scID Uses Discriminant Analysis to Identify Transcriptionally Equivalent Cell Types across Single-Cell RNA-Seq Data with Batch Effect
Sign Up to like & getrecommendations! Published in 2020 at "iScience"
DOI: 10.1016/j.isci.2020.100914
Abstract: Summary The power of single-cell RNA sequencing (scRNA-seq) stems from its ability to uncover cell type-dependent phenotypes, which rests on the accuracy of cell type identification. However, resolving cell types within and, thus, comparison of… read more here.
Keywords: single cell; seq data; cell types; batch effect ... See more keywords
Addressing the batch effect issue for LC/MS metabolomics data in data preprocessing
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-70850-0
Abstract: With the growth of metabolomics research, more and more studies are conducted on large numbers of samples. Due to technical limitations of the Liquid Chromatography–Mass Spectrometry (LC/MS) platform, samples often need to be processed in… read more here.
Keywords: batch; multiple batches; batch effect; effect issue ... See more keywords
PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac622
Abstract: Abstract Microbial communities are highly dynamic and sensitive to changes in the environment. Thus, microbiome data are highly susceptible to batch effects, defined as sources of unwanted variation that are not related to and obscure… read more here.
Keywords: batch effects; microbiome data; variation; plsda batch ... See more keywords
MultiBaC: An R package to remove batch effects in multi-omic experiments.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac132
Abstract: MOTIVATION Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics technologies. However, multi-omic… read more here.
Keywords: batch; multibac package; batch effect; batch effects ... See more keywords
Normalization of Large-Scale Transcriptome Data Using Heuristic Methods
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics and Biology Insights"
DOI: 10.1177/11779322231160397
Abstract: In this study, we introduce an artificial intelligent method for addressing the batch effect of a transcriptome data. The method has several clear advantages in comparison with the alternative methods presently in use. Batch effect… read more here.
Keywords: batch; batch effect; transcriptome data; distribution ... See more keywords
Influence of batch effect correction methods on drug induced differential gene expression profiles
Sign Up to like & getrecommendations! Published in 2019 at "BMC Bioinformatics"
DOI: 10.1186/s12859-019-3028-6
Abstract: BackgroundBatch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signature-based drug repositioning.… read more here.
Keywords: effect; effect correction; drug; batch effect ... See more keywords