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rprops edited this page Apr 21, 2017
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Welcome to the Phenoflow_package wiki!
| Functions | Actions |
|---|---|
| flowBasis | Function part of the flowFDA package (in development) which performes bivariate kernel density estimations on the phenotypic parameters |
| Diversity | Calculation of Hill diversities of order 0, 1 and 2 from fingerprint object |
| Diversity_rf | More accurate (i.e., smaller errors) calculation of Hill diversities from flowSet. It is slower than Diversity(). This calculation can be parallelized. |
| Diversity_16S | Calculation of Hill diversities from 16S amplicon data for comparison with Diversity(). This calculation can be parallelized. |
| Evenness | Calculation of pareto evenness (Wittebolle L. et al. (2009)) from fingerprint object (1 = maximum evenness, 0 = minimum evenness) |
| So | Calculation of Structural Organization parameter (Koch et al. (2014), Frontiers in Microbiology) |
| CV | Calculation of Coefficient of Variation (CV) of the fingerprint object |
| beta_diversity_fcm | Non-metric Multidimensional Scaling (NMDS) or PCoA of the phenotypic fingerprints |
| time_discretization | Function for subsetting .fcs files in time intervals and exporting them as new .fcs files. Designed for the analysis of on-line experiments. |
| FCS_resample | Resamples sample files from flowSet object to an equal number of cells. Standard is to the minimum sample size. |
| FCS_clean | Denoises all samples by means of automated identification and removal of fluorescence anomalies in flow cytometry data |
| Functions | Actions |
|---|---|
| flowRate | Calculation of growth rates of microbial populations from flow cytometry data. |
| flowInsilico |