R package with some convenience functions for CMETs NGS pipeline
library(devtools)
install_github("CMET-UGent/CMETNGS")
For more details on a function call ?functionname
| Function name | Description |
|---|---|
| highqualgraphR | export publication-grade graphics from ggplot2 object |
| makebargraphrawggplot2 | make stacked bar graphs from preformatted taxonomy |
| preformattax | preformat mothur taxonomies |
| coldiss | fast plots of dissimilarity matrices |
| cbindPad | function to combine unequal-length data frames (or vectors) into a dataframe |
| gg_color_hue | function to generate ggplot-like color pallettes |
| myround | alternative plotting function |
| fasta2dataframe | bioconductor-based readout of (mothur formatted) sequences into a dataframe |
| KimPalettes | Function to select a discrete color palette as created by Kim De Paepe |
| MakeEDABargraphs | create some exploratory stacked bargraphs based upon mothur output files and phyloseq, as created by Tim Lacoere |
| df2fasta | bioconductor-based inverse of fasta2dataframe (useful in case you did some filtering via fasta2dataframe but need a fasta output for downstream) |
| MakeExcelReport | R function that takes absolute (!) paths to a shared, taxonomy and optional otureps fasta and automatically creates an excel file from it. |
| myround | more robust rounding function |
| construct_phyloseq | create a phyloseq object from mothur output, according to CMET SOP (different from phyloseq::import_mothur in that it works with the final files from our current SOP, with support for metadata) |
| Analyze_Sangers | wrapper function for sangeranalyzeR package to deal with LGC/Tim Lacoere formatted data for 16S Sangers |