Package: ANCOMBC 2.15.0

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_2.15.0.tar.gz
ANCOMBC_2.15.0.zip(r-4.7)ANCOMBC_2.15.0.zip(r-4.6)ANCOMBC_2.15.0.zip(r-4.5)
ANCOMBC_2.15.0.tgz(r-4.6-any)ANCOMBC_2.15.0.tgz(r-4.5-any)
ANCOMBC_2.15.0.tar.gz(r-4.7-any)ANCOMBC_2.15.0.tar.gz(r-4.6-any)
ANCOMBC_2.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ANCOMBC/json (API)
NEWS

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

Bug tracker:https://github.com/frederickhuanglin/ancombc/issues

Datasets:
  • QMP - Quantitative Microbiome Project data

On BioConductor:ANCOMBC-2.15.0(bioc 3.24)ANCOMBC-2.14.0(bioc 3.23)

differentialexpressionmicrobiomenormalizationsequencingsoftwareancomancombcancombc2correlationdifferential-abundance-analysissecom

11.12 score 136 stars 1 packages 734 scripts 2.9k downloads 2 mentions 7 exports 120 dependencies

Last updated from:d823bf01e6. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING220
linux-devel-x86_64OK411
source / vignettesOK986
linux-release-x86_64OK356
macos-release-arm64OK219
macos-oldrel-arm64OK192
windows-develOK296
windows-releaseOK288
windows-oldrelOK261
wasm-releaseOK210

Exports:ancomancombcancombc2data_sanity_checksecom_distsecom_linearsim_plnm

Dependencies:askpassbackportsbase64encbitbit64bootbslibcachemcellrangercheckmateclassclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDescToolsdigestdoParalleldoRNGe1071energyevaluateExactexpmfarverfastmapfontawesomeforcatsforeachforeignFormulafsggplot2gldgluegridExtragslgtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelme4lmerTestlmommagrittrMASSMatrixmemoisemimeminqamultcompmvtnormnlmenloptrnnetnumDerivopensslpillarpkgconfigprettyunitsprogressproxyquadprogR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlreformulasrematchrlangrmarkdownrngtoolsrootSolverpartrstudioapiS7sandwichsassscalesstringistringrsurvivalsysTH.datatibbletidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunyamlzoo

ANCOM Tutorial

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered fromANCOM.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2024-10-21
Started: 2022-10-11

ANCOM-BC Tutorial

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered fromANCOMBC.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2024-10-21
Started: 2020-08-10

ANCOM-BC2 Tutorial

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered fromANCOMBC2.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-04-27
Started: 2022-10-11

SECOM Tutorial

Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered fromSECOM.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-01-07
Started: 2022-10-11

Tutorial on Data Sanity and Integrity Checks

Menglu Liang$^1$, Huang Lin$^1$, $^1$University of Maryland, College Park, MD 20742

Rendered fromdata_sanity_check.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-03-16
Started: 2024-10-21