Helena L. Crowell
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View article: On feature selection to disentangle cell type and state transcriptional programs
On feature selection to disentangle cell type and state transcriptional programs Open
Single-cell omics approaches profile molecular constituents of individual cells. Replicated multi-condition experiments in particular aim at studying how the molecular makeup and composition of cell subpopulations changes at the sample-lev…
View article: Analysis of anatomical multi-cellular structures from spatial omics data using <i>sosta</i>
Analysis of anatomical multi-cellular structures from spatial omics data using <i>sosta</i> Open
Spatial omics technologies enable high-resolution, large-scale quantification of molecular features while preserving the spatial context within tissues. Existing analysis methods largely focus on spatial arrangements of single cells, where…
View article: Differential detection workflows for multi-sample single-cell RNA-seq data
Differential detection workflows for multi-sample single-cell RNA-seq data Open
In single-cell transcriptomics, differential expression (DE) tools compare average expression between cell types or conditions. However, scRNA-seq technologies hold the promise to infer differences in other aspects of the expression distri…
View article: Harnessing the potential of spatial statistics for spatial omics data with <i>pasta</i>
Harnessing the potential of spatial statistics for spatial omics data with <i>pasta</i> Open
Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, give rise to very different data modalities. The cha…
View article: In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics
In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics Open
Copy number variations (CNVs) drive cancer progression. So far, spatial CNV inference has relied on whole transcriptome-based sequencing technologies. However, advances in image‐based spatial transcriptomics (iST) now enable high-plex gene…
View article: Tracing colorectal malignancy transformation from cell to tissue scale
Tracing colorectal malignancy transformation from cell to tissue scale Open
The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remains poorly resolved. Here, we survey col…
View article: STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging Open
Single-cell RNA sequencing has revolutionized our understanding of cellular diversity but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (singl…
View article: 1st SpatialData Developer Workshop
1st SpatialData Developer Workshop Open
This pre-print is aimed at sharing the results of the "1st SpatialData workshop," an in-person event organized by the SpatialData team and funded by the Chan Zuckerberg Initiative (CZI) that brought together expertise from different fields…
View article: On feature selection to disentangle cell type and state transcriptional programs
On feature selection to disentangle cell type and state transcriptional programs Open
Single-cell omics approaches profile molecular constituents of individual cells. Replicated multi-condition experiments in particular aim at studying how the molecular makeup and composition of cell subpopulations changes at the sample-lev…
View article: Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta Open
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can give rise to very different data modaliti…
View article: Author Correction: The shaky foundations of simulating single-cell RNA sequencing data
Author Correction: The shaky foundations of simulating single-cell RNA sequencing data Open
View article: Author Correction: Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease
Author Correction: Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease Open
View article: The<i>tidyomics</i>ecosystem: Enhancing omic data analyses
The<i>tidyomics</i>ecosystem: Enhancing omic data analyses Open
The growth of omic data presents evolving challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor 1 provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R p…
View article: Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease
Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease Open
View article: Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Open
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines…
View article: distinct: A novel approach to differential distribution analyses
distinct: A novel approach to differential distribution analyses Open
We present distinct, a general method for differential analysis of full distributions that is well suited to applications on single-cell data, such as single-cell RNA sequencing and high-dimensional flow or mass cytometry data. High-throug…
View article: The shaky foundations of simulating single-cell RNA sequencing data
The shaky foundations of simulating single-cell RNA sequencing data Open
View article: Additional file 1 of Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Additional file 1 of Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Open
Additional file 1. List of benchmarks with consolidate survey answers.
View article: Additional file 3 of Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Additional file 3 of Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Open
Additional file 3. Uneditedsurvey responses.
View article: Additional file 2 of Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Additional file 2 of Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Open
Additional file 2. Review form.
View article: Macrophage and neutrophil heterogeneity at single-cell spatial resolution in inflammatory bowel disease
Macrophage and neutrophil heterogeneity at single-cell spatial resolution in inflammatory bowel disease Open
Ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory intestinal diseases that show a perplexing heterogeneity in manifestations and response to treatment. The molecular basis for this heterogeneity remains uncharacteri…
View article: Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Open
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines…
View article: Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data"
Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data" Open
Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data" See description.txt, Supplementary Text, Methods and https://github.com/HelenaLC/simulation-comparison for further description of the files availa…
View article: Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data"
Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data" Open
Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data" See description.txt, Supplementary Text, Methods and https://github.com/HelenaLC/simulation-comparison for further description of the files availa…
View article: An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data
An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data Open
Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Current…
View article: SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor Open
Summary SpatialExperiment is a new data infrastructure for storing and accessing spatially-resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardi…
View article: Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma
Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Open
View article: Built on sand: the shaky foundations of simulating single-cell RNA sequencing data
Built on sand: the shaky foundations of simulating single-cell RNA sequencing data Open
With the emergence of hundreds of single-cell RNA-sequencing (scRNA-seq) datasets, the number of computational tools to analyse aspects of the generated data has grown rapidly. As a result, there is a recurring need to demonstrate whether …
View article: Supplementary Material for "Built on sand: the shaky foundations of simulating single-cell RNA sequencing data"
Supplementary Material for "Built on sand: the shaky foundations of simulating single-cell RNA sequencing data" Open
Supplementary Material for "Built on sand: the shaky foundations of simulating single-cell RNA sequencing data" See description.txt, Supplementary Text, Methods and https://github.com/HelenaLC/simulation-comparison for further description …
View article: Selenium-Binding Protein 1 (SELENBP1) as Biomarker for Adverse Clinical Outcome After Traumatic Spinal Cord Injury
Selenium-Binding Protein 1 (SELENBP1) as Biomarker for Adverse Clinical Outcome After Traumatic Spinal Cord Injury Open
Graphical Abstract The pathophysiology of traumatic spinal cord injury (TSCI) can be divided into two major phases. (A) The mechanical trauma is followed within minutes by a secondary phase consisting of local complex and intertwined acute…