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

Files in this package

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.

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