(Q35904373)

11 August 2017

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics (English)

1 reference

11 August 2017

0 references

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

author name string

Tobias Österlund

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Olle Nerman

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Erik Kristiansson

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

language of work or name

English

0 references

publication date

25 January 2016

1 reference

11 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

page(s)

78

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

11 June 2020

limma

object named as

Limma

2 references

22 June 2022

https://europepmc.org/article/PMC/4727335

based on heuristic

inferred from PubMed Central ID database lookup

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

DESeq2

object named as

DESeq2

1 reference

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

edgeR

object named as

edgeR

EdgeR

1 reference

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

edgeR

0 references

cites work

Tentacle: distributed quantification of genes in metagenomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Overview of a surface-ripened cheese community functioning by meta-omics analyses

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

A robust approach for identifying differentially abundant features in metagenomic samples

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

The effects of variable sample biomass on comparative metagenomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Binning metagenomic contigs by coverage and composition

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

STAMP: statistical analysis of taxonomic and functional profiles.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Differential abundance analysis for microbial marker-gene surveys

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Gut metagenome in European women with normal, impaired and diabetic glucose control

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Studying the microbiology of the indoor environment

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

A comparison of methods for differential expression analysis of RNA-seq data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

FANTOM: Functional and taxonomic analysis of metagenomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

The effect of correlation in false discovery rate estimation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

A metagenome-wide association study of gut microbiota in type 2 diabetes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Human gut microbiome viewed across age and geography

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Unlocking the potential of metagenomics through replicated experimental design

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

IMG/M: the integrated metagenome data management and comparative analysis system

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Accelerated Profile HMM Searches

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Metagenomic biomarker discovery and explanation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Accessing the soil metagenome for studies of microbial diversity.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Differential expression analysis for sequence count data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Metagenomics: Facts and Artifacts, and Computational Challenges*

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

A human gut microbial gene catalogue established by metagenomic sequencing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

A scaling normalization method for differential expression analysis of RNA-seq data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

11 July 2018

A primer on metagenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Identifying biologically relevant differences between metagenomic communities

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Statistical methods for detecting differentially abundant features in clinical metagenomic samples

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Weighted analysis of general microarray experiments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

IMG/M: a data management and analysis system for metagenomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Moderated statistical tests for assessing differences in tag abundance

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

An application of statistics to comparative metagenomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Metagenomics for studying unculturable microorganisms: cutting the Gordian knot

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Statistical significance for genomewide studies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

The TIGRFAMs database of protein families

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

BLAT—The BLAST-Like Alignment Tool

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Quantitative metagenomic analyses based on average genome size normalization

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

Average genome size: a potential source of bias in comparative metagenomics

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4727335

10.1186/S12864-016-2386-Y

24 September 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26810311%20AND%20SRC:MED&resulttype=core&format=json