Steps + Tools:
1. Node.js, JQuery web scraping from blockexplorer.com
2. C++ boost library regex to parse block/ transaction data
3. R programming language to manipulate data.
4. R network package "igraph" to create bitcoin network.
5. "rgexf" R package to export your graph to Gephi visualizer.
6. Visualize your graph in Gephi with awesome Gephi layout plugins.
Yep. It's actually part of my network research. First of all, you need to have the whole or part (it depends on your focus of analysis) of the bitcoin blockchain or block information json/html formatted files downloaded. So, in my case I scraped htmls using node.js from blockexplorer.com because then it's very easy to parse the information. You can do it from blockchain.info too. Or you can even manipulate the block chain level db databases that is constantly being downloaded in your computer by your bitcoin wallet. Such manipulator already exists such as Gavin's Bitcointools (https://github.com/gavinandresen/bitcointools) but outdated.
In my case, then all the block information as well as transaction information data are parsed from the html file using c++ boost library, basically regex. In fact you can use python, node.js, perl, ruby or even R to do these things. But obviously C++ is fast when you are dealing with massive data. The best combination will be C++ and R(RCpp package).
Now if you have parsed the transaction data, you need to create network edges. You can do it by pure R language and with useful R packages.
Then if you want to manipulate that network, the R package called "igraph"(http://igraph.sourceforge.net/screenshots.html) is the best one out there. With igraph you can plot nice graphs but not magnificently beautiful ones. There comes other visualization GUIs like gephi or graphviz.
I used gephi (https://gephi.org/). Now how do you take your graph to gephi from R,i.e. convert to .gexf file. There comes R to gephi exporter rgexf package(http://cran.fhcrc.org/web/packages/rgexf/index.html).
Once you get your network in gephi, then you will be astonished how many different things gephi can allow you to do. Gephi has so many plugins, layouts to create outstanding graphs, visualize and do other network analysis.
Finally, if anyone learns all these tools. They can manipulate anything in the web, any graphs. Hope this helps. Please post and share your works. Thank you.