbiRefSeq_sm.sort.mRNA.bed
    Untracked:  analysis/snake.config.notes.Rmd
    Untracked:  analysis/verifyBAM.Rmd
    Untracked:  analysis/verifybam_dubs.Rmd
    Untracked:  code/PeaksToCoverPerReads.py
    Untracked:  code/strober_pc_pve_heatmap_func.R
    Untracked:  data/18486.genecov.txt
    Untracked:  data/APApeaksYL.total.inbrain.bed
    Untracked:  data/ApaQTLs/
    Untracked:  data/ChromHmmOverlap/
    Untracked:  data/DistTXN2Peak_genelocAnno/
    Untracked:  data/GM12878.chromHMM.bed
    Untracked:  data/GM12878.chromHMM.txt
    Untracked:  data/LianoglouLCL/
    Untracked:  data/LocusZoom/
    Untracked:  data/NuclearApaQTLs.txt
    Untracked:  data/PeakCounts/
    Untracked:  data/PeakCounts_noMP_5perc/
    Untracked:  data/PeakCounts_noMP_genelocanno/
    Untracked:  data/PeakUsage/
    Untracked:  data/PeakUsage_noMP/
    Untracked:  data/PeakUsage_noMP_GeneLocAnno/
    Untracked:  data/PeaksUsed/
    Untracked:  data/PeaksUsed_noMP_5percCov/
    Untracked:  data/RNAkalisto/
    Untracked:  data/RefSeq_annotations/
    Untracked:  data/TotalApaQTLs.txt
    Untracked:  data/Totalpeaks_filtered_clean.bed
    Untracked:  data/UnderstandPeaksQC/
    Untracked:  data/WASP_STAT/
    Untracked:  data/YL-SP-18486-T-combined-genecov.txt
    Untracked:  data/YL-SP-18486-T_S9_R1_001-genecov.txt
    Untracked:  data/YL_QTL_test/
    Untracked:  data/apaExamp/
    Untracked:  data/apaQTL_examp_noMP/
    Untracked:  data/bedgraph_peaks/
    Untracked:  data/bin200.5.T.nuccov.bed
    Untracked:  data/bin200.Anuccov.bed
    Untracked:  data/bin200.nuccov.bed
    Untracked:  data/clean_peaks/
    Untracked:  data/comb_map_stats.csv
    Untracked:  data/comb_map_stats.xlsx
    Untracked:  data/comb_map_stats_39ind.csv
    Untracked:  data/combined_reads_mapped_three_prime_seq.csv
    Untracked:  data/diff_iso_GeneLocAnno/
    Untracked:  data/diff_iso_proc/
    Untracked:  data/diff_iso_trans/
    Untracked:  data/ensemble_to_genename.txt
    Untracked:  data/example_gene_peakQuant/
    Untracked:  data/explainProtVar/
    Untracked:  data/filtPeakOppstrand_cov_noMP_GeneLocAnno_5perc/
    Untracked:  data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.bed
    Untracked:  data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.noties.bed
    Untracked:  data/first50lines_closest.txt
    Untracked:  data/gencov.test.csv
    Untracked:  data/gencov.test.txt
    Untracked:  data/gencov_zero.test.csv
    Untracked:  data/gencov_zero.test.txt
    Untracked:  data/gene_cov/
    Untracked:  data/joined
    Untracked:  data/leafcutter/
    Untracked:  data/merged_combined_YL-SP-threeprimeseq.bg
    Untracked:  data/molPheno_noMP/
    Untracked:  data/mol_overlap/
    Untracked:  data/mol_pheno/
    Untracked:  data/nom_QTL/
    Untracked:  data/nom_QTL_opp/
    Untracked:  data/nom_QTL_trans/
    Untracked:  data/nuc6up/
    Untracked:  data/nuc_10up/
    Untracked:  data/other_qtls/
    Untracked:  data/pQTL_otherphen/
    Untracked:  data/peakPerRefSeqGene/
    Untracked:  data/perm_QTL/
    Untracked:  data/perm_QTL_GeneLocAnno_noMP_5percov/
    Untracked:  data/perm_QTL_GeneLocAnno_noMP_5percov_3UTR/
    Untracked:  data/perm_QTL_opp/
    Untracked:  data/perm_QTL_trans/
    Untracked:  data/perm_QTL_trans_filt/
    Untracked:  data/protAndAPAAndExplmRes.Rda
    Untracked:  data/protAndAPAlmRes.Rda
    Untracked:  data/protAndExpressionlmRes.Rda
    Untracked:  data/reads_mapped_three_prime_seq.csv
    Untracked:  data/smash.cov.results.bed
    Untracked:  data/smash.cov.results.csv
    Untracked:  data/smash.cov.results.txt
    Untracked:  data/smash_testregion/
    Untracked:  data/ssFC200.cov.bed
    Untracked:  data/temp.file1
    Untracked:  data/temp.file2
    Untracked:  data/temp.gencov.test.txt
    Untracked:  data/temp.gencov_zero.test.txt
    Untracked:  data/threePrimeSeqMetaData.csv
    Untracked:  data/threePrimeSeqMetaData55Ind.txt
    Untracked:  data/threePrimeSeqMetaData55Ind.xlsx
    Untracked:  data/threePrimeSeqMetaData55Ind_noDup.txt
    Untracked:  data/threePrimeSeqMetaData55Ind_noDup.xlsx
    Untracked:  data/threePrimeSeqMetaData55Ind_noDup_WASPMAP.txt
    Untracked:  data/threePrimeSeqMetaData55Ind_noDup_WASPMAP.xlsx
    Untracked:  output/picard/
    Untracked:  output/plots/
    Untracked:  output/qual.fig2.pdf

Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/CompareLianoglouData.Rmd
    Modified:   analysis/NewPeakPostMP.Rmd
    Modified:   analysis/apaQTLoverlapGWAS.Rmd
    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/coloc_apaQTLs_protQTLs.Rmd
    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/explainpQTLs.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/flash2mash.Rmd
    Modified:   analysis/mispriming_approach.Rmd
    Modified:   analysis/overlapMolQTL.Rmd
    Modified:   analysis/overlapMolQTL.opposite.Rmd
    Modified:   analysis/overlap_qtls.Rmd
    Modified:   analysis/peakOverlap_oppstrand.Rmd
    Modified:   analysis/peakQCPPlots.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/pipeline_55Ind.Rmd
    Modified:   analysis/swarmPlots_QTLs.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   analysis/test.smash.Rmd
    Modified:   analysis/understandPeaks.Rmd
    Modified:   code/Snakefile

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.