Package: ANCOMBC 2.9.0

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_2.9.0.tar.gz
ANCOMBC_2.9.0.zip(r-4.5)ANCOMBC_2.9.0.zip(r-4.4)ANCOMBC_2.9.0.zip(r-4.3)
ANCOMBC_2.9.0.tgz(r-4.4-any)ANCOMBC_2.9.0.tgz(r-4.3-any)
ANCOMBC_2.9.0.tar.gz(r-4.5-noble)ANCOMBC_2.9.0.tar.gz(r-4.4-noble)
ANCOMBC_2.9.0.tgz(r-4.4-emscripten)ANCOMBC_2.9.0.tgz(r-4.3-emscripten)
ANCOMBC.pdf |ANCOMBC.html✨
ANCOMBC/json (API)
NEWS

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

Peer review:

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

Datasets:
  • QMP - Quantitative Microbiome Project data

On BioConductor:ANCOMBC-2.9.0(bioc 3.21)ANCOMBC-2.8.0(bioc 3.20)

differentialexpressionmicrobiomenormalizationsequencingsoftwareancomancombcancombc2correlationdifferential-abundance-analysissecom

10.61 score 110 stars 1 packages 408 scripts 2.3k downloads 2 mentions 7 exports 127 dependencies

Last updated 2 months agofrom:6c44bf5ef2. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winOKDec 19 2024
R-4.5-linuxOKDec 19 2024
R-4.4-winOKDec 19 2024
R-4.4-macOKDec 19 2024
R-4.3-winOKDec 19 2024
R-4.3-macOKDec 19 2024

Exports:ancomancombcancombc2data_sanity_checksecom_distsecom_linearsim_plnm

Dependencies:askpassbackportsbase64encbitbit64bootbslibcachemcellrangercheckmateclassclicliprclustercodetoolscolorspacecpp11crayoncurlCVXRdata.tableDescToolsdigestdoParalleldoRNGe1071ECOSolveRenergyevaluateExactexpmfansifarverfastmapfontawesomeforcatsforeachforeignFormulafsggplot2gldgluegmpgridExtragslgtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelme4lmerTestlmommagrittrMASSMatrixmemoisemgcvmimeminqamultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslosqppillarpkgconfigprettyunitsprogressproxyR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlrematchrlangrmarkdownRmpfrrngtoolsrootSolverpartrstudioapisandwichsassscalesscsstringistringrsurvivalsysTH.datatibbletidyselecttinytextzdbutf8vctrsviridisviridisLitevroomwithrxfunyamlzoo

ANCOM Tutorial

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

Rendered fromANCOM.Rmdusingknitr::rmarkdownon Dec 19 2024.

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 Dec 19 2024.

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 Dec 19 2024.

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

SECOM Tutorial

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

Rendered fromSECOM.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-10-21
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 Dec 19 2024.

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