CSA is developed for the whole process of ChIP-Seq analysis, which covers mapping (BWA[1], Bowtie, Bowtie2[2], SOAP[3], BLAST, Subread[4], NGM[5]), quality control (multiBamSummary[6]), peak calling (MACS[7], MACS2, PeakSeq[8], PeakRanger[9], SICER[10], FindPeaks[11], Fseq[12], AREM, BroadPeak, BCP, PePr[13], diffReps[14], SISSRs[15]), and downstream analysis (findMotifs, annotatePeaks, iPAGE[16]). In addition, CSA provides a customization function for users to define their own workflow. Moreover, the visualization of mapping, peak calling, motif finding, and pathway analysis results is also supplied in CSA.
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[12]Boyle, A. P., Guinney, J., Crawford, G. E., & Furey, T. S. (2008). Bioinformatics, 24(21), 2537-2538.
[13]Zhang, Y., Lin, Y. H., Johnson, T. D., et al (2014). Bioinformatics, 30(18), 2568-2575.
[14]Shen, L., Shao, N. Y., Liu, X., Maze, I., Feng, J., & Nestler, E. J. (2012). Plos One, 8(6), e65598.
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[16]Goodarzi, H., Elemento, O., & Tavazoie, S. (2009).  Molecular Cell, 36(5), 900-911.
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