MBECS: Microbiome Batch Effects Correction Suite: BMC Bioinformatics

M. Olbrich; A. Künstner; H. Busch

doi:10.1186/s12859-023-05252-w

MBECS: Microbiome Batch Effects Correction Suite: BMC Bioinformatics

M. Olbrich
, A. Künstner
, H. Busch

University of Lübeck

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the Microbiome Batch Effects Correction Suite development that integrates several BECAs and evaluation metrics into a software package for the statistical computation framework R. © 2023, The Author(s).

Original language	British English
Journal	BMC Bioinform.
Volume	24
Issue number	1
DOIs	https://doi.org/10.1186/s12859-023-05252-w
State	Published - 2023

Keywords

Batch effects
Bioconductor
Microbiome
phyloseq
R-package
Algorithms
Microbiota
Software
Molecular biology
Batch effect
Bioconductors
Effect corrections
Evaluation metrics
Phyloseq
Statistical computations
algorithm
article
microbiome
nonhuman
software
microflora
Biotechnology

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10.1186/s12859-023-05252-w

https://www.scopus.com/inward/record.uri?eid=2-s2.0-85158042636&doi=10.1186%2fs12859-023-05252-w&partnerID=40&md5=5ec3bd58bde795ecde719af25b83b536

Cite this

@article{36ed2f6efd434b07b6d83c4bb2b682b8,

title = "MBECS: Microbiome Batch Effects Correction Suite: BMC Bioinformatics",

abstract = "Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the Microbiome Batch Effects Correction Suite development that integrates several BECAs and evaluation metrics into a software package for the statistical computation framework R. {\textcopyright} 2023, The Author(s).",

keywords = "Batch effects, Bioconductor, Microbiome, phyloseq, R-package, Algorithms, Microbiota, Software, Molecular biology, Batch effect, Bioconductors, Effect corrections, Evaluation metrics, Phyloseq, Statistical computations, algorithm, article, microbiome, nonhuman, software, microflora, Biotechnology",

author = "M. Olbrich and A. K{\"u}nstner and H. Busch",

note = "Export Date: 11 January 2024; Cited By: 0; Correspondence Address: M. Olbrich; L{\"u}beck Institute for Experimental Dermatology, University of L{\"u}beck, L{\"u}beck, Germany; email: [email protected]; H. Busch; L{\"u}beck Institute for Experimental Dermatology, University of L{\"u}beck, L{\"u}beck, Germany; email: [email protected]; CODEN: BBMIC",

year = "2023",

doi = "10.1186/s12859-023-05252-w",

language = "British English",

volume = "24",

journal = "BMC Bioinform.",

issn = "1471-2105",

publisher = "BioMed Central Ltd.",

number = "1",

}

TY - JOUR

T1 - MBECS: Microbiome Batch Effects Correction Suite

T2 - BMC Bioinformatics

AU - Olbrich, M.

AU - Künstner, A.

AU - Busch, H.

N1 - Export Date: 11 January 2024; Cited By: 0; Correspondence Address: M. Olbrich; Lübeck Institute for Experimental Dermatology, University of Lübeck, Lübeck, Germany; email: [email protected]; H. Busch; Lübeck Institute for Experimental Dermatology, University of Lübeck, Lübeck, Germany; email: [email protected]; CODEN: BBMIC

PY - 2023

Y1 - 2023

N2 - Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the Microbiome Batch Effects Correction Suite development that integrates several BECAs and evaluation metrics into a software package for the statistical computation framework R. © 2023, The Author(s).

AB - Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the Microbiome Batch Effects Correction Suite development that integrates several BECAs and evaluation metrics into a software package for the statistical computation framework R. © 2023, The Author(s).

KW - Batch effects

KW - Bioconductor

KW - Microbiome

KW - phyloseq

KW - R-package

KW - Algorithms

KW - Microbiota

KW - Software

KW - Molecular biology

KW - Batch effect

KW - Bioconductors

KW - Effect corrections

KW - Evaluation metrics

KW - Phyloseq

KW - Statistical computations

KW - algorithm

KW - article

KW - microbiome

KW - nonhuman

KW - software

KW - microflora

KW - Biotechnology

U2 - 10.1186/s12859-023-05252-w

DO - 10.1186/s12859-023-05252-w

M3 - Article

C2 - 37138207

SN - 1471-2105

VL - 24

JO - BMC Bioinform.

JF - BMC Bioinform.

IS - 1

ER -

MBECS: Microbiome Batch Effects Correction Suite: BMC Bioinformatics

Abstract

Keywords

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