I just came across this software suite HOMER , it seems to be quite good.
I would like to have an opinion on this software from the people who are working with NGS data analysis (specially with ChIP Seq and with RNA seq data analysis) and where they rank it in comparison with other softwares (GREAT, completeMotifs etc).
My advice will be, ' Stick to R and Bioconductors" and rest of the tools for ChIP seq analysis could be used for extended analysis.
Note: Since no one answered, so I thought of writing down few lines. Which could help any new comer in ChIPseq analysis field. HOMER is not extra ordinary, just normal.