Pooling across cells to normalize single-cell RNA sequencing data with many zero counts von Lun, Aaron T L, Bach, Karsten, Marioni, John C

Volltext

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data von Lun, Aaron T L, Riesenfeld, Samantha, Andrews, Tallulah, Dao, The Phuong, Gomes, Tomas, Marioni, John C

Volltext

Orchestrating single-cell analysis with Bioconductor von Amezquita, Robert A., Lun, Aaron T. L., Becht, Etienne, Carey, Vince J., Carpp, Lindsay N., Geistlinger, Ludwig, Marini, Federico, Rue-Albrecht, Kevin, Risso, Davide, Soneson, Charlotte, Waldron, Levi, Pagès, Hervé, Smith, Mike L., Huber, Wolfgang, Morgan, Martin, Gottardo, Raphael, Hicks, Stephanie C.

Volltext

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; peer review: 5 approved] von Chen, Yunshun, Lun, Aaron T. L, Smyth, Gordon K

Volltext

Transcription-factor-mediated supervision of global genome architecture maintains B cell identity von Johanson, Timothy M., Lun, Aaron T. L., Coughlan, Hannah D., Tan, Tania, Smyth, Gordon K., Nutt, Stephen L., Allan, Rhys S.

Volltext

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

Volltext

Locus-specific expression of transposable elements in single cells with CELLO-seq von Berrens, Rebecca V., Yang, Andrian, Laumer, Christopher E., Lun, Aaron T. L., Bieberich, Florian, Law, Cheuk-Ting, Lan, Guocheng, Imaz, Maria, Bowness, Joseph S., Brockdorff, Neil, Gaffney, Daniel J., Marioni, John C.

Volltext

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division von Stojic, Lovorka, Lun, Aaron T. L., Mascalchi, Patrice, Ernst, Christina, Redmond, Aisling M., Mangei, Jasmin, Barr, Alexis R., Bousgouni, Vicky, Bakal, Chris, Marioni, John C., Odom, Duncan T., Gergely, Fanni

Volltext

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors von Haghverdi, Laleh, Lun, Aaron T L, Morgan, Michael D, Marioni, John C

Volltext

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R von McCarthy, Davis J, Campbell, Kieran R, Lun, Aaron T L, Wills, Quin F

Volltext

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows von Lun, Aaron T L, Smyth, Gordon K

Volltext

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types von Lun, Aaron T L, Pagès, Hervé, Smith, Mike L

Volltext

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

Volltext

Detection and removal of barcode swapping in single-cell RNA-seq data von Griffiths, Jonathan A., Richard, Arianne C., Bach, Karsten, Lun, Aaron T. L., Marioni, John C.

Volltext

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data von Lun, Aaron T L, Smyth, Gordon K

Volltext

Publisher Correction: Orchestrating single-cell analysis with Bioconductor von Amezquita, Robert A., Lun, Aaron T. L., Becht, Etienne, Carey, Vince J., Carpp, Lindsay N., Geistlinger, Ludwig, Marini, Federico, Rue-Albrecht, Kevin, Risso, Davide, Soneson, Charlotte, Waldron, Levi, Pagès, Hervé, Smith, Mike L., Huber, Wolfgang, Morgan, Martin, Gottardo, Raphael, Hicks, Stephanie C.

Volltext

T cell cytolytic capacity is independent of initial stimulation strength von Richard, Arianne C., Lun, Aaron T. L., Lau, Winnie W. Y., Göttgens, Berthold, Marioni, John C., Griffiths, Gillian M.

Volltext

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations von Taberlay, Phillippa C, Achinger-Kawecka, Joanna, Lun, Aaron T L, Buske, Fabian A, Sabir, Kenneth, Gould, Cathryn M, Zotenko, Elena, Bert, Saul A, Giles, Katherine A, Bauer, Denis C, Smyth, Gordon K, Stirzaker, Clare, O'Donoghue, Sean I, Clark, Susan J

Volltext

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly von Lun, Aaron T L, Smyth, Gordon K

Volltext

EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival von Fu, Nai Yang, Rios, Anne C., Pal, Bhupinder, Soetanto, Rina, Lun, Aaron T. L., Liu, Kevin, Beck, Tamara, Best, Sarah A., Vaillant, François, Bouillet, Philippe, Strasser, Andreas, Preiss, Thomas, Smyth, Gordon K., Lindeman, Geoffrey J., Visvader, Jane E.

Volltext