From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data

por Lun, Aaron T. L., Smyth, Gordon K.
Publicado 2016

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

por Lun, Aaron T. L., Marioni, John C.
Publicado 2017

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

por Lun, Aaron T.L., Smyth, Gordon K.
Publicado 2014

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

por Lun, Aaron T.L., Smyth, Gordon K.
Publicado 2015

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

por Lun, Aaron T.L., Smyth, Gordon K.
Publicado 2016

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

por Lun, Aaron T. L., Perry, Malcolm, Ing-Simmons, Elizabeth
Publicado 2016

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

por Chen, Yunshun, Lun, Aaron T. L., Smyth, Gordon K.
Publicado 2016

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

por Lun, Aaron T. L., Pagès, Hervé, Smith, Mike L.
Publicado 2018

Testing for differential abundance in mass cytometry data

por Lun, Aaron T. L., Richard, Arianne C., Marioni, John C.
Publicado 2017

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

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

iSEE: Interactive SummarizedExperiment Explorer

por Rue-Albrecht, Kevin, Marini, Federico, Soneson, Charlotte, Lun, Aaron T.L.
Publicado 2018

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

por McCarthy, Davis J, Campbell, Kieran R, Lun, Aaron T L, Wills, Quin F
Publicado 2017

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

por Griffiths, Jonathan A., Richard, Arianne C., Bach, Karsten, Lun, Aaron T. L., Marioni, John C.
Publicado 2018

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

por Lun, Aaron T. L., Riesenfeld, Samantha, Andrews, Tallulah, Dao, The Phuong, Gomes, Tomas, Marioni, John C.
Publicado 2019

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

por Lun, Aaron T.L., Calero-Nieto, Fernando J., Haim-Vilmovsky, Liora, Göttgens, Berthold, Marioni, John C.
Publicado 2017

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium

por Holik, Aliaksei Z., Galvis, Laura A., Lun, Aaron T.L., Ritchie, Matthew E., Asselin-Labat, Marie-Liesse
Publicado 2015

T cell cytolytic capacity is independent of initial stimulation strength

por Richard, Arianne C., Lun, Aaron T. L., Lau, Winnie W. Y., Göttgens, Berthold, Marioni, John C., Griffiths, Gillian M.
Publicado 2018

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

por Stojic, Lovorka, Lun, Aaron T L, Mangei, Jasmin, Mascalchi, Patrice, Quarantotti, Valentina, Barr, Alexis R, Bakal, Chris, Marioni, John C, Gergely, Fanni, Odom, Duncan T
Publicado 2018

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

por Righelli, Dario, Weber, Lukas M, Crowell, Helena L, Pardo, Brenda, Collado-Torres, Leonardo, Ghazanfar, Shila, Lun, Aaron T L, Hicks, Stephanie C, Risso, Davide
Publicado 2022

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

por Johanson, Timothy M., Coughlan, Hannah D., Lun, Aaron T. L., Bediaga, Naiara G., Naselli, Gaetano, Garnham, Alexandra L., Harrison, Leonard C., Smyth, Gordon K., Allan, Rhys S.
Publicado 2018