Detecting and correcting systematic variation in large-scale RNA sequencing data (Q30844399)

15 October 2017

Detecting and correcting systematic variation in large-scale RNA sequencing data (English)

1 reference

15 October 2017

Danielle Thierry-Mieg

11

Danielle Thierry-Mieg

0 references

D Kreil

13

David P Kreil

1 reference

15 October 2017

May Wang

9

0 references

Paweł P Łabaj

Paweł P Łabaj

2

0 references

Jean Thierry-Mieg

Jean Thierry-Mieg

12

0 references

Christopher E. Mason

14

Christopher E Mason

1 reference

15 October 2017

Sheng Li

1

1 reference

15 October 2017

Paul Zumbo

3

1 reference

15 October 2017

Peter Sykacek

4

1 reference

15 October 2017

Wei Shi

5

1 reference

15 October 2017

Leming Shi

6

1 reference

15 October 2017

John Phan

7

1 reference

15 October 2017

Po-Yen Wu

8

1 reference

15 October 2017

Charles Wang

10

1 reference

15 October 2017

24 August 2014

1 reference

15 October 2017

1 reference

15 October 2017

32

1 reference

15 October 2017

9

1 reference

15 October 2017

888-895

1 reference

describes a project that uses

15 October 2017

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4160374

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Transcriptomic dissection of myogenic differentiation signature in caprine by RNA-Seq.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Software for computing and annotating genomic ranges

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Systematic biases in DNA copy number originate from isolation procedures

14 July 2018

1 reference

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Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

STAR: ultrafast universal RNA-seq aligner

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

SERE: single-parameter quality control and sample comparison for RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

RSeQC: quality control of RNA-seq experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

RNA-SeQC: RNA-seq metrics for quality control and process optimization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Performance comparison of benchtop high-throughput sequencing platforms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Summarizing and correcting the GC content bias in high-throughput sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

GC-content normalization for RNA-Seq data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Using control genes to correct for unwanted variation in microarray data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Field guide to next‐generation DNA sequencers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

BamTools: a C API and toolkit for analyzing and managing BAM files

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Improving RNA-Seq expression estimates by correcting for fragment bias

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

A pipeline for RNA-seq data processing and quality assessment

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

A survey of sequence alignment algorithms for next-generation sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Biases in Illumina transcriptome sequencing caused by random hexamer priming

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Understanding mechanisms underlying human gene expression variation with RNA sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

BEDTools: a flexible suite of utilities for comparing genomic features

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Disease signatures are robust across tissues and experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

The Sequence Alignment/Map format and SAMtools

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Capturing heterogeneity in gene expression studies by surrogate variable analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Moderated statistical tests for assessing differences in tag abundance

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Data quality in genomics and microarrays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

AceView: a comprehensive cDNA-supported gene and transcripts annotation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

MGED standards: work in progress

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

A study of inter-lab and inter-platform agreement of DNA microarray data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Assessing the accuracy of prediction algorithms for classification: an overview

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4160374

Multiple-laboratory comparison of microarray platforms

14 July 2018

1 reference

The Genotype-Tissue Expression (GTEx) project

21 January 2018

1 reference

The NIH Roadmap Epigenomics Mapping Consortium

21 January 2018

1 reference

A polygenic burden of rare disruptive mutations in schizophrenia

21 January 2018

1 reference

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

21 January 2018

1 reference

21 January 2018

Prepare for the deluge

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25150837

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Empowering microarrays in the regulatory setting

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25150837

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NBT.3000

1 reference

Dimensions Publication ID

15 October 2017

0 references

1 reference

15 October 2017

PubMed publication ID

25150837

1 reference