CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data (Q30989599)

14 October 2017

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data (English)

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14 October 2017

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Praveen Kumar Raj Kumar

1

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14 October 2017

Thanh V Hoang

2

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14 October 2017

Michael L Robinson

3

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14 October 2017

Panagiotis A Tsonis

4

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14 October 2017

Chun Liang

5

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14 October 2017

language of work or name

English

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publication date

25 August 2015

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14 October 2017

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14 October 2017

5

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14 October 2017

13443

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Creative Commons Attribution 4.0 International

14 October 2017

start time

25 August 2015

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

DESeq2

object named as

DESeq

DESeq2

1 reference

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

DESeq2

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cites work

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

1 reference

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Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses 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=4548254

Systematic evaluation of spliced alignment programs 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=4548254

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

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=4548254

14 July 2018

1 reference

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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=4548254

Tools for mapping high-throughput sequencing 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=4548254

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

14 July 2018

1 reference

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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=4548254

Using Tablet for visual exploration of second-generation sequencing 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=4548254

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

Repetitive DNA and next-generation sequencing: computational challenges and solutions

14 July 2018

1 reference

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Computational methods for transcriptome annotation and quantification using 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=4548254

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

Quality control and preprocessing of metagenomic datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

Integrative genomics viewer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

From RNA-seq reads to differential expression results

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

Differential expression analysis for sequence count 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=4548254

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=4548254

Fast and SNP-tolerant detection of complex variants and splicing in short reads

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

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=4548254

Fast and accurate short read alignment with Burrows-Wheeler transform

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

Next-generation DNA 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=4548254

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4548254

Mapping and quantifying mammalian transcriptomes 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=4548254

Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

14 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP13443

21 January 2018

Identifiers

DOI

10.1038/SREP13443

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Dimensions Publication ID

14 October 2017

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14 October 2017

PubMed publication ID

26304587

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