metaMix: Bayesian Mixture Analysis for Metagenomic Community Profiling

Resolves complex metagenomic mixtures by analysing deep sequencing data, using a mixture model based approach. The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture.

AuthorSofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
Date of publication2015-03-15 14:03:01
MaintainerSofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
LicenseGPL-3
Version0.2

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Files in this package

metaMix
metaMix/inst
metaMix/inst/extdata
metaMix/inst/extdata/PT_plots.RData
metaMix/inst/extdata/gi_taxid_prot_example.dmp
metaMix/inst/extdata/blastOut_custom.tab
metaMix/inst/extdata/read_lengths.tab
metaMix/inst/extdata/read_weights.tab
metaMix/inst/extdata/blastOut_default.tab
metaMix/inst/extdata/dat1
metaMix/inst/extdata/dat1/step4.RData
metaMix/inst/extdata/dat1/step2.RData
metaMix/inst/extdata/dat1/gi_taxid_prot_example.dmp
metaMix/inst/extdata/dat1/step3.RData
metaMix/inst/extdata/dat1/blastOut2.tab
metaMix/inst/extdata/dat1/read_lengths.tab
metaMix/inst/extdata/dat1/removeID.tab
metaMix/inst/extdata/dat1/read_weights.tab
metaMix/inst/extdata/dat1/blastOut_old.tab
metaMix/inst/extdata/dat1/remove.sh
metaMix/inst/extdata/dat1/blastOut.tab
metaMix/inst/extdata/dat1/names_example.dmp.bck
metaMix/inst/extdata/dat1/names_example.dmp
metaMix/inst/extdata/names_example.dmp
metaMix/inst/doc
metaMix/inst/doc/guide.Rnw
metaMix/inst/doc/guide.R
metaMix/inst/doc/guide.pdf
metaMix/src
metaMix/src/fast_multinom_weight.cpp
metaMix/NAMESPACE
metaMix/data
metaMix/data/step2.RData
metaMix/data/step3.RData
metaMix/data/step1.RData
metaMix/R
metaMix/R/step3_parallelTemper_nucl.R metaMix/R/Gibbs.R metaMix/R/step2_allInclusive_MM.R metaMix/R/step1_preprocess.R metaMix/R/getArgs.R metaMix/R/step4_bayesModelAver.R
metaMix/R/metaMix-package.r
metaMix/R/EM.R metaMix/R/logmean.R metaMix/R/computePenalty.R metaMix/R/step3_parallelTemper.R metaMix/R/zzz.R
metaMix/vignettes
metaMix/vignettes/guide.Rnw
metaMix/vignettes/guide.Rnw.bck
metaMix/MD5
metaMix/build
metaMix/build/vignette.rds
metaMix/DESCRIPTION
metaMix/man
metaMix/man/bayes.model.aver.Rd metaMix/man/step2.Rd metaMix/man/step3.Rd metaMix/man/generative.prob.Rd metaMix/man/parallel.temper.Rd metaMix/man/parallel.temper.nucl.Rd metaMix/man/reduce.space.Rd metaMix/man/step1.Rd

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