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

Por Lun, Aaron T. L., Smyth, Gordon K.
Publicado no F1000Res (2016)

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 em 2014

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

Por Lun, Aaron T.L., Smyth, Gordon K.
Publicado no BMC Bioinformatics (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 no Nucleic Acids Res (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 no F1000Res (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 no F1000Res (2016)

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 no F1000Res (2016)

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 no Bioinformatics (2017)

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 no Genome Res (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 no Genom Data (2015)

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

Por Galvis, Laura A., Holik, Aliaksei Z., Short, Kieran M., Pasquet, Julie, Lun, Aaron T. L., Blewitt, Marnie E., Smyth, Ian M., Ritchie, Matthew E., Asselin-Labat, Marie-Liesse
Publicado no Development (2015)

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

Por 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.
Publicado no Genome Res (2016)

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

Por Welby, Emily, Lakowski, Jorn, Di Foggia, Valentina, Budinger, Dimitri, Gonzalez-Cordero, Anai, Lun, Aaron T.L., Epstein, Michael, Patel, Aara, Cuevas, Elisa, Kruczek, Kamil, Naeem, Arifa, Minneci, Federico, Hubank, Mike, Jones, David T., Marioni, John C., Ali, Robin R., Sowden, Jane C.
Publicado no Stem Cell Reports (2017)