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simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry
The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10081176/ https://www.ncbi.nlm.nih.gov/pubmed/37034702 http://dx.doi.org/10.1101/2023.03.28.534653 |
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author | He, Dongze Patro, Rob |
author_facet | He, Dongze Patro, Rob |
author_sort | He, Dongze |
collection | PubMed |
description | The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools. |
format | Online Article Text |
id | pubmed-10081176 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-100811762023-04-08 simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry He, Dongze Patro, Rob bioRxiv Article The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools. Cold Spring Harbor Laboratory 2023-03-29 /pmc/articles/PMC10081176/ /pubmed/37034702 http://dx.doi.org/10.1101/2023.03.28.534653 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article He, Dongze Patro, Rob simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
title | simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
title_full | simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
title_fullStr | simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
title_full_unstemmed | simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
title_short | simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
title_sort | simpleaf: a simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10081176/ https://www.ncbi.nlm.nih.gov/pubmed/37034702 http://dx.doi.org/10.1101/2023.03.28.534653 |
work_keys_str_mv | AT hedongze simpleafasimpleflexibleandscalableframeworkforsinglecelltranscriptomicsdataprocessingusingalevinfry AT patrorob simpleafasimpleflexibleandscalableframeworkforsinglecelltranscriptomicsdataprocessingusingalevinfry |