Package: MicEco 0.9.19

Jakob Russel

MicEco: Various functions for microbial community data

Collection of functions for microbiome analyses. E.g. fitting neutral models and standardized effect sizes of phylogenetic beta diversities, and much more.

Authors:Jakob Russel [aut, cre]

MicEco_0.9.19.tar.gz
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MicEco_0.9.19.tgz(r-4.4-any)MicEco_0.9.19.tgz(r-4.3-any)
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MicEco.pdf |MicEco.html✨
MicEco/json (API)

# Install 'MicEco' in R:
install.packages('MicEco', repos = c('https://metagenlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/russel88/miceco/issues

Datasets:
  • gg_13_5_16S - 16S copy numbers for GreenGenes 13_5 database OTUs

On CRAN:

16samplicon-sequencingmicrobial-communitiesmicrobial-ecologymicrobiomemicrobiome-analysisnull-model

4.15 score 41 stars 69 scripts 28 exports 117 dependencies

Last updated 2 years agofrom:91f8e6f5d6. Checks:OK: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winWARNINGNov 06 2024
R-4.5-linuxWARNINGNov 06 2024
R-4.4-winWARNINGNov 06 2024
R-4.4-macWARNINGNov 06 2024
R-4.3-winWARNINGNov 06 2024
R-4.3-macWARNINGNov 06 2024

Exports:adonis_OmegaSqclrcomdist.parcomdistnt.parcommunity_rrnaneutral.fitneutral.randproportionalityps_eulerps_pheatmapps_pruneps_refactorps_tax_cleanps_vennrarefy_rrnararefy_rrna.matrixrarefy_rrna.phyloseqrcurveses.comdistses.comdist2ses.comdistntses.comdistnt2ses.mntd.parses.mpd.parses.permtestses.UniFracUniFrac.multiWdS.test

Dependencies:abindade4apeaskpassbackportsbase64encbbmlebdsmatrixBiobaseBiocGenericsbiomformatBiostringsbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestdoSNOWeulerrevaluatefansifarverfastmapfontawesomeforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataGenSAggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemulttestmunsellmvtnormnlmennetnumDerivopensslpermutepheatmapphyloseqpicantepillarpixmappkgconfigplyrpolyclippolylabelrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangrmarkdownrpartrstudioapiS4VectorssassscalessnowspstringistringrsurvivalsystibbletinytexUCSC.utilsutf8vctrsveganviridisviridisLitewithrxfunXVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Calculate (partial) Omega-squared (effect-size calculation) for PERMANOVA and add it to the input objectadonis_OmegaSq
CLR transformation of community matrix, with multiplicative zero replacementclr
Inter-community mean pairwise distancecomdist.par
Inter-community mean nearest taxon distancecomdistnt.par
Calculate the community/sample-wise mean 16S rRNA copy numberscommunity_rrna
16S copy numbers for GreenGenes 13_5 database OTUsgg_13_5_16S
Fit Sloan et al. (2006) Neutral Modelneutral.fit
Fit Sloan et al. (2006) Neutral Model several timesneutral.rand
Calculate proportionality between all pairs of OTUs, for network analysisproportionality
Make Euler diagram of shared taxa (ASVs, OTUs) across sample groupsps_euler
Make pheatmap directly from a phyloseq objectps_pheatmap
Prune taxa from phyloseq object by their prevalence or abundanceps_prune
Relevel the Sample variable in a psmelted phyloseq objectps_refactor
Clean tax_table such that NAs are replaced with names of the most specific known taxonomy prefixed with the rank.ps_tax_clean
Make Venn diagram of shared taxa (ASVs, OTUs) across sample groupsps_venn
Rarefy and normalize based on 16S rRNA copy numbersrarefy_rrna rarefy_rrna.matrix rarefy_rrna.phyloseq
Rarefaction curve on phyloseq object Theoretical richness with vegan's rarefy functionrcurve
Standardized effect size of inter-community MPD (betaMPD, betaNRI)ses.comdist
Standardized effect size of inter-community MPD (betaMPD, betaNRI)ses.comdist2
Standardized effect size of inter-community MNTD (betaMNTD, betaNTI)ses.comdistnt
Standardized effect size of inter-community MNTD (betaMNTD, betaNTI)ses.comdistnt2
Standardized effect size of MNTDses.mntd.par
Standardized effect size of MPDses.mpd.par
Permutation test of z-matrixses.permtest
Standardized effect size of unifracses.UniFrac
Run 'UniFrac' multiple times in parallel and take the averageUniFrac.multi
Permutation test of Wd* - robust distance-based multivariate analysis of varianceWdS.test