OSCR

Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § STAR★Methods › Method details › Xenium data analysis ↔ vignettes/Seurat.Rmd, lines 227–236 · score 0.67 · FindNeighbors, FindClusters, dimensionality reduction, resolutions, Seurat, embeddings
  2. [2] § STAR★Methods › Method details › Batch correction of scRNA-seq data ↔ vignettes/Seurat.Rmd, lines 227–236 · score 0.54 · FindNeighbors, FindClusters, resolutions, Seurat, embeddings, Harmony

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

R Markdown · 275 lines · 13 KB · no license · 2 matches

The registry keeps no copy of this file: its repository has no license, so its authors keep all their rights to it. Your browser shows it from its source, with JavaScript.

It can be read at the source: vignettes/Seurat.Rmd.

Overview

Authors: Beatrix S Wang1,2,3, Konstantina Karamboulas2, Nareh Tahmasian2,3, Daniel J Dennis2, David R Kaplan2,3,4,5, Freda D Miller1,2,3,4,5
ORCID iDs: Beatrix S Wang
  1. Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
  2. Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
  3. Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
  4. Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
  5. Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
Institutions: University of British Columbia (Canada); University of Toronto (Canada); Hospital for Sick Children (Canada)
Journal: Stem cell reports, volume 21, issue 7, article 102967
Dates: received 30 January 2026; accepted 19 May 2026; published online 18 June 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.stemcr.2026.102967 · PMID 42314674 · PMCID PMC13385433 · OpenAlex W7165128621
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), mouse (organism), developmental (subfield)
Methods: Preprocessing, Statistics, Smoothing, state filtering, decompositions, Connectivity, Machine learning, fMRI & imaging
Keywords: neural stem cells, cortical development, stem cell development, single-cell transcriptomics, single-cell spatial transcriptomics, single-cell epigenetics, stem cell epigenetics, radial glia, olfactory neurogenesis
MeSH: Adult Stem Cells*, Embryonic Stem Cells*, Epigenesis, Genetic*, Neural Stem Cells*, Single-Cell Analysis*, Transcription, Genetic*, Animals, Cell Differentiation, Gene Expression Regulation, Developmental, Mice, Multiomics, Neurodevelopment, Neurogenesis, Single-Cell Gene Expression Analysis, Transcriptome (* major topic)
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: Canadian Institutes of Health Research
Citations: not cited yet (Europe PMC); 59 references in the paper
Research resources: 2002) and R26Eyfpfl/fl RRID:IMSR_JAX, RRID:IMSR_JAX:005628, RRID:IMSR_JAX:006148, R Project for Statistical Computing (v4) RRID:SCR_001905, GraphPad Prism 10 RRID:SCR_002798, Adobe Illustrator RRID:SCR_010279, Adobe Photoshop RRID:SCR_014199, Monocle R Package (v2) RRID:SCR_016339, Seurat R Package (v4) RRID:SCR_016341, Cell Ranger (v4) RRID:SCR_017344, ArchR R Package (v1) RRID:SCR_020982, Harmony R Package (v1.2.0) RRID:SCR_022206, Cell Ranger ARC (v2) RRID:SCR_023897, Xenium Explorer (v1.3–4) RRID:SCR_025847, Xenium Ranger (v3) RRID:SCR_028191

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

immunogenomics/harmony

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: df19af23ae0639bd6ea2da63898f973f08c85862, 5 June 2026
Languages: R (22), C/C++ (5), C++ (4)
Size: 69 files, 31 scripts
Software Heritage: archived
Found in: the resources table
Holds: README, environment (DESCRIPTION), tests, continuous integration, documentation, 7 notebooks
Not found: license file, CITATION.cff
Tools: Harmony (14 files), tidyverse (10 files), cowplot (7 files), ggplot2 (6 files), Seurat (4 files), data.table (3 files), patchwork (3 files), SingleCellExperiment (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
32 files, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit df19af2, when its fingerprint is the one OSCR verified. How this works.

At the source: github.com/immunogenomics/harmony/

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 31 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1016/j.stemcr.2026.102967.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 9 keywords, 15 MeSH terms, 1 funder, 59 references, 15 RRIDs.

