Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (Q29547403)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

Wolfgang Huber

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

Simon Anders

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

author name string

Love MI

1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

Huber W

2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

Anders S

3

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

language of work or name

1 reference

23 April 2017

publication date

1 January 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

volume

15

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

page(s)

550

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

issue

12

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

25 February 2020

copyright license

start time

1 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

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

DESeq2

1 reference

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

DESeq2

0 references

limma

object named as

limma

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-014-0550-8

0 references

cites work

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Differential expression analysis for sequence count data

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Bioconductor: open software development for computational biology and bioinformatics

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

HTSeq--a Python framework to work with high-throughput sequencing data

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Differential analysis of gene regulation at transcript resolution with RNA-seq

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Regularization Paths for Generalized Linear Models via Coordinate Descent

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Understanding mechanisms underlying human gene expression variation with RNA sequencing

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Robustly detecting differential expression in RNA sequencing data using observation weights

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Design and analysis of Bar-seq experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Software for computing and annotating genomic ranges

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

easyRNASeq: a bioconductor package for processing RNA-Seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Detecting differential usage of exons from RNA-seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Identifying differentially expressed transcripts from RNA-seq data with biological variation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Removing technical variability in RNA-seq data using conditional quantile normalization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

GC-content normalization for RNA-Seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Significance testing in ridge regression for genetic data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

A powerful and flexible approach to the analysis of RNA sequence count data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Independent filtering increases detection power for high-throughput experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Testing significance relative to a fold-change threshold is a TREAT.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Moderated statistical tests for assessing differences in tag abundance

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

A variance-stabilizing transformation for gene-expression microarray data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Complete alternative splicing events are bubbles in splicing graphs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Comparison of Affymetrix GeneChip expression measures.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4302049

Dimensions Publication ID

26 November 2018

Identifiers

1015222646

0 references

Mendeley publication ID

322a7f85-8dba-3322-a147-b7b5e5bf2382

1 reference

https://www.mendeley.com/catalogue/322a7f85-8dba-3322-a147-b7b5e5bf2382/

title

Moderated estimation of fold chan... preview & related info | Mendeley (British English)

8 October 2022

48027

1 reference

48027

419026

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

3 references

23 April 2017

419026

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25516281%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25516281

23 April 2017

419026