matR: Metagenomics Analysis Tools for R

An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. matR integrates easily with other R packages and non-R software.

AuthorDaniel Braithwaite [aut, cre], Kevin Keegan [aut], University of Chicago [cph]
Date of publication2014-10-23 11:50:13
MaintainerDaniel Braithwaite <contact.dtb@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version0.9
https://github.com/MG-RAST/matR/

View on CRAN

Man pages

BIOMannotations: Search and change row or column annotations of BIOM data

BIOMmerge: Merge BIOM data

BIOMrename: Change row and column identifiers of BIOM data

BIOMretrieval: Get annotation information of samples as BIOM data

BIOMsubset: Take part of (subset) BIOM data

boxplot.biom: Summarize BIOM data in boxplots

buildDemoSets: Build objects containing metagenome annotations as BIOM data

collapse: Collapse character vectors to a single string

demoObjects: BIOM annotation data for certain metagenomes and projects

demoSets: Get paths to files of metagenome and project IDs

dependencies: Install recommended packages

dir.MGRAST: List directory of projects

distx: Calculate distances with optional grouping and other features

getMetColumns: Get single field from column metadata

getMetRows: Get single field from row metadata

hazPackages: Check for presence of recommended packages

IDsets: Handle sets of metagenome and project IDs

image.biom: Display heatmap of BIOM data with optional dendrograms

metadata.character: Get metadata of projects and metagenomes

parAuto: Provide automatic par values

parMap: Determine par values according to a provided metadata mapping

princomp.biom: Compute and plot principal coordinates of BIOM data

rowstats: Apply selected significance test across rows

search.MGRAST: Find metagenomes matching specified criteria

stepper: Step through a demo line-by-line

step.through: Step through a demo line-by-line

subMetadata: Substitute for reference to row or column metadata

transform.biom: Apply mathematical transformations to BIOM data

Functions

[.biom Man page
biom.environment Man page
biomRequest Man page
boxplot Man page
boxplot.biom Man page
buildDemoSets Man page
collapse Man page
columns Man page
columns<- Man page
demoObjects Man page
demoSets Man page
dependencies Man page
dimnames<-.biom Man page
dir.MGRAST Man page
distx Man page
distx.biom Man page
distx.matrix Man page
expandSet Man page
getMetColumns Man page
getMetRows Man page
hazPackages Man page
IDsets Man page
image Man page
image.biom Man page
merge.biom Man page
metadata Man page
metadata.character Man page
parAuto Man page
parMap Man page
princomp Man page
princomp.biom Man page
readSet Man page
rows Man page
rows<- Man page
rowstats Man page
rowstats.biom Man page
rowstats.matrix Man page
scrapeSet Man page
scrubSet Man page
search.MGRAST Man page
stepper Man page
step.through Man page
subColumn Man page
subRow Man page
t_ColCenter Man page
t_ColScale Man page
t_Log Man page
t_NA2Zero Man page
transform Man page
transform.biom Man page
t_Threshold Man page
xx1 Man page
xx2 Man page
xx3 Man page
xx4 Man page
yy1 Man page
yy2 Man page
yy3 Man page
yy4 Man page

Files

matR
matR/inst
matR/inst/extdata
matR/inst/extdata/set-4.tsv
matR/inst/extdata/set-6.tsv
matR/inst/extdata/set-1.tsv
matR/inst/extdata/set-7.tsv
matR/inst/extdata/set-2.tsv
matR/inst/extdata/set-3.tsv
matR/inst/extdata/set-5.tsv
matR/tests
matR/tests/data-test.R
matR/tests/graphics-test.R
matR/tests/analysis-test.R
matR/tests/client-test.R
matR/tests/input-form-test.R
matR/tests/biom-ext-test.R
matR/NAMESPACE
matR/demo
matR/demo/simple.R
matR/demo/functions.R
matR/demo/00Index
matR/demo/ant.R
matR/demo/API.R
matR/demo/whyR.R
matR/data
matR/data/demoObjects.rda
matR/R
matR/R/utils.R matR/R/graphics.R matR/R/boxplot.R matR/R/biom-ext.R matR/R/analysis-support.R matR/R/init.R matR/R/client.R matR/R/image.R matR/R/princomp.R matR/R/distx.R matR/R/analysis-misc.R matR/R/transform.R matR/R/rowstats.R
matR/README.md
matR/MD5
matR/DESCRIPTION
matR/man
matR/man/distx.Rd matR/man/demoObjects.Rd matR/man/getMetColumns.Rd matR/man/BIOMsubset.Rd matR/man/parAuto.Rd matR/man/BIOMannotations.Rd matR/man/BIOMrename.Rd matR/man/search.MGRAST.Rd matR/man/stepper.Rd matR/man/BIOMmerge.Rd matR/man/dependencies.Rd matR/man/hazPackages.Rd matR/man/getMetRows.Rd matR/man/buildDemoSets.Rd matR/man/subMetadata.Rd matR/man/IDsets.Rd matR/man/demoSets.Rd matR/man/dir.MGRAST.Rd matR/man/metadata.character.Rd matR/man/transform.biom.Rd matR/man/step.through.Rd matR/man/boxplot.biom.Rd matR/man/image.biom.Rd matR/man/collapse.Rd matR/man/BIOMretrieval.Rd matR/man/parMap.Rd matR/man/rowstats.Rd matR/man/princomp.biom.Rd
matR/LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.