References

[KFS+17]

Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R Kulkarni, Ge Tan, and others. Jaspar 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res., 46(D1):D260–D266, 2017. doi:10.1093/nar/gkx1126.

[KRG+18]

Anja Kiesel, Christian Roth, Wanwan Ge, Maximilian Wess, Markus Meier, and Johannes Söding. The bamm web server for de-novo motif discovery and regulatory sequence analysis. Nucleic Acids Research, 46(W1):W215–W220, 2018. doi:10.1093/nar/gky431.

[KVG+17]

Michelle M Kudron, Alec Victorsen, Louis Gevirtzman, LaDeana W Hillier, William W Fisher, Dionne Vafeados, Matt Kirkey, Ann S Hammonds, Jeffery Gersch, Haneen Ammouri, and others. The modern resource: genome-wide binding profiles for hundreds of drosophila and caenorhabditis elegans transcription factors. Genetics, pages genetics–300657, 2017. doi:10.1534/genetics.117.300657.

[KVY+18]

Ivan V Kulakovskiy, Ilya E Vorontsov, Ivan S Yevshin, Ruslan N Sharipov, Alla D Fedorova, Eugene I Rumynskiy, Yulia A Medvedeva, Arturo Magana-Mora, Vladimir B Bajic, Dmitry A Papatsenko, and et al. Hocomoco: towards a complete collection of transcription factor binding models for human and mouse via large-scale chip-seq analysis. Nucleic Acids Res., 46(D1):D252–D259, 2018. doi:10.1093/nar/gkx1106.

[Qui14]

Aaron R Quinlan. Bedtools: the swiss-army tool for genome feature analysis. Current protocols in bioinformatics, pages 11–12, 2014. doi:10.1002/0471250953.bi1112s47.

[QH10]

Aaron R Quinlan and Ira M Hall. Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6):841–842, 2010. doi:10.1093/bioinformatics/btq033.

[SSoding16]

Matthias Siebert and Johannes Söding. Bayesian markov models consistently outperform pwms at predicting motifs in nucleotide sequenc es. Nucleic Acids Res., 44(13):6055–6069, Jul 2016. doi:10.1093/nar/gkw521.

[Str08]

Korbinian Strimmer. fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics, 24(12):1461–1462, 2008. doi:10.1093/bioinformatics/btn209.

[YSV+16]

Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, and Fedor Kolpakov. Gtrd: a database of transcription factor binding sites identified by chip-seq experiments. Nucleic Acids Res., pages gkw951, 2016. doi:10.1093/nar/gkw951.