A. Lun

发表

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

J. Marioni, A. Lun, 2016, bioRxiv.

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

Laleh Haghverdi, John C Marioni, Aaron T L Lun, 2018, Nature Biotechnology.

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

Davis J. McCarthy, J. Marioni, A. Lun, 2016, F1000Research.

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry.

J. W. Wong, A. Lun, K. Swaminathan, 2013, Analytical chemistry.

Testing for differential abundance in mass cytometry data

John C. Marioni, Aaron T. L. Lun, J. Marioni, 2017, Nature Methods.

T cell cytolytic capacity is independent of initial stimulation strength

J. Marioni, B. Göttgens, A. Lun, 2018, Nature Immunology.

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Samantha Riesenfeld, John C Marioni, Aaron T L Lun, 2019, Genome Biology.

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution

J. Marioni, W. Reik, A. Lun, 2019, Cell reports.

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

J. Marioni, B. Göttgens, A. Lun, 2017, bioRxiv.

Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance

A. Lun, C. Martinez-Jimenez, M. Narita, 2022, Genes & development.

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

Berthold Göttgens, John C Marioni, Aaron T L Lun, 2017, bioRxiv.

Erythropoietin‐stimulated endothelial cells support erythroid cell differentiation of CD34(+) haematopoietic progenitors

C. Frömmel, A. Lun, A. Moldenhauer, 2013, Vox sanguinis.

Additional file 2 of Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

J. Marioni, K. Bach, A. Lun, 2016 .

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

Helena L. Crowell, D. Risso, A. Lun, 2021, bioRxiv.

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

David T. Jones, J. Marioni, A. Lun, 2017, Stem cell reports.

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

Aaron T. L. Lun, Davis J. McCarthy, Kieran R. Campbell, 2017, Bioinform..

Orchestrating single-cell analysis with Bioconductor

Raphael Gottardo, Charlotte Soneson, Stephanie C. Hicks, 2019, Nature Methods.

Overcoming systematic errors caused by log-transformation of normalized single-cell RNA sequencing data

Aaron Lun, A. Lun, 2018, bioRxiv.

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types

Aaron T. L. Lun, Hervé Pagès, Mike L. Smith, 2018, PLoS Comput. Biol..

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Aaron T. L. Lun, John C. Marioni, Samantha Riesenfeld, 2018 .

beachmat: a Bioconductor C++ API for accessing single-cell genomics data from a variety of R matrix types

Aaron T. L. Lun, Hervé Pagès, Mike L. Smith, 2017, bioRxiv.

Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours

John C. Marioni, Michael D. Morgan, Laleh Haghverdi, 2017, bioRxiv.

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

John C Marioni, Davis J. McCarthy, Aaron T L Lun, 2016, F1000Research.

Single-cell data analysis in the browser

Jayaram Kancherla, A. Lun, 2022 .

Detection and removal of barcode swapping in single-cell RNA-seq data

Aaron T. L. Lun, John C. Marioni, Karsten Bach, 2017, bioRxiv.

Detection and removal of barcode swapping in single-cell RNA-seq data

John C Marioni, Karsten Bach, Jonathan A Griffiths, 2017, Nature Communications.

Doublet identification in single-cell sequencing data using scDblFinder

Mark D. Robinson, Pierre-Luc Germain, Aaron Lun, 2021, F1000Research.

csaw: ChIP-seq analysis with windows User's Guide

Aaron Lun, A. Lun, 2015 .

Locus-specific expression of transposable elements in single cells with CELLO-seq

Daniel J. Gaffney, J. Marioni, N. Brockdorff, 2021, Nature Biotechnology.

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments

A. Lun, Elizabeth Ing-Simmons, M. Perry, 2016, F1000Research.

iSEE: Interactive SummarizedExperiment Explorer

Kevin Rue-Albrecht, Charlotte Soneson, Aaron T L Lun, 2018, F1000Research.

T cell cytolytic capacity is independent of initial stimulation strength

J. Marioni, B. Göttgens, A. Lun, 2018, Nature Immunology.

Powering single-cell analyses in the browser with WebAssembly

Jayaram Kancherla, A. Lun, 2023, bioRxiv.

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry

J. W. Wong, A. Lun, K. Downard, 2012, BMC Bioinformatics.

Doublet identification in single-cell sequencing data using scDblFinder.

M. Robinson, P. Germain, A. Lun, 2021, F1000Research.

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments

Elizabeth Ing-Simmons, Aaron T L Lun, A. Lun, 2016, F1000Research.

Package 'diffhic' Title Differential Analyis of Hi-c Data

A. Lun, Aaron Maintainer, Lun, 2017 .

diffHic: Differential analysis of Hi-C data User's Guide

Aaron Lun, A. Lun, 2016 .

basilisk: a Bioconductor package for managing Python environments

A. Lun, 2022, J. Open Source Softw..

gesel: a JavaScript package for client-side gene set enrichment

Jayaram Kancherla, A. Lun, 2023, J. Open Source Softw..