Concepedia

Target analysis by integration of transcriptome and ChIP-seq data with BETA

Su Wang, Hanfei Sun, Jian Ma, Chongzhi Zang, Chenfei Wang, Juan Wang, Qianzi Tang, Clifford A. Meyer, Yong Zhang, X. Shirley Liu

Nature Protocols · 2013 · 582 citations · 40 references

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References

40

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha et al. · Proceedings of the National Academy of Sciences · 2005 · 56.7K citations · Full text

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop et al. · Genome biology · 2009 · 23K citations · Full text

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Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer et al. · Genome biology · 2008 · 19.9K citations · Full text

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell, Adam Roberts, Loyal A. Goff et al. · Nature Protocols · 2012 · 12.9K citations · Full text

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The Human Genome Browser at UCSC

W. James Kent, Charles W. Sugnet, Terrence S. Furey et al. · Genome Research · 2002 · 10.9K citations · Full text

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