(Q31144565)

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Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies.

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

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based on heuristic

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Jonathan Thorsen

1

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28 March 2020

2

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Martin Mortensen

3

1 reference

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28 March 2020

Morten Arendt Rasmussen

4

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Europe PubMed Central

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28 March 2020

5

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Europe PubMed Central

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28 March 2020

Søren J Sørensen

7

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28 March 2020

8

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Europe PubMed Central

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28 March 2020

9

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Europe PubMed Central

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28 March 2020

author name string

Waleed Abu Al-Soud

6

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28 March 2020

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25 November 2016

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28 March 2020

1 reference

Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

4

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28 March 2020

1

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28 March 2020

62

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Europe PubMed Central

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28 March 2020

describes a project that uses

object named as

ggplot2

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5123278

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

object named as

phyloseq

R package phyloseq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

0 references

object named as

DESeq2

DESeq

DEseq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

0 references

object named as

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

https://scigraph.springernature.com/pub.10.1186/s40168-016-0208-8

0 references

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Rethinking "enterotypes".

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Waste not, want not: why rarefying microbiome data is inadmissible

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Deep phenotyping of the unselected COPSAC2010 birth cohort study.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Differential abundance analysis for microbial marker-gene surveys

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Structure, function and diversity of the healthy human microbiome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Comparisons of distance methods for combining covariates and abundances in microbiome studies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Enterotypes of the human gut microbiome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

pROC: an open-source package for R and S+ to analyze and compare ROC curves

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Differential expression analysis for sequence count data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Search and clustering orders of magnitude faster than BLAST

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Vaginal microbiome of reproductive-age women

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

A human gut microbial gene catalogue established by metagenomic sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Generalized linear mixed models: a practical guide for ecology and evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Moderated statistical tests for assessing differences in tag abundance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

UniFrac: a new phylogenetic method for comparing microbial communities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5123278

21 June 2018

Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology

1 reference

https://api.crossref.org/works/10.1186%2FS40168-016-0208-8

21 January 2018

An Ordination of the Upland Forest Communities of Southern Wisconsin

1 reference

https://api.crossref.org/works/10.1186%2FS40168-016-0208-8

21 January 2018

A fair comparison

1 reference

https://api.crossref.org/works/10.1186%2FS40168-016-0208-8

21 January 2018

Reply to: "a fair comparison".

1 reference

https://api.crossref.org/works/10.1186%2FS40168-016-0208-8

21 January 2018

Mixed effects models and extensions in ecology with R

1 reference

https://api.crossref.org/works/10.1186%2FS40168-016-0208-8

21 January 2018

Identifiers

10.1186/S40168-016-0208-8

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Dimensions Publication ID

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/s40168-016-0208-8

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27884206%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

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