momr: Mining Metaomics Data (MetaOMineR)

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'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.

Author
Edi Prifti, Emmanuelle Le Chatelier
Date of publication
2015-07-27 12:42:14
Maintainer
Edi Prifti <edi.prifti@gmail.com>
License
Artistic-2.0
Version
1.1

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

Files in this package

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