ArticleNature methods2024
Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- Post-vaccination expansion of extrafollicular Th10 and regulatory Tfr cells distinguishes strong from weak influenza vaccine responses in older adults.medRxiv : the preprint server for health sciences · 2026Article
- Recurrent intra-tumour heterogeneity is a hallmark of metastatic prostate cancer.Nature communications · 2026Article
- Article
- A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC data.G3 (Bethesda, Md.) · 2026Article
- Dose-dependent IFN programs in myeloid cells after mRNA and adenovirus COVID-19 vaccination.JCI insight · 2026Article
- Regulatory element modules as universal features for single-cell chromatin analysis.bioRxiv : the preprint server for biology · 2025Article
- simPIC:flexible simulation of paired-insertion counts for single-cell ATAC sequencing data.bioRxiv : the preprint server for biology · 2025Article
- Establishing a continuum of cell types in the visual cortex.bioRxiv : the preprint server for biology · 2025Article
- A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.Genome biology · 2025Article
- Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data.Bioinformatics (Oxford, England) · 2025Article
- scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data.Nature communications · 2025Article
- Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome.Cell systems · 2025Article
- Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS.Nature communications · 2025Article
- Epigenetic control of antigen presentation failure in osteosarcoma: from single-cell chromatin maps to therapeutic strategies.Frontiers in immunology · 2025Review
- Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?bioRxiv : the preprint server for biology · 2024Article
- Concepts and new developments in droplet-based single cell multi-omics.Trends in biotechnology · 2024Review
- Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Existing approaches to scoring single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) feature matrices from sequencing reads are inconsistent, affecting downstream analyses and displaying artifacts. We show that, even with sparse single-cell data, quantitative counts are informative for estimating the regulatory state of a cell, which calls for a consistent treatment. We propose Paired-Insertion Counting as a uniform method for snATAC-seq feature characterization and provide a probability model for inferring latent insertion dynamics from snATAC-seq count matrices.
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.