Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68378050%3A_____%2F23%3A00574419" target="_blank" >RIV/68378050:_____/23:00574419 - isvavai.cz</a>
Result on the web
<a href="https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad089/7220500?login=true" target="_blank" >https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad089/7220500?login=true</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/bioadv/vbad089" target="_blank" >10.1093/bioadv/vbad089</a>

Result language
angličtina
Original language name
Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis
Original language description
Motivation: While the workflow for primary analysis of single-cell RNA-seq (scRNA-seq) data is well established, the secondary analysis of the feature-barcode matrix is usually done by custom scripts. There is no fully automated pipeline in the R statistical environment, which would follow the current best programming practices and requirements for reproducibility. Results: We have developed scdrake, a fully automated workflow for secondary analysis of scRNA-seq data, which is fully implemented in the R language and built within the drake framework. The pipeline includes quality control, cell and gene filtering, normalization, detection of highly variable genes, dimensionality reduction, clustering, cell type annotation, detection of marker genes, differential expression analysis and integration of multiple samples. The pipeline is reproducible and scalable, has an efficient execution, provides easy extendability and access to intermediate results and outputs rich HTML reports. Scdrake is distributed as a Docker image, which provides a straightforward setup and enhances reproducibility.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10608 - Biochemistry and molecular biology

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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