(Q40204689)

18 September 2017

RNA-Seq workflow: gene-level exploratory analysis and differential expression (English)

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18 September 2017

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2

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18 September 2017

4

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18 September 2017

Michael I Love

1

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author name string

Vladislav Kim

series ordinal

3

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18 September 2017

14 October 2015

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18 September 2017

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18 September 2017

4

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18 September 2017

1070

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Creative Commons Attribution 4.0 International

18 September 2017

start time

14 October 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

ggplot2

object named as

ggplot2

ggplot

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=4670015

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

DESeq2

object named as

DESeq2

DESeq

1 reference

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

cites work

Orchestrating high-throughput genomic analysis with Bioconductor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

svaseq: removing batch effects and other unwanted noise from sequencing data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

PROPER: comprehensive power evaluation for differential expression using RNA-seq

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

Normalization of RNA-seq data using factor analysis of control genes or samples

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

A global non-coding RNA system modulates fission yeast protein levels in response to stress.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

Software for computing and annotating genomic ranges

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

STAR: ultrafast universal RNA-seq aligner

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

Differential expression analysis for sequence count data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

Independent filtering increases detection power for high-throughput experiments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

The Sequence Alignment/Map format and SAMtools

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

The human genome browser at UCSC

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4670015

10.12688/F1000RESEARCH.7035.1

20 August 2018

Identifiers

DOI

1 reference

18 September 2017

1 reference

PMC publication ID

4670015

18 September 2017

PubMed publication ID

26674615

1 reference

PMC publication ID

4670015