momr: Mining Metaomics Data (MetaOMineR)

'MetaOMineR' suite is a set of R packages that offers many functions and modules needed for the analyses of quantitative metagenomics data. 'momr' is the core package and contains routines for biomarker identification and exploration. Developed since the beginning of field, 'momr' has evolved and is structured around the different modules such as preprocessing, analysis, vizualisation, etc. See package help for more information.

AuthorEdi Prifti, Emmanuelle Le Chatelier
Date of publication2015-07-27 12:42:14
MaintainerEdi Prifti <edi.prifti@gmail.com>
LicenseArtistic-2.0
Version1.1

View on CRAN

Man pages

abondanceScore: abondanceScore

aggregateProfiles: aggregateProfiles

buildMgsFinal: buildMgsFinal @date December 20th 2013

computeFilteredVectors: computeFilteredVectors

computeSignalMetrics: computeSignalMetrics

computeUpsizedGC: computeUpsizedGC

connectivity: connectivity

countSampledGenes: countSampledGenes

countSampledGenesGC: countSampledGenesGC

deleteData: deleteData

downsizedRichnessL2T: downsizedRichnessL2T

downsizeGC: downsizeGC

downsizeGC.all: downsizeGC.all

downsizeMatrix: downsizeMatrix

extractProfiles: extractProfiles

extractSignificant: extractSignificant

filterListGenebags: filterListGenebags

filterMat: filterMat

filt.hierClust: filt.hierClust

hierClust: hierClust

hs_3.3_metahit_genesize: hs_3.3_metahit_genesize

hs_3.3_metahit_sample_dat_freq: hs_3.3_metahit_sample_dat_freq

hs_3.3_metahit_sample_dat_raw: hs_3.3_metahit_sample_dat_raw

indexReads: indexReads

indexReadsGC: indexReadsGC

launchTask: launchTask

lmp: lmp

mapResults: mapResults

mgs_hs_3.3_metahit_sup500: mgs_hs_3.3_metahit_sup500

momr-package: Mining Metaomics Data In R

normFreqRPKM: normFreqRPKM

normFreqTC: normFreqTC

phenoPairwiseRelations: phenoPairwiseRelations

plotBarcode: plotBarcode

plotBarcode2: plotBarcode2

plotBarcodeBW: plotBarcodeBW

plotCors: plotCors

plotCors2: plotCors2

plotMGSQuality: plotMGSQuality

plotPvals: plotPvals

presenceScore: presenceScore

profiles2Genebags: profiles2Genebags

projectOntoMGS: projectOntoMGS

sampleRandomly: sampleRandomly

selectListSize: selectListSize

splitData: splitData

testRelations: testRelations

watchProgress: watchProgress

Functions

abondanceScore Man page
aggregateProfiles Man page
buildMgsFinal Man page
computeFilteredVectors Man page
computeSignalMetrics Man page
computeUpsizedGC Man page
connectivity Man page
countSampledGenes Man page
countSampledGenesGC Man page
deleteData Man page
downsizedRichnessL2T Man page
downsizeGC Man page
downsizeGC.all Man page
downsizeMatrix Man page
extractProfiles Man page
extractSignificant Man page
filterListGenebags Man page
filterMat Man page
filt.hierClust Man page
hierClust Man page
hs_3.3_metahit_genesize Man page
hs_3.3_metahit_sample_dat_freq Man page
hs_3.3_metahit_sample_dat_raw Man page
indexReads Man page
indexReadsGC Man page
launchTask Man page
lmp Man page
mapResults Man page
mgs_hs_3.3_metahit_sup500 Man page
momr Man page
momr-package Man page
normFreqRPKM Man page
normFreqTC Man page
phenoPairwiseRelations Man page
plotBarcode Man page
plotBarcode2 Man page
plotBarcodeBW Man page
plotCors Man page
plotCors2 Man page
plotMGSQuality Man page
plotPvals Man page
presenceScore Man page
profiles2Genebags Man page
projectOntoMGS Man page
sampleRandomly Man page
selectListSize Man page
splitData Man page
testRelations Man page
watchProgress Man page

Files

momr
momr/inst
momr/inst/CITATION
momr/inst/usage.R
momr/inst/momr_introduction.Rmd
momr/inst/momr_introduction.tex
momr/inst/momr_introduction.pdf
momr/NAMESPACE
momr/data
momr/data/hs_3.3_metahit_genesize.rda
momr/data/mgs_hs_3.3_metahit_sup500.rda
momr/data/hs_3.3_metahit_sample_dat_freq.rda
momr/data/datalist
momr/data/hs_3.3_metahit_sample_dat_raw.rda
momr/R
momr/R/querries.R momr/R/analyses.R momr/R/normalization.R momr/R/data.R momr/R/visualization.R momr/R/filtering.R momr/R/downsizing.R momr/R/mapreduce.R
momr/MD5
momr/DESCRIPTION
momr/man
momr/man/plotBarcodeBW.Rd momr/man/mapResults.Rd momr/man/watchProgress.Rd momr/man/launchTask.Rd momr/man/splitData.Rd momr/man/countSampledGenes.Rd momr/man/abondanceScore.Rd momr/man/projectOntoMGS.Rd momr/man/connectivity.Rd momr/man/momr-package.Rd momr/man/profiles2Genebags.Rd momr/man/selectListSize.Rd momr/man/plotPvals.Rd momr/man/filterListGenebags.Rd momr/man/buildMgsFinal.Rd momr/man/computeSignalMetrics.Rd momr/man/plotMGSQuality.Rd momr/man/phenoPairwiseRelations.Rd momr/man/downsizeGC.Rd momr/man/computeFilteredVectors.Rd momr/man/hs_3.3_metahit_genesize.Rd momr/man/mgs_hs_3.3_metahit_sup500.Rd momr/man/hs_3.3_metahit_sample_dat_raw.Rd momr/man/sampleRandomly.Rd momr/man/plotBarcode.Rd momr/man/deleteData.Rd momr/man/indexReadsGC.Rd momr/man/plotCors2.Rd momr/man/extractSignificant.Rd momr/man/downsizeMatrix.Rd momr/man/extractProfiles.Rd momr/man/normFreqTC.Rd momr/man/indexReads.Rd momr/man/filterMat.Rd momr/man/downsizedRichnessL2T.Rd momr/man/computeUpsizedGC.Rd momr/man/plotBarcode2.Rd momr/man/lmp.Rd momr/man/plotCors.Rd momr/man/filt.hierClust.Rd momr/man/normFreqRPKM.Rd momr/man/hierClust.Rd momr/man/testRelations.Rd momr/man/presenceScore.Rd momr/man/hs_3.3_metahit_sample_dat_freq.Rd momr/man/aggregateProfiles.Rd momr/man/downsizeGC.all.Rd momr/man/countSampledGenesGC.Rd

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

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