ebimetagenomics: EBI Metagenomics Portal

Functions for querying the EBI Metagenomics Portal (https://www.ebi.ac.uk/metagenomics/). The current main focus is on taxa abundance data, but the intention is that this package should evolve into a general purpose package for working with EBI Metagenomics data using R.

Author
Darren Wilkinson
Date of publication
2016-10-20 06:30:13
Maintainer
Darren Wilkinson <darren.wilkinson@ncl.ac.uk>
License
LGPL-3
Version
0.3

View on R-Forge

Man pages

convertOtuTad
Converts an OTU count data frame to a TAD data frame
getProjectsList
Download the EMG projects list into a data frame
getProjectSummary
Download an EMG project summary into a data frame
getRunOtu
Downloads OTU count data associated with a EMG run
getSampleOtu
Downloads and merges all of the OTU count data associated...
mergeOtu
Merges two OTU count data data frames to produce a combined...
plotOtu
Plots OTU count data
projectRuns
Find runs associated with an EMG project
projectSamples
Find samples associated with an EMG project
read.otu.tsv
Reads OTU count data associated with a EMG run
read.project.csv
Read an EMG project summary into a data frame
runsBySample
Find runs associated with a particular sample ID within an...

Files in this package

ebimetagenomics/DESCRIPTION
ebimetagenomics/NAMESPACE
ebimetagenomics/R
ebimetagenomics/R/emg.R
ebimetagenomics/man
ebimetagenomics/man/convertOtuTad.Rd
ebimetagenomics/man/getProjectSummary.Rd
ebimetagenomics/man/getProjectsList.Rd
ebimetagenomics/man/getRunOtu.Rd
ebimetagenomics/man/getSampleOtu.Rd
ebimetagenomics/man/mergeOtu.Rd
ebimetagenomics/man/plotOtu.Rd
ebimetagenomics/man/projectRuns.Rd
ebimetagenomics/man/projectSamples.Rd
ebimetagenomics/man/read.otu.tsv.Rd
ebimetagenomics/man/read.project.csv.Rd
ebimetagenomics/man/runsBySample.Rd