ReviewNature protocols2025
kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq.
Review in Nature protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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
42 citing papers in PubMed.
- Prefibrotic bone marrow microenvironment is a hallmark of clonal hematopoiesis.Nature immunology · 2026Article
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- Bioinformatics and multi-omics approaches in male infertility: implications for diagnosis and assisted reproduction.Journal of assisted reproduction and genetics · 2026Review
- Consensus Pituitary Atlas, a scalable resource for annotation, novel marker discovery, and analyses in mouse pituitary gland research.Cell reports · 2026Article
- Regulatory logic underlying neural crest contributions to the head versus the heart.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transcriptomic responses to endurance exercise training in rats.BMC genomic data · 2026Article
- Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Article
- Article
- Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation.Cell genomics · 2026Article
- Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity ineLife · 2026Article
- Tumor-suppressive circRNAs in colorectal cancer spheroids and patients.Journal of the Chinese Medical Association : JCMA · 2026Article
- Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating Reelin and ciliary gene regulatory networks.Cell reports · 2026Article
- Cellular and molecular landscapes of human tendons across the lifespan revealed by spatial and single-cell transcriptomics.Cell reports · 2026Article
- Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's disease.iScience · 2026Article
- Uniform pre-processing of bacterial single-cell RNA-seq.bioRxiv : the preprint server for biology · 2026Article
- Long-Read Sequencing Reveals Cell- and State-Specific Alternative Splicing in 293T and A549 Cell Transcriptomes.International journal of molecular sciences · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Agnostic viral detection at single-cell resolution reveals novel viruses.Nature biotechnology · 2026Article
- Sequence and structural determinants of efficaciousbioRxiv : the preprint server for biology · 2025Article
Corrections and comments
- Update of
Authors and funding
12 authors.
Funding
Abstract
The term 'RNA-seq' refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto, bustools and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data. Execution of this protocol requires basic familiarity with a command line environment. With this protocol, quantification of a moderately sized RNA-seq dataset can be completed within minutes.
Indexed as
Identifiers
39390263What 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.