README.md

In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

CMETNGS_package

R package with some convenience functions for CMETs NGS pipeline

Installation

library(devtools)
install_github("CMET-UGent/CMETNGS")

Available functions

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

CMET-UGent/CMETNGS documentation built on Dec. 12, 2020, 8:22 a.m.