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HTSeq--a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W. Anders S, et al. Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25. Bioinformatics. 2015. PMID: 25260700 Free PMC article.
Visualization of genomic data with the Hilbert curve.
Anders S. Anders S. Bioinformatics. 2009 May 15;25(10):1231-5. doi: 10.1093/bioinformatics/btp152. Epub 2009 Mar 17. Bioinformatics. 2009. PMID: 19297348 Free PMC article.
This article argues that the so-called Hilbert curve visualization can complement genome browsers and help to get further insights into the structure of one's data. ...
This article argues that the so-called Hilbert curve visualization can complement genome browsers and help to get further insights into the …
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. Morgan M, et al. Bioinformatics. 2009 Oct 1;25(19):2607-8. doi: 10.1093/bioinformatics/btp450. Epub 2009 Aug 3. Bioinformatics. 2009. PMID: 19654119 Free PMC article.
Differential expression analysis for sequence count data.
Anders S, Huber W. Anders S, et al. Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27. Genome Biol. 2010. PMID: 20979621 Free PMC article.
Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions.
Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO. Schlattl A, et al. Genome Res. 2011 Dec;21(12):2004-13. doi: 10.1101/gr.122614.111. Epub 2011 Aug 23. Genome Res. 2011. PMID: 21862627 Free PMC article.
Detecting differential usage of exons from RNA-seq data.
Anders S, Reyes A, Huber W. Anders S, et al. Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111. Epub 2012 Jun 21. Genome Res. 2012. PMID: 22722343 Free PMC article.
An efficient method for genome-wide polyadenylation site mapping and RNA quantification.
Wilkening S, Pelechano V, Järvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM. Wilkening S, et al. Nucleic Acids Res. 2013 Mar 1;41(5):e65. doi: 10.1093/nar/gks1249. Epub 2013 Jan 7. Nucleic Acids Res. 2013. PMID: 23295673 Free PMC article.
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.
Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J. Zarnack K, et al. Cell. 2013 Jan 31;152(3):453-66. doi: 10.1016/j.cell.2012.12.023. Cell. 2013. PMID: 23374342 Free PMC article.
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor.
Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD. Anders S, et al. Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. Epub 2013 Aug 22. Nat Protoc. 2013. PMID: 23975260
Drift and conservation of differential exon usage across tissues in primate species.
Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W. Reyes A, et al. Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15377-82. doi: 10.1073/pnas.1307202110. Epub 2013 Sep 3. Proc Natl Acad Sci U S A. 2013. PMID: 24003148 Free PMC article.
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