(Q34812367)

4 August 2017

title

ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq (English)

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4 August 2017

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4

Gregor Reid

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4 August 2017

Andrew D Fernandes

1

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4 August 2017

Jean M Macklaim

series ordinal

2

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4 August 2017

Thomas G Linn

series ordinal

3

1 reference

4 August 2017

Gregory B Gloor

series ordinal

5

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4 August 2017

language of work or name

English

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publication date

2 July 2013

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4 August 2017

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4 August 2017

volume

8

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4 August 2017

issue

7

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4 August 2017

page(s)

e67019

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Creative Commons Attribution 4.0 International

4 August 2017

copyright license

start time

2 July 2013

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

edgeR

object named as

edgeR

1 reference

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

DESeq2

object named as

DESeq

1 reference

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

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Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution

8 July 2018

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Hypothesis testing and power calculations for taxonomic-based human microbiome data

8 July 2018

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Inferring correlation networks from genomic survey data

8 July 2018

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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

8 July 2018

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Dirichlet multinomial mixtures: generative models for microbial metagenomics

8 July 2018

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A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

8 July 2018

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The real cost of sequencing: higher than you think!

8 July 2018

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TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

8 July 2018

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RNA-seq: technical variability and sampling.

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Predicting a human gut microbiota's response to diet in gnotobiotic mice

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Full-length transcriptome assembly from RNA-Seq data without a reference genome

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

A comparison of analog and Next-Generation transcriptomic tools for mammalian studies.

8 July 2018

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RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture

8 July 2018

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Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel

8 July 2018

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Aligning short sequencing reads with Bowtie

8 July 2018

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De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology

8 July 2018

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Differential expression analysis for sequence count data

8 July 2018

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Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

8 July 2018

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MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

8 July 2018

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Most "dark matter" transcripts are associated with known genes

8 July 2018

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Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

8 July 2018

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

8 July 2018

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Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

8 July 2018

1 reference

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Identifying biologically relevant differences between metagenomic communities

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

A review of statistical methods for preprocessing oligonucleotide microarrays.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Sex-specific and lineage-specific alternative splicing in primates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

8 July 2018

1 reference

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ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Statistical methods for detecting differentially abundant features in clinical metagenomic samples

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

TopHat: discovering splice junctions with RNA-Seq

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Effect size, confidence interval and statistical significance: a practical guide for biologists

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

An application of statistics to comparative metagenomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3699591

The formal definition of reference priors

8 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0067019

Comparative analysis of transcriptional and physiological responses of Bacillus cereus to organic and inorganic acid shocks

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0067019

Ordered group reference priors with application to the multinomial problem

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0067019

10.1371/JOURNAL.PONE.0067019

21 January 2018

Identifiers

DOI

1 reference

4 August 2017

0 references

1 reference

4 August 2017

1 reference