Research graph
References from Data pre-processing for analyzing microbiome data – A mini review. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/nm.4517
10.1038/nm.4517 · External reference
10.1016/j.cell.2012.01.035
10.1016/j.cell.2012.01.035 · External reference
Gut microbiome and its role in colorectal cancer
10.1186/s12885-021-09054-2 · 2021 · External reference
The role of intestinal microbiota in colorectal cancer
10.3389/fphar.2021.674807 · 2021 · External reference
Field guide to next-generation DNA sequencers: field guide to next-gen sequencers
10.1111/j.1755-0998.2011.03024.x · 2011 · External reference
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
10.1186/s12859-016-0976-y · 2016 · External reference
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
10.1038/s41467-019-13036-1 · 2019 · External reference
10.1126/science.1124234
10.1126/science.1124234 · External reference
10.1073/pnas.1117018109
10.1073/pnas.1117018109 · External reference
10.1038/nrg.2016.49
10.1038/nrg.2016.49 · External reference
Normalization and microbial differential abundance strategies depend upon data characteristics
10.1186/s40168-017-0237-y · 2017 · External reference
10.1371/journal.pbio.1002533
10.1371/journal.pbio.1002533 · External reference
Normalization and microbial differential abundance strategies depend upon data characteristics
10.1186/s40168-017-0237-y · 2017 · External reference
10.1038/nmeth.4468
10.1038/nmeth.4468 · External reference
10.1371/journal.pcbi.1004226
10.1371/journal.pcbi.1004226 · External reference
Advances and challenges in metatranscriptomic analysis
10.3389/fgene.2019.00904 · 2019 · External reference
10.1016/j.tim.2017.11.002
10.1016/j.tim.2017.11.002 · External reference
10.1146/annurev-biodatasci-031121-103035
10.1146/annurev-biodatasci-031121-103035 · External reference
Metaproteomics characterizes human gut microbiome function in colorectal cancer
10.1038/s41522-020-0123-4 · 2020 · External reference
10.1038/s41564-017-0084-4
10.1038/s41564-017-0084-4 · External reference
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10.1093/bioinformatics/btu170
10.1093/bioinformatics/btu170 · External reference
10.14806/ej.17.1.200
10.14806/ej.17.1.200 · External reference
Unresolved reference
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ComBat-seq: batch effect adjustment for RNA-seq count data
10.1093/nargab/lqaa078 · 2020 · External reference
10.1093/nar/gkv007
10.1093/nar/gkv007 · External reference
10.1186/s13059-014-0550-8
10.1186/s13059-014-0550-8 · External reference
Batch effects correction for microbiome data with Dirichlet-multinomial regression
10.1093/bioinformatics/bty729 · 2019 · External reference
10.1093/bioinformatics/bts034
10.1093/bioinformatics/bts034 · External reference
10.1038/s41592-019-0619-0
10.1038/s41592-019-0619-0 · External reference
10.1038/nbt.4091
10.1038/nbt.4091 · External reference
10.1016/j.cell.2019.05.006
10.1016/j.cell.2019.05.006 · External reference
PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data
10.1093/bib/bbac622 · 2023 · External reference
10.1038/s41467-022-33071-9
10.1038/s41467-022-33071-9 · External reference
10.1371/journal.pone.0061217
10.1371/journal.pone.0061217 · External reference
Missing value imputation in high-dimensional phenomic data: imputable or not, and how?