Cite

This paper

Wang, B. S., Karamboulas, K., Tahmasian, N., Dennis, D. J., Kaplan, D. R., & Miller, F. D. (2026). Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells. Stem cell reports, 21(7), 102967. https://doi.org/10.1016/j.stemcr.2026.102967

BibTeX

@article{wang2026single,
author = {Wang, Beatrix S and Karamboulas, Konstantina and Tahmasian, Nareh and Dennis, Daniel J and Kaplan, David R and Miller, Freda D},
title = {{Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells}},
journal = {Stem cell reports},
year = {2026},
month = jun,
volume = {21},
number = {7},
pages = {102967},
publisher = {Elsevier},
issn = {2213-6711},
doi = {10.1016/j.stemcr.2026.102967},
url = {https://doi.org/10.1016/j.stemcr.2026.102967},
pmid = {42314674},
pmcid = {PMC13385433}
}

RIS

TY - JOUR
AU - Wang, Beatrix S
AU - Karamboulas, Konstantina
AU - Tahmasian, Nareh
AU - Dennis, Daniel J
AU - Kaplan, David R
AU - Miller, Freda D
TI - Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells
T2 - Stem cell reports
J2 - Stem Cell Reports
PY - 2026
DA - 2026/06/18
VL - 21
IS - 7
SP - 102967
SN - 2213-6711
PB - Elsevier
DO - 10.1016/j.stemcr.2026.102967
UR - https://doi.org/10.1016/j.stemcr.2026.102967
LA - en
ER -

CSL-JSON

{
"id": "10.1016/j.stemcr.2026.102967",
"type": "article-journal",
"title": "Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells",
"container-title": "Stem cell reports",
"author": [
{
"family": "Wang",
"given": "Beatrix S"
},
{
"family": "Karamboulas",
"given": "Konstantina"
},
{
"family": "Tahmasian",
"given": "Nareh"
},
{
"family": "Dennis",
"given": "Daniel J"
},
{
"family": "Kaplan",
"given": "David R"
},
{
"family": "Miller",
"given": "Freda D"
}
],
"container-title-short": "Stem Cell Reports",
"volume": "21",
"issue": "7",
"page": "102967",
"DOI": "10.1016/j.stemcr.2026.102967",
"PMID": "42314674",
"PMCID": "PMC13385433",
"ISSN": "2213-6711",
"publisher": "Elsevier",
"URL": "https://doi.org/10.1016/j.stemcr.2026.102967",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
18
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1016/j.xcrm.2026.102766 [code]
A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.
Journal: Cell reports. Medicine
In common: Harmony, SingleCellExperiment, Seurat, 5 other tools, genetics / omics, 5 references
[2] doi:10.1038/s41597-026-07185-4 [code]
A multi-center cross-platform single-cell multimodal atlas of the mouse cerebral cortex.
Journal: Scientific data
In common: Harmony, Seurat, cowplot, 4 other tools, genetics / omics, mouse, 5 references
[3] doi:10.1371/journal.pcbi.1014424 [code]
Combinatorial multiomic analysis from a pedigree of Sox10Dom Hirschsprung mice identifies multiple high confidence candidate modifiers of Enteric Nervous System development.
Journal: PLoS computational biology
In common: Harmony, Seurat, cowplot, 4 other tools, genetics / omics, mouse, 4 references
[4] doi:10.1093/brain/awaf426 [code]
Single-nucleus multiome shows motor neuron glutamate overactivation in amyotrophic lateral sclerosis.
Journal: Brain : a journal of neurology
In common: Harmony, SingleCellExperiment, Seurat, 4 other tools, genetics / omics, 3 references
[5] doi:10.1002/imt2.70163 [code]
Spatial multi-omics unveils sphingolipid metabolic reprogramming within the retinal pathological niche.
Journal: iMeta
In common: Harmony, SingleCellExperiment, Seurat, 5 other tools, genetics / omics, mouse, 1 reference
[6] doi:10.1038/s41586-026-10612-6 [code]
Acquired genetic and cell-state changes in IDH-mutant glioma progression.
Journal: Nature
In common: Harmony, SingleCellExperiment, Seurat, 5 other tools, 2 references
[7] doi:10.1016/j.cell.2026.05.026 [code]
The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM.
Journal: Cell
In common: Harmony, SingleCellExperiment, Seurat, 5 other tools, genetics / omics, 2 references
[8] doi:10.1038/s41593-026-02367-0 [code]
A reproducible three-dimensional model of human brain tissue to investigate physiological and disease-associated microglia phenotypes.
Journal: Nature neuroscience
In common: Harmony, SingleCellExperiment, Seurat, 5 other tools, 2 references
[9] doi:10.1002/advs.77986 [code]
DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.
Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
In common: Harmony, SingleCellExperiment, Seurat, 4 other tools, genetics / omics, 2 references
[10] doi:10.1038/s41467-026-73007-1 [code]
Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states.
Journal: Nature communications
In common: Seurat, data.table, patchwork, 2 other tools, genetics / omics, 5 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.