Evidence map›Paper›PMID 40060564›Full record

ArticlebioRxiv : the preprint server for biology2025

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment.

Lambda Moses, Alik Huseynov, Joseph M Rich, Lior Pachter

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Lambda MosesDivision of Biology and Biological Engineering, California Institute of Technology; Present address: Department of Statistics, Irving Institute of Cancer Dynamics, Columbia University.ORCID 0000-0002-7092-9427
Alik HuseynovSingle Cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany; Present address: Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany.ORCID 0000-0002-1438-4389
Joseph M RichDivision of Biology and Biological Engineering, California Institute of Technology.ORCID 0000-0003-1400-8479
Lior PachterDivision of Biology and Biological Engineering, California Institute of Technology.ORCID 0000-0002-9164-6231

Funding

Center for Mouse Genomic Variation at Single Cell ResolutionUM1HG012077 · NHGRI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Seyed Ali Mortazavi, BARBARA J WOLD · 2021 to 2026
$13.7M
NHGRI NIH HHS UM1 HG012077
6 · The paper itself

Abstract

SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for working with spatial -omics data. SpatialFeatureExperiment can be used to store and analyze a variety of spatial -omics data types, including data from the Visium, Xenium, MERFISH, SeqFish, and Slide-seq platforms, bringing spatial operations to the SingleCellExperiment ecosystem.

Identifiers

PMID40060564
PMCPMC11888365

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.