Package: ANCOMBC 2.7.0

Huang Lin

ANCOMBC: Microbiome differential abudance and correlation analyses with bias correction

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

Authors:Huang Lin [cre, aut]

ANCOMBC_2.7.0.tar.gz
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ANCOMBC_2.7.0.tgz(r-4.4-any)ANCOMBC_2.7.0.tgz(r-4.3-any)
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ANCOMBC.pdf |ANCOMBC.html✨
ANCOMBC/json (API)
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Bug tracker:https://github.com/frederickhuanglin/ancombc/issues

On BioConductor:ANCOMBC-2.7.0(bioc 3.20)ANCOMBC-2.6.0(bioc 3.19)

bioconductor-package

6 exports 1.31 score 212 dependencies 2 dependents 2 mentions

Last updated 2 months agofrom:607faaadc8

Exports:ancomancombcancombc2secom_distsecom_linearsim_plnm

Dependencies:abindapeaskpassbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64blusterbootbslibcachemCairocellrangercheckmateclasscliclustercodetoolscolorspacecpp11crayoncurlCVXRdata.tableDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsDescToolsdigestDirichletMultinomialdoParalleldoRNGdplyrdqrnge1071ECOSolveRenergyevaluateExactexpmfansifarverfastmapFNNfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgldgluegmpgridExtragslgtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphIRangesirlbaisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclelme4lmerTestlmomlpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmediationmemoisemgcvmiamimeminqamultcompMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnumDerivopensslopenxlsxosqppermutepheatmappillarpkgconfigplyrpngprettyunitsprogressproxypurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsrbiomRColorBrewerRcppRcppAnnoyRcppEigenRcppHNSWRcppMLRcppParallelRcppProgressRdpackreadxlrematchreshape2rjsonrlangrmarkdownRmpfrrngtoolsrootSolverpartRSpectrarstudioapirsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscsscuttleSingleCellExperimentsitmoslamsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttidytreetinytextreeioTreeSummarizedExperimentUCSC.utilsutf8uwotvctrsveganviporviridisviridisLitewithrxfunXVectoryamlyulab.utilszipzlibbioczoo