ArticleBioinformatics (Oxford, England)2023
simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- QCatch: a framework for quality control assessment and analysis of single-cell sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Single-cell RNA sequencing data processing using cloud-based serverless computing.GigaByte (Hong Kong, China) · 2026Article
- Brain tumors induce widespread disruption of calvarial bone and alteration of skull marrow immune landscape.Nature neuroscience · 2025Article
- The loss of microRNA-26b promotes aortic calcification through the regulation of cell-specific target genes.Cardiovascular research · 2025Article
- Metastatic small cell lung cancer arises from TP53/RB1-deficient and MYC overproduction hESC-derived PNECs.eLife · 2025Article
- Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.Bioinformatics (Oxford, England) · 2025Article
- T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis.Cell reports. Medicine · 2025Article
- Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.Nucleic acids research · 2025Article
- Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.Bioinformatics (Oxford, England) · 2024Article
- Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads.bioRxiv : the preprint server for biology · 2024Article
- scCensus: Off-target scRNA-seq reads reveal meaningful biology.bioRxiv : the preprint server for biology · 2024Article
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
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Abstract
summaryThe 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. AVAILABILITY AND IMPLEMENTATION: Simpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation for simpleaf is available at https://simpleaf.readthedocs.io/en/latest/ and tutorials for simpleaf that have been developed can be accessed at https://combine-lab.github.io/alevin-fry-tutorials.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.