10.1186/s12859-014-0346-6 · 2014 · External reference
imputeTS: Time series missing value imputation in R
10.32614/rj-2017-009 · 2017 · External reference
mbImpute: an accurate and robust imputation method for microbiome data
10.1186/s13059-021-02400-4 · 2021 · External reference
10.1038/s41467-020-17041-7
10.1038/s41467-020-17041-7 · External reference
10.1038/nmeth.2658
10.1038/nmeth.2658 · External reference
10.1186/gb-2010-11-3-r25
10.1186/gb-2010-11-3-r25 · External reference
10.1038/s41587-019-0209-9
10.1038/s41587-019-0209-9 · External reference
10.1128/aem.01541-09
10.1128/aem.01541-09 · External reference
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
10.1038/s41587-023-01688-w · 2023 · External reference
10.1101/gr.5969107
10.1101/gr.5969107 · External reference
10.1186/gb-2014-15-3-r46
10.1186/gb-2014-15-3-r46 · External reference
10.1038/ncomms11257
10.1038/ncomms11257 · External reference
10.1038/nmeth.2276
10.1038/nmeth.2276 · External reference
10.1186/s40168-018-0605-2
10.1186/s40168-018-0605-2 · External reference
10.1186/s12915-014-0087-z
10.1186/s12915-014-0087-z · External reference
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10.1016/s0004-3702(97)00043-x
10.1016/s0004-3702(97)00043-x · External reference
10.1111/j.1600-0587.2012.07348.x
10.1111/j.1600-0587.2012.07348.x · External reference
10.1038/s41586-020-2095-1
10.1038/s41586-020-2095-1 · External reference
Major data analysis errors invalidate cancer microbiome findings
10.1101/2023.07.28.550993 · 2023 · External reference
Identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability in microbiome research
10.1128/mbio.00525-18 · 2018 · External reference
Managing batch effects in microbiome data
10.1093/bib/bbz105 · 2020 · External reference
10.1038/s41586-020-2881-9
10.1038/s41586-020-2881-9 · External reference
10.1038/nrg2825
10.1038/nrg2825 · External reference
10.1371/journal.pcbi.1006102
10.1371/journal.pcbi.1006102 · External reference
Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed
10.1093/biostatistics/kxv026 · 2016 · External reference
10.1073/pnas.97.18.10101
10.1073/pnas.97.18.10101 · External reference
Unresolved reference
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Are batch effects still relevant in the age of big data?
10.1016/j.tibtech.2022.02.005 · 2022 · External reference
Why batch effects matter in omics data, and how to avoid them
10.1016/j.tibtech.2017.02.012 · 2017 · External reference
How missing value imputation is confounded with batch effects and what you can do about it
10.1016/j.drudis.2023.103661 · 2023 · External reference
The importance of batch sensitization in missing value imputation
10.1038/s41598-023-30084-2 · 2023 · External reference
HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values
10.1038/s41467-022-31007-x · 2022 · External reference
Statistics or biology: the zero-inflation controversy about scRNA-seq data
10.1186/s13059-022-02601-5 · 2022 · External reference
Analysis of microbiome data in the presence of excess zeros
2017 · External reference
Analysis of composition of microbiomes: a novel method for studying microbial composition
2015 · External reference
10.1093/bioinformatics/btw308
10.1093/bioinformatics/btw308 · External reference
Model uncertainty, data mining and statistical inference
10.2307/2983440 · 1995 · External reference
DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation
10.1093/bioinformatics/btad286 · 2023 · External reference
Analysis of microbial compositions: a review of normalization and differential abundance analysis
10.1038/s41522-020-00160-w · 2020 · External reference
10.1046/j.1461-0248.2001.00230.x
10.1046/j.1461-0248.2001.00230.x · External reference
Methods for normalizing microbiome data: an ecological perspective
10.1111/2041-210x.13115 · 2019 · External reference
10.1186/s13059-019-1716-1
10.1186/s13059-019-1716-1 · External reference
10.1186/s13059-020-02078-0
10.1186/s13059-020-02078-0 · External reference
‘compositions’: a unified R package to analyze compositional data
10.1016/j.cageo.2006.11.017 · 2008 · External reference
metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models
10.1186/s12859-019-2744-2 · 2019 · External reference
MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data
10.1371/journal.pone.0243609 · 2020 · External reference
Large-scale microbiome data integration enables robust biomarker identification
10.1038/s43588-022-00247-8 · 2022 · External reference
10.1186/s13059-022-02753-4
10.1186/s13059-022-02753-4 · External reference
10.1038/s41591-022-01698-2
10.1038/s41591-022-01698-2 · External reference
10.1016/j.cell.2018.08.041
10.1016/j.cell.2018.08.041 · External reference
10.1038/s41467-022-28525-z
10.1038/s41467-022-28525-z · External reference
10.1016/j.clnu.2022.09.012
10.1016/j.clnu.2022.09.012 · External reference
10.3390/nu12103221
10.3390/nu12103221 · External reference
Associations between maternal obesity and offspring gut microbiome in the first year of life
10.1111/ijpo.12921 · 2022 · External reference
10.3390/nu11030666
10.3390/nu11030666 · External reference
Unique gut microbiome signatures among adult patients with moderate to severe atopic dermatitis in Southern Chinese
10.3390/ijms241612856 · 2023 · External reference
10.1016/j.chom.2023.03.010
10.1016/j.chom.2023.03.010 · External reference