ArticleNAR genomics and bioinformatics2021
Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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Who cites it
29 citing papers in PubMed, 51 citations in OpenAlex.
- crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis.BMC genomics · 2026Article
- Decoding autoimmune disease with single-cell immune repertoire and transcriptome sequencing: mechanisms and therapeutic opportunities.Frontiers in immunology · 2026Review
- Tumor-infiltrating B cells produce tumor-specific antibodies and may contribute to suppressing tumor in head and neck squamous cell carcinoma.Oncoimmunology · 2025Article
- The co-inhibitory receptor TIGIT promotes tissue-protective functions in T cells.Nature immunology · 2025Article
- Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.Research square · 2025Article
- Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.bioRxiv : the preprint server for biology · 2025Article
- Immune profiling in subclinical secondary dengue-infected cases reveals adaptive immune signatures correlated to protection from severe dengue.Cell host & microbe · 2025Article
- Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline.NAR genomics and bioinformatics · 2025Article
- T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis.Cell reports. Medicine · 2025Article
- bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data.NAR genomics and bioinformatics · 2024Article
- Article
- TCR clustering by contrastive learning on antigen specificity.Briefings in bioinformatics · 2024Article
- Single-cell immune repertoire analysis.Nature methods · 2024Review
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
- Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.Nature biotechnology · 2024Article
- ePlatypus: an ecosystem for computational analysis of immunogenomics data.Bioinformatics (Oxford, England) · 2023Article
- Article
- Persistent virus-specific and clonally expanded antibody-secreting cells respond to induced self-antigen in the CNS.Acta neuropathologica · 2023Article
- Expansion of CD4+ cytotoxic T lymphocytes with specific gene expression patterns may contribute to suppression of tumor immunity in oral squamous cell carcinoma: single-cell analysis andFrontiers in immunology · 2023Article
- B-cell receptor repertoire sequencing: Deeper digging into the mechanisms and clinical aspects of immune-mediated diseases.iScience · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput single-cell sequencing (scSeq) technologies are revolutionizing the ability to molecularly profile B and T lymphocytes by offering the opportunity to simultaneously obtain information on adaptive immune receptor repertoires (VDJ repertoires) and transcriptomes. An integrated quantification of immune repertoire parameters, such as germline gene usage, clonal expansion, somatic hypermutation and transcriptional states opens up new possibilities for the high-resolution analysis of lymphocytes and the inference of antigen-specificity. While multiple tools now exist to investigate gene expression profiles from scSeq of transcriptomes, there is a lack of software dedicated to single-cell immune repertoires. Here, we present Platypus, an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. Platypus provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. To showcase the capabilities of Platypus, we use it to analyze and visualize single-cell immune repertoires and transcriptomes from B and T cells from convalescent COVID-19 patients, revealing unique insight into the repertoire features and transcriptional profiles of clonally expanded lymphocytes. Platypus will expedite progress by facilitating the analysis of single-cell immune repertoire and transcriptome sequencing.
Identifiers
What OpenQuestion holds
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.