Aaron T. L. Lun
YOU?
Author Swipe
View article: Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states
Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states Open
View article: edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets Open
edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form of read counts for genes or genomic features. Over the past 15 years, edgeR has been a popular choice for statistical analysis of data fro…
View article: CRISPR activation screens identify the SWI/SNF ATPases as suppressors of ferroptosis
CRISPR activation screens identify the SWI/SNF ATPases as suppressors of ferroptosis Open
Ferroptosis is an iron-dependent cell death mechanism characterized by the accumulation of toxic lipid peroxides and cell membrane rupture. GPX4 (glutathione peroxidase 4) prevents ferroptosis by reducing these lipid peroxides into lipid a…
View article: Systematic perturbation screens decode regulators of inflammatory macrophage states and identify a role for<i>TNF</i>mRNA m6A modification
Systematic perturbation screens decode regulators of inflammatory macrophage states and identify a role for<i>TNF</i>mRNA m6A modification Open
Macrophages adopt dynamic cell states with distinct effector functions to maintain tissue homeostasis and respond to environmental challenges. During chronic inflammation, macrophage polarization is subverted towards sustained inflammatory…
View article: Systemic inflammatory response syndrome triggered by blood-borne pathogens induces prolonged dendritic cell paralysis and immunosuppression
Systemic inflammatory response syndrome triggered by blood-borne pathogens induces prolonged dendritic cell paralysis and immunosuppression Open
Blood-borne pathogens can cause systemic inflammatory response syndrome (SIRS) followed by protracted, potentially lethal immunosuppression. The mechanisms responsible for impaired immunity post-SIRS remain unclear. We show that SIRS trigg…
View article: edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets Open
edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form of read counts for genes or genomic features. Over the past 15 years, edgeR has been a popular choice for statistical analysis of data fro…
View article: Epiregulon: Inference of single-cell transcription factor activity to predict drug response and drivers of cell state
Epiregulon: Inference of single-cell transcription factor activity to predict drug response and drivers of cell state Open
Transcription factors (TFs) and transcriptional coregulators represent an emerging class of therapeutic targets in oncology. Gene regulatory networks (GRNs) can be used to evaluate pharmacological agents targeting these factors and to iden…
View article: gesel: a JavaScript package for client-side gene setenrichment
gesel: a JavaScript package for client-side gene setenrichment Open
gesel is a JavaScript package for performing gene set enrichment analyses within the browser.All calculations are performed on the client device, without any no need for a dedicated backend server.This eliminates concerns around cost, scal…
View article: Powering single-cell analyses in the browser withWebAssembly
Powering single-cell analyses in the browser withWebAssembly Open
We present kana, a web application for interactive single-cell 'omics data analysis in the browser.Like, literally, in the browser: kana leverages web technologies such as WebAssembly to efficiently perform the relevant computations on the…
View article: basilisk: a Bioconductor package for managing Pythonenvironments
basilisk: a Bioconductor package for managing Pythonenvironments Open
basilisk is an R/Bioconductor package for managing Python environments within the Bioconductor package ecosystem.Developers of other Bioconductor packages can use basilisk to automatically provision and load custom Python environments, pro…
View article: A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies
A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies Open
View article: Doublet identification in single-cell sequencing data using scDblFinder
Doublet identification in single-cell sequencing data using scDblFinder Open
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed to detect them. Building on the strengths of existing approaches, we developed scDblFinder, a f…
View article: Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance
Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance Open
Senescence is a stress-responsive tumor suppressor mechanism associated with expression of the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells trigger their own immune-mediated elimination, which if evad…
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: The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies
The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies Open
The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR moda…
View article: Powering single-cell analyses in the browser with WebAssembly
Powering single-cell analyses in the browser with WebAssembly Open
We present kana, a web application for interactive single-cell ‘omics data analysis in the browser. Like, literally, in the browser: kana leverages web technologies such as WebAssembly to efficiently perform the relevant computations on th…
View article: Locus-specific expression of transposable elements in single cells with CELLO-seq
Locus-specific expression of transposable elements in single cells with CELLO-seq Open
View article: Doublet identification in single-cell sequencing data using scDblFinder
Doublet identification in single-cell sequencing data using scDblFinder Open
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed to detect them. Building on the strengths of existing approaches, we developed scDblFinder, a f…
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: Transposable element expression at unique loci in single cells with CELLO-seq
Transposable element expression at unique loci in single cells with CELLO-seq Open
The role of Transposable Elements (TEs) in regulating diverse biological processes, from early development to cancer, is becoming increasing appreciated. However, unlike other biological processes, next generation single-cell sequencing te…
View article: A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division Open
View article: iSEE workshop – package and functionality
iSEE workshop – package and functionality Open
View article: Publisher Correction: Orchestrating single-cell analysis with Bioconductor
Publisher Correction: Orchestrating single-cell analysis with Bioconductor Open
View article: Orchestrating single-cell analysis with Bioconductor
Orchestrating single-cell analysis with Bioconductor Open
View article: A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division Open
Genome stability relies on proper coordination of mitosis and cytokinesis, where dynamic microtubules capture and faithfully segregate chromosomes into daughter cells. The role of long noncoding RNAs (lncRNAs) in controlling these processe…
View article: Orchestrating Single-Cell Analysis with Bioconductor
Orchestrating Single-Cell Analysis with Bioconductor Open
Recent developments in experimental technologies such as single-cell RNA sequencing have enabled the profiling a high-dimensional number of genome-wide features in individual cells, inspiring the formation of large-scale data generation pr…
View article: EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data Open
View article: Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution
Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution Open
View article: Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT
Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT Open
View article: Additional file 2 of EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Additional file 2 of EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data Open
The list of participants in the 1st Human Cell Atlas Jamboree. (TSV 1 kb)