ArticleNucleic acids research2018
SCPortalen: human and mouse single-cell centric database.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Human Cancer Single-Cell RNA-Seq Datasets Using the IMMUcan Database.Cancer research · 2023Pooled it
- Dear-OMG: An Omics-General Compression Method for Genomics, Proteomics and Metabolomics Data.Interdisciplinary sciences, computational life sciences · 2026Article
- Immune regulation and therapeutic targets in sepsis: insights from single-cell transcriptomics.Frontiers in immunology · 2026Review
- hECA v2.0: an AI-ready ensemble cell atlas of single-cell RNA and ATAC sequencing data.Scientific data · 2025Article
- Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era.Biomarker research · 2024Review
- starTracer is an accelerated approach for precise marker gene identification in single-cell RNA-Seq analysis.Communications biology · 2024Article
- A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations.ArXiv · 2024Article
- Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment.Nature reviews. Urology · 2024Review
- Progress in single-cell multimodal sequencing and multi-omics data integration.Biophysical reviews · 2024Review
- SCAN: Spatiotemporal Cloud Atlas for Neural cells.Nucleic acids research · 2024Article
- A systematic overview of single-cell transcriptomics databases, their use cases, and limitations.Frontiers in bioinformatics · 2024Review
- ImmunoPET imaging of Trop2 expression in solid tumors with nanobody tracers.European journal of nuclear medicine and molecular imaging · 2024Article
- SINGLE-CELL TRANSCRIPTOME ANALYSIS IN HEALTH AND DISEASE.Shock (Augusta, Ga.) · 2024Article
- Transcriptional profiles reveal histologic origin and prognosis across 33 The Cancer Genome Atlas tumor types.Translational cancer research · 2023Article
- ABC portal: a single-cell database and web server for blood cells.Nucleic acids research · 2023Article
- HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses.Nucleic acids research · 2023Article
- Article
- SC2sepsis: sepsis single-cell whole gene expression database.Database : the journal of biological databases and curation · 2022Article
- scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data.Genome biology · 2022Article
- SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data.iScience · 2022Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database 'SCPortalen' (http://single-cell.clst.riken.jp/). The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available. The target users of SCPortalen are all researchers interested in specific cell types or population heterogeneity. Through the web interface of SCPortalen users are easily able to search, explore and download the single-cell datasets of their interests.
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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.