Man pages for cpauvert/psadd
Additions to phyloseq package for microbiome analysis

adaptative_threshold_otuRelevel taxa/OTU to 0 according to a taxa/OTU wise threshold.
ctrl_samples_statsGenerate taxa/OTU statistics to compare control samples with...
get_taxa_nomyTaxa/OTU abundance in a given sample coupled with rank and...
id2hashConvert taxa/ID through a correspondence table
multiple_rrarefyPerforms rarefying multiple times and returns averaged OTU...
plot_kronaInteractive Taxonomy plot with Krona from a phyloseq object
plot_mvPlot Mean Variance OTU in order to evaluate overdispersion
plot_piePie Plot Taxonomy Assignations from Phyloseq
plot_pie_vectorPie Plot Taxonomy Assignations from Two Abundance Vector
plot_pie_with_legendPlot Taxonomy Assignations from Phyloseq with legend.
plot_sparsityPlot taxa/OTU table to evaluate sparsity.
plot_violinViolin distribution plot
relative_abd_without_specific_sampleCompute taxa/OTU abundance relative to the total dataset
relative_abundanceCompute taxa/OTU abundance relative to the total dataset
rename_otuOTU renaming: from hash to rank abundance prefix
sample_prevTaxa/OTU number in all samples
sample_statsApply statistics function to samples.
subset_samples_no_zeroSubset samples and prune taxa/OTU with zero abundance
taxa_prevOTU/Species prevalence in all samples
taxa_statsApply statistics function to taxa abundance vector
cpauvert/psadd documentation built on May 13, 2019, 10:54 p.m.