Author(s)
Nicolas Descostes
Published 6 Projects
genomics epigenetics Bioinformatics Biochemistry Cancer Biology
Danny Reinberg
Published 16 Projects
Polycomb Spreading Biochemistry Molecular Biology Nucleation
Content
Video Abstract (AI generated) (01:20) Paper PreprintMotivation: Chromatin Immuno-Precipitation followed by Sequencing (ChIP-Seq)is used to determine the binding sites of any protein of interest. ChIP-Seq data suffer from being more qualitative than quantitative. The recent use of spike-in controls along with the standard protocol tackled this problem. However, no dedicated tool is available for a robust evaluation of this new ChIP-Seq approach. Results: We developed ChIPSeqSpike, an R/Bioconductor package that enables ChIP-Seq spike-in normalization, assessment and analysis. Ready to use scaled bigwig files and scaling factors values are obtained as output. ChIPSeqSpike also provides tools for ChIP-Seq spike-in assessment and analysis through a versatile collection of graphical functions. Availability: The package is implemented in R (as of version 3.4) and is available from Bioconductor at the URL: https://www.bioconductor.org/packages/3.7/bioc/html/ChIPSeqSpike.html, where installation and usage instructions can be found.
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Danny Reinberg. (2021, Nov 7).ChIPSeqSpike: A R Bioconductor package for ChIP-Seq data scaling according to spike-in control[Video]. Scitok. https://scitok.com/project/p/2fac3940
Descostes Nicolas. "ChIPSeqSpike: A R Bioconductor package for ChIP-Seq data scaling according to spike-in control" Scitok, uploaded by Reinberg Danny, 7 Nov, 2021, https://scitok.com/project/p2fac3940
Danny Reinberg. "ChIPSeqSpike: A R Bioconductor package for ChIP-Seq data scaling according to spike-in control" Scitok. (Nov 7, 2021). https://scitok.com/project/p/2fac3940
Danny Reinberg (Nov 7, 2021). ChIPSeqSpike: A R Bioconductor package for ChIP-Seq data scaling according to spike-in control Scitok. https://scitok.com/project/p/2fac3940
Danny Reinberg. ChIPSeqSpike: A R Bioconductor package for ChIP-Seq data scaling according to spike-in control[video]. 2021 Nov 7. https://scitok.com/project/p/2fac3940
@online{al2006link, title={ ChIPSeqSpike: A R Bioconductor package for ChIP-Seq data scaling according to spike-in control }, author={ Reinberg, Danny }, organization={Scitok}, month={ Nov }, day={ 7 }, year={ 2021 }, url = {https://scitok.com/project/p/2fac3940}, }