Scipediacontent: Scipediacontent moved page Draft Content 762462665 to Robinson et al 2020a

2021-02-12T13:47:11Z

Scipediacontent moved page Draft Content 762462665 to Robinson et al 2020a

Scipediacontent: Created page with " == Abstract == We present pipeComp ( https://github.com/plger/pipeComp ), a flexible R framework for pipeline comparison handling interactions between analysis steps and re..."

2021-02-12T13:47:09Z

Created page with " == Abstract == We present pipeComp ( https://github.com/plger/pipeComp ), a flexible R framework for pipeline comparison handling interactions between analysis steps and re..."

New page

== Abstract ==

We present pipeComp ( https://github.com/plger/pipeComp ), a flexible R framework for pipeline comparison handling interactions between analysis steps and relying on multi-level evaluation metrics. We apply it to the benchmark of single-cell RNA-sequencing analysis pipelines using simulated and real datasets with known cell identities, covering common methods of filtering, doublet detection, normalization, feature selection, denoising, dimensionality reduction, and clustering. pipeComp can easily integrate any other step, tool, or evaluation metric, allowing extensible benchmarks and easy applications to other fields, as we demonstrate through a study of the impact of removal of unwanted variation on differential expression analysis.

Document type: Article

== Full document ==
<pdf>Media:Draft_Content_762462665-beopen410-9031-document.pdf</pdf>

== Original document ==

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

* [http://dx.doi.org/10.3929/ethz-b-000439493 http://dx.doi.org/10.3929/ethz-b-000439493] under the license http://creativecommons.org/licenses/by/4.0/

* [http://europepmc.org/articles/PMC7465801 http://europepmc.org/articles/PMC7465801] under the license https://creativecommons.org/licenses/by/4.0/legalcode

* [http://hdl.handle.net/20.500.11850/439493 http://hdl.handle.net/20.500.11850/439493]

* [https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02136-7 https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02136-7] under the license http://creativecommons.org/licenses/by/4.0/

* [http://link.springer.com/article/10.1186/s13059-020-02136-7 http://link.springer.com/article/10.1186/s13059-020-02136-7],
: [https://doaj.org/toc/1474-760X https://doaj.org/toc/1474-760X] under the license cc-by

* [http://link.springer.com/content/pdf/10.1186/s13059-020-02136-7.pdf http://link.springer.com/content/pdf/10.1186/s13059-020-02136-7.pdf],
: [http://link.springer.com/article/10.1186/s13059-020-02136-7/fulltext.html http://link.springer.com/article/10.1186/s13059-020-02136-7/fulltext.html],
: [http://dx.doi.org/10.1186/s13059-020-02136-7 http://dx.doi.org/10.1186/s13059-020-02136-7]

* [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02136-7 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02136-7],
: [https://www.research-collection.ethz.ch/handle/20.500.11850/439493 https://www.research-collection.ethz.ch/handle/20.500.11850/439493],
: [https://europepmc.org/article/PPR/PPR111323 https://europepmc.org/article/PPR/PPR111323],
: [https://academic.microsoft.com/#/detail/3081957388 https://academic.microsoft.com/#/detail/3081957388] under the license http://creativecommons.org/licenses/by/4.0/

DOIS: 10.1186/s13059-020-02136-7 10.3929/ethz-b-000439493

← Older revision	Revision as of 13:47, 12 February 2021
(No difference)

Robinson et al 2020a - Revision history

Scipediacontent: Scipediacontent moved page Draft Content 762462665 to Robinson et al 2020a

Scipediacontent: Created page with " == Abstract == We present pipeComp ( https://github.com/plger/pipeComp ), a flexible R framework for pipeline comparison handling interactions between analysis steps and re..."