A benchmark for RNA-seq quantification pipelines (Q39827876)

15 September 2017

A benchmark for RNA-seq quantification pipelines (English)

1 reference

Erratum to: A benchmark for RNA-seq quantification pipelines.

15 September 2017

1 reference

1 reference

corrigendum / erratum

0 references

Erratum to: A benchmark for RNA-seq quantification pipelines.

0 references

Mingxiang Teng

1

0 references

Michael I Love

Michael I Love

2

0 references

Christopher E. Mason

8

Christopher E Mason

1 reference

15 September 2017

14

Rafael A Irizarry

1 reference

15 September 2017

5

Alexander Dobin

1 reference

15 September 2017

Carrie A Davis

3

1 reference

15 September 2017

Sarah Djebali

4

1 reference

15 September 2017

Brenton R Graveley

6

1 reference

15 September 2017

Sheng Li

7

1 reference

15 September 2017

Sara Olson

9

1 reference

15 September 2017

Dmitri Pervouchine

10

1 reference

15 September 2017

Cricket A Sloan

11

1 reference

15 September 2017

Xintao Wei

12

1 reference

15 September 2017

Lijun Zhan

13

1 reference

15 September 2017

23 April 2016

1 reference

15 September 2017

1 reference

15 September 2017

17

1 reference

15 September 2017

74

1 reference

describes a project that uses

15 September 2017

edgeR

edgeR

1 reference

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

DESeq2

DESeq2

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-016-0940-1

0 references

cites work

Near-optimal probabilistic RNA-seq quantification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Comparative assessment of methods for the computational inference of transcript isoform abundance from 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=4842274

limma powers differential expression analyses for RNA-sequencing and microarray studies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

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=4842274

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=4842274

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

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=4842274

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Transcriptome and genome sequencing uncovers functional variation in humans

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Human housekeeping genes, revisited

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

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=4842274

Revisiting global gene expression analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

GENCODE: the reference human genome annotation for The ENCODE Project

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Fast gapped-read alignment with Bowtie 2

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Synthetic spike-in standards for 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=4842274

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Mapping and analysis of chromatin state dynamics in nine human cell types

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Tackling the widespread and critical impact of batch effects in high-throughput 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=4842274

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Transcriptome genetics using second generation sequencing in a Caucasian population

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

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=4842274

Consolidated strategy for the analysis of microarray spike-in 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=4842274

Mapping and quantifying mammalian transcriptomes by 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=4842274

The ENCODE (ENCyclopedia Of DNA Elements) Project

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Exploration, normalization, and summaries of high density oligonucleotide array probe level 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=4842274

Analyzing a portion of the ROC curve

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Polyester: simulating RNA-seq datasets with differential transcript expression

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Streaming fragment assignment for real-time analysis of sequencing experiments

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

The self-assessment trap: can we all be better than average?

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Comparison of Affymetrix GeneChip expression measures.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

A benchmark for Affymetrix GeneChip expression measures

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4842274

Multiple-laboratory comparison of microarray platforms

20 August 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0940-1

Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0940-1

An introduction to ROC analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0940-1

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0940-1

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27107712

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-016-0940-1

1 reference

15 September 2017

1 reference

15 September 2017

1 reference