ArticleBioinformatics (Oxford, England)2020
alona: a web server for single-cell RNA-seq analysis.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Mapping Cell Identity from scRNA-seq: A primer on computational methods.Computational and structural biotechnology journal · 2025Review
- VICTOR: Validation and inspection of cell type annotation through optimal regression.Computational and structural biotechnology journal · 2024Article
- ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems.BMC bioinformatics · 2024Article
- Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis.Molecular biology and evolution · 2023Article
- Evaluation of single-cell RNAseq labelling algorithms using cancer datasets.Briefings in bioinformatics · 2023Article
- Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.Computational and structural biotechnology journal · 2023Review
- SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data.Computational and structural biotechnology journal · 2023Article
- scCloudMine: A cloud-based app for visualization, comparison, and exploration of single-cell transcriptomic data.Plant communications · 2022Article
- Article
- Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells.Scientific reports · 2022Article
- Mouse genomic and cellular annotations.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- scMRMA: single cell multiresolution marker-based annotation.Nucleic acids research · 2022Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Article
- Asc-Seurat: analytical single-cell Seurat-based web application.BMC bioinformatics · 2021Article
- Targeting the tumor microenvironment in B-cell lymphoma: challenges and opportunities.Journal of hematology & oncology · 2021Review
- Article
- Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods.Nature protocols · 2021Review
- WASP: a versatile, web-accessible single cell RNA-Seq processing platform.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
summarySingle-cell RNA sequencing (scRNA-seq) is a technology to measure gene expression in single cells. It has enabled discovery of new cell types and established cell type atlases of tissues and organs. The widespread adoption of scRNA-seq has created a need for user-friendly software for data analysis. We have developed a web server, alona that incorporates several of the most popular single-cell analysis algorithms into a flexible pipeline. alona can perform quality filtering, normalization, batch correction, clustering, cell type annotation and differential gene expression analysis. Data are visualized in the web browser using an interface based on JavaScript, allowing the user to query genes of interest and visualize the cluster structure. alona accepts a compressed gene expression matrix and identifies cell clusters with a graph-based clustering strategy. Cell types are identified from a comprehensive collection of marker genes or by specifying a custom set of marker genes. AVAILABILITY AND IMPLEMENTATION: The service runs at https://alona.panglaodb.se and the Python package can be downloaded from https://oscar-franzen.github.io/adobo/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.