The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Reproducible RNA-seq analysis using recount2
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c 16. Köster, J. & Rahmann, S. Bioinformatics 28, 2520– 2522 (2012). 17. Di Tommaso, P. et al. PeerJ 3, e1273 (2015). 18. Goecks, J., Nekrutenko, A. & Taylor, J. Genome Biol. 11, R86 (2010). 19. Blankenberg, D. et al. Genome Biol. 15, 403 (2014). 20. Vivian, J. et al. Preprint at bioRxiv http://biorxiv.org/ content/early/2016/07/07/062497 (2016). 21. Stamatakis, A. Bioinformatics 22, 2688–2690 (2006). 22. Byron, S.A., Van Keuren-Jensen, K.R., Engelthaler, D.M., Carpten, J.D. & Craig, D.W. Nat. Rev. Genet. 17, 257–271 (2016).
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,172
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011) · Psychological Science · doi:10.1177/0956797611417632 · Cited by 6,567
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155
limma: Linear Models for Microarray Data
Smyth, G. K. (2005) · Statistics for Biology and Health · doi:10.1007/0-387-29362-0_23 · Cited by 5,796
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Massive mining of publicly available RNA-seq data from human and mouse
Lachmann, A., Torre, D., Keenan, A. B., Jagodnik, K. M., Lee, H. J., Wang, L., Silverstein, M. C., & Ma’ayan, A. (2018) · Nature Communications · doi:10.1038/s41467-018-03751-6 · Cited by 701
A practical guide to methods controlling false discoveries in computational biology
Korthauer, K., Kimes, P. K., Duvallet, C., Reyes, A., Subramanian, A., Teng, M., Shukla, C., Alm, E. J., & Hicks, S. C. (2019) · Genome Biology · doi:10.1186/s13059-019-1716-1 · Cited by 436
Cloud computing for genomic data analysis and collaboration
Langmead, B., & Nellore, A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.113 · Cited by 310
“61 ) efforts used AWS and a custom cloud-enabled RNA-seq aligner 62 to reanalyse over 70,000 human samples spanning TCGA, GTEx and the SRA, releasing expres-sion-level summaries at the level of splice junctions, exons, genes and individual genomic bases.”
MethodSelf-citationDream: powerful differential expression analysis for repeated measures designs
Hoffman, G. E., & Roussos, P. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btaa687 · Cited by 319
Metadata
- Authors
- Collado-Torres, L., Nellore, A., Kammers, K., Ellis, S. E., Taub, M. A., Hansen, K. D., Jaffe, A. E., Langmead, B., & Leek, J. T.
- Venue
- Nature Biotechnology
- Published
- 2017-04
- Volume
- 35
- Issue
- 4
- Pages
- 319-321
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2606715885
- Cited by
- 458
- References
- 46
- FWCI
- 14.56
- Type
- journal article
- Language
- en
- Open access
- green
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