Evidence map›Paper›PMID 41908069›Full record

ArticleSoftwareX2025

scSpatialSIM: a simulator of spatial single-cell molecular data.

Alex C Soupir, Julia Wrobel, Jordan H Creed, Oscar E Ospina, Christopher M Wilson, Brandon J Manley, Lauren C Peres, Brooke L Fridley

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in SoftwareX, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

8 authors.

Alex C SoupirDepartment of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, United States.ORCID 0000-0003-1251-9179
Julia WrobelDepartment of Biostatistics, Emory University, Atlanta, GA, United States.
Jordan H CreedDepartment of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, United States.
Oscar E OspinaDepartment of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, United States.
Christopher M WilsonDepartment of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, United States.
Brandon J ManleyDepartment of Biostatistics, Emory University, Atlanta, GA, United States.
Lauren C PeresDepartment of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, United States.
Brooke L FridleyDivision of Health Services and Outcomes Research, Children's Mercy, Kansas City, MO, United States.

Funding

Spatial and Bayesian modeling methods for assessment of the tumor immune microenvironment and survival of women with ovarian cancerR01CA279065 · NCI · H. LEE MOFFITT CANCER CTR & RES INST · PI Brooke L Fridley, Lauren Cole Peres · 2023 to 2026
$2.2M
Analytical tools for studying the tumor microenvironment leveraging spatial transcriptomicsU01CA274489 · NCI · H. LEE MOFFITT CANCER CTR & RES INST · PI FRIDLEY, BROOKE L, YU, XIAOQING · 2022 to 2024
$1.2M
NCI NIH HHS R01 CA279065NCI NIH HHS U01 CA274489
6 · The paper itself

Abstract

The increasing use of spatial molecular technologies such as multiplex immunofluorescence (mIF) and spatial transcriptomics (SRT) has driven the need for robust statistical methods to analyze the spatial architecture of tissues. However, a lack of consensus on "gold standard" approaches present challenges for benchmarking and comparison. To address this gap, we developed "scSpatialSIM", an

Indexed as

Cell clusteringCell co-localizationSpatial molecular dataSpatial single-cell simulationsSpatial statistics benchmarking

Identifiers

PMID41908069
PMCPMC13021152

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.