Scipediacontent: Scipediacontent moved page Draft Content 254731846 to Irizarry et al 2016a

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Scipediacontent moved page Draft Content 254731846 to Irizarry et al 2016a

Scipediacontent: Created page with " == Abstract == Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about w..."

2021-02-15T09:44:26Z

Created page with " == Abstract == Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about w..."

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== Abstract ==

Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance due in part to a lack of sensitive assessment metrics. We present a series of statistical summaries and plots to evaluate the performance in terms of specificity and sensitivity, available as a R/Bioconductor package (http://bioconductor.org/packages/rnaseqcomp). Using two independent datasets, we assessed seven competing pipelines. Performance was generally poor, with two methods clearly underperforming and RSEM slightly outperforming the rest. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0940-1) contains supplementary material, which is available to authorized users.

Document type: Article

== Full document ==
<pdf>Media:Draft_Content_254731846-beopen790-6377-document.pdf</pdf>

== Original document ==

The different versions of the original document can be found in:

* [http://dx.doi.org/10.1186/s13059-016-0940-1 http://dx.doi.org/10.1186/s13059-016-0940-1] under the license http://creativecommons.org/licenses/by/4.0/

* [http://europepmc.org/articles/PMC4842274 http://europepmc.org/articles/PMC4842274]

* [http://hdl.handle.net/10230/27924 http://hdl.handle.net/10230/27924]

* [http://nrs.harvard.edu/urn-3:HUL.InstRepos:26860249 http://nrs.harvard.edu/urn-3:HUL.InstRepos:26860249] under the license http://creativecommons.org/licenses/by/4.0/

* [https://dx.doi.org/10.1186/s13059-016-0940-1 https://dx.doi.org/10.1186/s13059-016-0940-1]

* [https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-016-0940-1 https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-016-0940-1]

* [http://link.springer.com/content/pdf/10.1186/s13059-016-0940-1.pdf http://link.springer.com/content/pdf/10.1186/s13059-016-0940-1.pdf],
: [http://link.springer.com/article/10.1186/s13059-016-0940-1/fulltext.html http://link.springer.com/article/10.1186/s13059-016-0940-1/fulltext.html],
: [http://link.springer.com/content/pdf/10.1186/s13059-016-0940-1 http://link.springer.com/content/pdf/10.1186/s13059-016-0940-1],
: [http://dx.doi.org/10.1186/s13059-016-0940-1 http://dx.doi.org/10.1186/s13059-016-0940-1] under the license cc-by

* [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0940-1 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0940-1],
: [https://www.ncbi.nlm.nih.gov/pubmed/27107712 https://www.ncbi.nlm.nih.gov/pubmed/27107712],
: [https://link.springer.com/article/10.1186/s13059-016-0940-1 https://link.springer.com/article/10.1186/s13059-016-0940-1],
: [https://paperity.org/p/76211203/a-benchmark-for-rna-seq-quantification-pipelines https://paperity.org/p/76211203/a-benchmark-for-rna-seq-quantification-pipelines],
: [http://europepmc.org/abstract/MED/27107712 http://europepmc.org/abstract/MED/27107712],
: [https://core.ac.uk/display/33028458 https://core.ac.uk/display/33028458],
: [https://dash.harvard.edu/handle/1/26860249 https://dash.harvard.edu/handle/1/26860249],
: [https://jhu.pure.elsevier.com/en/publications/a-benchmark-for-rna-seq-quantification-pipelines https://jhu.pure.elsevier.com/en/publications/a-benchmark-for-rna-seq-quantification-pipelines],
: [https://repositori.upf.edu/handle/10230/27924 https://repositori.upf.edu/handle/10230/27924],
: [http://repository.cshl.edu/id/eprint/32618 http://repository.cshl.edu/id/eprint/32618],
: [http://www.ncbi.nlm.nih.gov/pubmed/27107712 http://www.ncbi.nlm.nih.gov/pubmed/27107712],
: [https://publications.hse.ru/en/articles/202280175 https://publications.hse.ru/en/articles/202280175],
: [http://genomebiology.com/content/pdf/s13059-016-0940-1.pdf http://genomebiology.com/content/pdf/s13059-016-0940-1.pdf],
: [https://academic.microsoft.com/#/detail/2340210804 https://academic.microsoft.com/#/detail/2340210804] under the license http://creativecommons.org/licenses/by/4.0/

DOIS: 10.1186/s13059-016-0940-1 10.1186/s13059-016-0940-1.

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Irizarry et al 2016a - Revision history

Scipediacontent: Scipediacontent moved page Draft Content 254731846 to Irizarry et al 2016a

Scipediacontent: Created page with " == Abstract == Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about w..."