ArticlePLoS computational biology2025
scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- Trial
- A single-cell profile of the porcine immune repertoire: concurrent profiling of T cell receptor and B cell receptor V(D)J sequences in health.Advanced biotechnology · 2026Article
- Intrathecal Allogeneic B7-H3-Targeted CAR γδ T Cells for Leptomeningeal Metastasis from Solid Tumors: Safety, Efficacy, and Immunologic Dynamics in a Phase I Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- αTIGIT-guided IL-15 mimetics drive potent and safe antitumor immunity by restoring tumor-infiltrating T cells.Cellular & molecular immunology · 2026Article
- Human memory CD4bioRxiv : the preprint server for biology · 2026Article
- Structural basis of IgLON5 autoantibody recognition in autoimmune encephalitis.Nature communications · 2026Article
- Single-cell RNA sequencing reveals clonally expanded CD4+ tissue-resident memory T cells in histidyl-tRNA synthetase-induced myositis.JCI insight · 2026Article
- GPR15-guided CD8Nature · 2026Article
- Case of complete response to immunotherapy in MMR-deficient prostate cancer associated with NK-like and CD4Cell reports. Medicine · 2026Article
- Refined single-cell profiling captures a CCR5EBioMedicine · 2026Article
- Functional and dysfunctional T regulatory cell states in human tissues in RA and other autoimmune arthritic diseases.Nature immunology · 2026Article
- Distinct immune microenvironment in HER2-low triple-negative breast cancer underlies inferior response to immunotherapy.NPJ precision oncology · 2026Article
- Congenital cytomegalovirus infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- HIV-1 BG505 SOSIP immunization induced B cell expansion targeting the 465-glycan hole, with neutralizing antibodies exhibiting distinct binding modes and mechanisms of virus inhibition.PLoS pathogens · 2026Article
- Highly focused human CD8+ T-cell response in the lower airways during acute influenza infection.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- CNS1-dependent regulatory T cells shape recovery from acute lung injury.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- CKS1B is a tumor-intrinsic factor driving CD8Science advances · 2026Article
- AKAP12-LMOD1 signaling defines stromal CAF activation and epithelial junction loss in colorectal cancer.Scientific reports · 2026Article
- Mapping breast cancer lineage in radiation and immunotherapy using the REMAP mouse.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and spatial transcriptomics analyses reveal tumor microenvironment-driven proliferation of NF2-associated vestibular schwannomas.Journal of neuroinflammation · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) and single-cell RNA sequencing (scRNA-seq) provide a transformative approach to profiling immune responses at unprecedented resolution across diverse pathophysiologic contexts. This work presents scRepertoire 2, a substantial update to our R package for analyzing and visualizing single-cell immune receptor data. This new version introduces an array of features designed to enhance both the depth and breadth of immune receptor analysis, including improved workflows for clonotype tracking, repertoire diversity metrics, and novel visualization modules that facilitate longitudinal and comparative studies. Additionally, scRepertoire 2 offers seamless integration with contemporary single-cell analysis frameworks like Seurat and SingleCellExperiment, allowing users to conduct end-to-end single-cell immune profiling with transcriptomic data. Performance optimizations in scRepertoire 2 resulted in a 85.1% increase in speed and a 91.9% reduction in memory usage from the first version over the range repertoire size tested in benchmarking, addressing the demands of the ever-increasing size and scale of single-cell studies. This release marks an advancement in single cell immunogenomics, equipping researchers with a robust toolset to uncover immune dynamics in health and disease.
Indexed as
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.