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.
Reference
[1]Li, H., & Durbin, R. (2010). Bioinformatics, 25(5), 1754-1760.
[2]Langmead, B., & Salzberg, S. L. (2012). Nature Methods, 9(4), 357.
[3]Li, R., Yu, C., et al. (2009). Bioinformatics, 25(15), 1966-1967.
[4]Liao, Y., Smyth, G. K., & Shi, W. (2013). Nucleic Acids Research, 41(10), 89-94.
[5]Sedlazeck, F. J. (2013). Bioinformatics, 29(21), 2790-1.
[6]Ramírez, F., Dündar, F., Diehl, S., et al. (2014). Nucleic Acids Research, 42(W1), 187-91.
[7]Zhang, Y., Liu, T., et al. (2008). Genome Biology, 9(9), : R137.
[8]Rozowsky, J., Euskirchen, G., et al. (2009). Nature Biotechnology, 27(1), 66-75.
[9]Feng, X., Grossman, R., & Stein, L. (2011). BMC Bioinformatics, 12(1), 139.
[10]Xu, S., Grullon, S., Ge, K., & Peng, W. (2014). 1150, 97-111.
[11]Fejes, A. P., Robertson, G., Bilenky, M., et al (2008). Bioinformatics, 24(15), 1729.
[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.
[15]Jothi, R., Cuddapah, S., Barski, A., Cui, K., & Zhao, K. (2008). Nucleic Acids Research, 36(16), 5221.
[16]Goodarzi, H., Elemento, O., & Tavazoie, S. (2009).  Molecular Cell, 36(5), 900-911.
  • Firefox and Chrome are recommended to get better interface display.