References

[BBC+11]

S. Behnel, R. Bradshaw, C. Citro, L. Dalcin, D.S. Seljebotn, and K. Smith. Cython: the best of both worlds. Computing in Science Engineering, 13(2):31 –39, 2011. doi:10.1109/MCSE.2010.118.

[CYK+14]

Beibei Chen, Jonghyun Yun, Min Soo Kim, Joshua T Mendell, and Yang Xie. Pipe-clip: a comprehensive online tool for clip-seq data analysis. Genome biology, 15(1):R18, 2014.

[CSP15]

Federico Comoglio, Cem Sievers, and Renato Paro. Sensitive and highly resolved identification of rna-protein interaction sites in par-clip data. BMC bioinformatics, 16(1):32, 2015.

[CGM+11]

David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, and Uwe Ohler. Paralyzer: definition of rna binding sites from par-clip short-read sequence data. Genome biology, 12(8):R79, 2011.

[DDS+13]

Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R Gingeras. Star: ultrafast universal rna-seq aligner. Bioinformatics, 29(1):15–21, 2013.

[FK14]

Matthew B Friedersdorf and Jack D Keene. Advancing the functional utility of par-clip by quantifying background binding to mrnas and lncrnas. Genome biology, 15(1):R2, 2014.

[HLB+10]

Markus Hafner, Markus Landthaler, Lukas Burger, Mohsen Khorshid, Jean Hausser, Philipp Berninger, Andrea Rothballer, Manuel Ascano, Anna-Carina Jungkamp, Mathias Munschauer, and others. Transcriptome-wide identification of rna-binding protein and microrna target sites by par-clip. Cell, 141(1):129–141, 2010.

[Hun07]

J. D. Hunter. Matplotlib: a 2d graphics environment. Computing In Science & Engineering, 9(3):90–95, 2007. doi:10.1109/MCSE.2007.55.

[JLDZ14]

Hongshan Jiang, Rong Lei, Shou-Wei Ding, and Shuifang Zhu. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC bioinformatics, 15(1):182, 2014.

[Lan10]

Ben Langmead. Aligning short sequencing reads with bowtie. Current protocols in bioinformatics, pages 11–7, 2010.

[LHW+09]

Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, and others. The sequence alignment/map format and samtools. Bioinformatics, 25(16):2078–2079, 2009.

[LHSoding12]

Sebastian Luehr, Holger Hartmann, and Johannes Söding. The xxmotif web server for exhaustive, weight matrix-based motif discovery in nucleotide sequences. Nucleic acids research, 40(W1):W104–W109, 2012.

[PWS13]

Vicent Pelechano, Wu Wei, and Lars M Steinmetz. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature, 497(7447):127–131, 2013.

[SSK+13]

Daniel Schulz, Bjoern Schwalb, Anja Kiesel, Carlo Baejen, Phillipp Torkler, Julien Gagneur, Johannes Soeding, and Patrick Cramer. Transcriptome surveillance by selective termination of noncoding rna synthesis. Cell, 155(5):1075–1087, 2013.

[SHS17]

Tom Smith, Andreas Heger, and Ian Sudbery. Umi-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome research, 27(3):491–499, 2017.

[Str08]

Korbinian Strimmer. Fdrtool: a versatile r package for estimating local and tail area-based false discovery rates. Bioinformatics, 24(12):1461–1462, 2008.

[Tor15]

Phillipp Torkler. STAMMP. PhD thesis, lmu, 2015.

[WCV11]

Stéfan van der Walt, S Chris Colbert, and Gael Varoquaux. The numpy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2):22–30, 2011.