Man pages for eclarke/SarcoidMicrobiome
Figures for the Clarke et al sarcoid microbiome paper

cairo_failsafeTry to use 'cairo_pdf', but fall back to 'pdf' if that...
counts_matrixCreates a counts matrix from an agglomerated data frame....
ExtractSignificantResultsExtracts the significant results from...
fct_anon_deterministicNon-random version of 'forcats::fct_anon'
LinkMatchedControlsLinks matched samples and (environmental) controls via the...
load_dataLoad datasets.
LoadDataLoad datasets (memoized).
MakeBarchartDataGroups taxa into top members and samples by their larger...
MakeHeatmapDataPrepare agglomerated dataframe for heatmap display by...
MakePCOADataPerforms principle coordinates analysis on a GUniFrac...
MakeTopBarchartDataPrepares data for making the summary barcharts showing the...
MakeUnifracDataCalculates the generalized UniFrac distances for an...
min_rankCreates a MinRank vector from an agglomerated data frame...
PCoAChunkWrapper for UniFrac calculations, PERMANOVA testing and PCoA...
PlotBarchartPlots the results of MakeBarchartData as a set of grouped...
PlotHeatmapPlot the results of MakeHeatmapData.
PlotPCOAStandardized PCoA plot.
PlotTopBarchartsPlots data prepared by MakeTopBarchartData.
root_treeRoot a tree using a random node as the root.
RunDESeq2Test differences between study groups using DESeq2.
RunGLMMTest differences between study groups using the generalized...
StandardizeMetadataStandardize a metadata table (s) to be compatible with...
TestMatchedControlMixedModelCreate and test a mixed effect model between two sample types...
TestPermanovaPerforms PERMANOVA on the given terms using the unifrac...
eclarke/SarcoidMicrobiome documentation built on May 15, 2019, 7:53 p.m.