Metagenomics Analysis Tools

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Documentation for package ‘matR’ version 0.9.1

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biom.environment Get annotation information of samples as BIOM data
biomRequest Get annotation information of samples as BIOM data
boxplot Summarize BIOM data in boxplots
boxplot.biom Summarize BIOM data in boxplots
columns Search and change row or column annotations of BIOM data
columns<- Search and change row or column annotations of BIOM data
demoObjects BIOM annotation data for certain metagenomes and projects
dimnames<-.biom Change row and column identifiers of BIOM data
dir.MGRAST List directory of projects
distx Calculate distances with optional grouping and other features
distx.biom Calculate distances with optional grouping and other features
distx.matrix Calculate distances with optional grouping and other features
expandSet Handle sets of metagenome and project IDs
IDsets Handle sets of metagenome and project IDs
image Display heatmap of BIOM data with optional dendrograms
image.biom Display heatmap of BIOM data with optional dendrograms
merge.biom Merge BIOM data
metadata Get metadata of projects and metagenomes
metadata.character Get metadata of projects and metagenomes
princomp Compute and plot principal coordinates of BIOM data
princomp.biom Compute and plot principal coordinates of BIOM data
readSet Handle sets of metagenome and project IDs
rows Search and change row or column annotations of BIOM data
rows<- Search and change row or column annotations of BIOM data
rowstats Apply selected significance test across rows
rowstats.biom Apply selected significance test across rows
rowstats.matrix Apply selected significance test across rows
scrapeSet Handle sets of metagenome and project IDs
scrubSet Handle sets of metagenome and project IDs
search.MGRAST Find metagenomes matching specified criteria
transform Apply mathematical transformations to BIOM data
transform.biom Apply mathematical transformations to BIOM data
t_ColCenter Apply mathematical transformations to BIOM data
t_ColScale Apply mathematical transformations to BIOM data
t_Log Apply mathematical transformations to BIOM data
t_NA2Zero Apply mathematical transformations to BIOM data
t_Threshold Apply mathematical transformations to BIOM data
xx1 BIOM annotation data for certain metagenomes and projects
xx2 BIOM annotation data for certain metagenomes and projects
xx3 BIOM annotation data for certain metagenomes and projects
xx4 BIOM annotation data for certain metagenomes and projects
yy1 BIOM annotation data for certain metagenomes and projects
yy2 BIOM annotation data for certain metagenomes and projects
yy3 BIOM annotation data for certain metagenomes and projects
yy4 BIOM annotation data for certain metagenomes and projects
[.biom Take part of (subset) BIOM data