Home > Resources > Whitepapers > White paper on the Transcription Factor ChIP-Seq

White paper on the Transcription Factor ChIP-Seq

In this White Paper we present a performance analysis on the new Transcription Factor ChIP-seq tool available in CLC Genomics Workbench and CLC Genomics Server (version 7.5 and up), and in Biomedical Genomics Worbench and Server. Using an independent manually curated benchmark dataset [Rye et al., 2011] we show that the CLC implementation of the shape-based peak caller ranks well among popular state-of-the-art peak callers while requiring a minimum of intervention and parameterization from the user. We describe the algorithmic principles underlying the implementation and provide an evaluation in terms of receiver-operator characteristic (ROC) plots. Finally, we identify the most promising avenues for further developments and future application areas.

Spotlight

AltheaDx

AltheaDx is a commercial stage molecular diagnostics company specializing in the field of pharmacogenetics, or PGx.

OTHER WHITEPAPERS

Could DNA be the next big thing in data storage?

whitePaper | August 19, 2021

DNA storage technology is advancing rapidly. Atos is closely monitoring the development of this technology in the hope that future developments will make it a scalable, cost effective and crucially a decarbonized alternative to today’s carbon intensive technologies.

Making the Promise of mRNA a Reality: OvercomingScale-Up Challenges

whitePaper | March 22, 2023

If scaling issues strike you as obvious or even boring, you should read “On Being the Right Size,” a 1926 essay by geneticist J.B.S. Haldane. It makes the case that a difference in scale—a seemingly simple matter—may demand subtle changes in form and function.

2022 Biosimilars Report: The U.S. Journey and Path Ahead

whitePaper | June 8, 2022

Cardinal Health is fortunate to sit at the crossroads of the United States (U.S.) healthcare system, engaging with stakeholders from across the industry including healthcare

How advanced purification technologies are speeding the hunt for new protections against disease

whitePaper | November 24, 2022

Smallpox was the first infectious disease for which an effective vaccine was developed. In the late 1700s, British doctor Edward Jenner devised a method to inoculate people with cowpox pus to give them immunity against smallpox, a much more deadly disease.