Lun AT - Search Results

1

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

Lun AT, McCarthy DJ, Marioni JC. Lun AT, et al. F1000Res. 2016 Aug 31;5:2122. doi: 10.12688/f1000research.9501.2. eCollection 2016. F1000Res. 2016. PMID: 27909575 Free PMC article.

2

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

McCarthy DJ, Campbell KR, Lun AT, Wills QF. McCarthy DJ, et al. Among authors: lun at. Bioinformatics. 2017 Apr 15;33(8):1179-1186. doi: 10.1093/bioinformatics/btw777. Bioinformatics. 2017. PMID: 28088763 Free PMC article.

3

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

Lun ATL, Marioni JC. Lun ATL, et al. Biostatistics. 2017 Jul 1;18(3):451-464. doi: 10.1093/biostatistics/kxw055. Biostatistics. 2017. PMID: 28334062 Free PMC article.

4

Testing for differential abundance in mass cytometry data.

Lun ATL, Richard AC, Marioni JC. Lun ATL, et al. Nat Methods. 2017 Jul;14(7):707-709. doi: 10.1038/nmeth.4295. Epub 2017 May 15. Nat Methods. 2017. PMID: 28504682 Free PMC article.

5

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

Lun ATL, Calero-Nieto FJ, Haim-Vilmovsky L, Göttgens B, Marioni JC. Lun ATL, et al. Genome Res. 2017 Nov;27(11):1795-1806. doi: 10.1101/gr.222877.117. Epub 2017 Oct 13. Genome Res. 2017. PMID: 29030468 Free PMC article.

6

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

Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T; participants in the 1st Human Cell Atlas Jamboree; Marioni JC. Lun ATL, et al. Genome Biol. 2019 Mar 22;20(1):63. doi: 10.1186/s13059-019-1662-y. Genome Biol. 2019. PMID: 30902100 Free PMC article.

7

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

Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC. Welby E, et al. Stem Cell Reports. 2017 Dec 12;9(6):1898-1915. doi: 10.1016/j.stemcr.2017.10.018. Epub 2017 Nov 16. Stem Cell Reports. 2017. PMID: 29153988 Free PMC article.

8

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

Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Stojic L, et al. Nucleic Acids Res. 2018 Jul 6;46(12):5950-5966. doi: 10.1093/nar/gky437. Nucleic Acids Res. 2018. PMID: 29860520 Free PMC article.

9

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

Chen Y, Lun AT, Smyth GK. Chen Y, et al. Among authors: lun at. F1000Res. 2016 Jun 20;5:1438. doi: 10.12688/f1000research.8987.2. eCollection 2016. F1000Res. 2016. PMID: 27508061 Free PMC article.

10

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

Lun AT, Perry M, Ing-Simmons E. Lun AT, et al. F1000Res. 2016 May 20;5:950. doi: 10.12688/f1000research.8759.2. eCollection 2016. F1000Res. 2016. PMID: 27303634 Free PMC article.

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