Which open source software is best for network data analysis?

My favorite is igraph package in R/Python. But it requires knowledge of R or Python...

If you are familiar with Python, there is also NetworkX.

There is an easier, but less powerful, alternative: NodeXL. Wich is an Excel addon.

You might also wanna try igraph http://igraph.sourceforge.net/ which is available in R and in Python. It is easy to combine networkx http://networkx.lanl.gov/ with igraph. For pure illustration purposes I recommend http://gephi.org/.

I would suggest NetworkX. I have also tried Network Workbench (http://nwb.cns.iu.edu/) that is a good tool but that unfortunately it is not periodically updated such as NetworkX, iGraph and Gephi.

I would recomend Gephi, as long as you have a decent system to run it on it can visualize 100,000+ nodes easily.

Check out Tulip http://tulip.labri.fr/TulipDrupal/

I am teaching a course on SNA. The students use Pajek - it is a good introduction to SNA and the program has an extensive user manual, a book actually. For my research, I am leaning toward Gephi, but in a previous research we relied on Cytoscape.

For a quick check of the data, I would recommend Pajek or Gephi.

BTW there is a good freed online course on Social Network Analysis coming up in March by Lada Adamic. She uses Gephi and iGraph. https://www.coursera.org/course/sna

Pajek

I recommend the sna and igraph packages in R.

I use gephi (free), ucinet, netdraw

I want to say thanks to all friends that answer my question and guide me.

If you have budget i2 Workstation has some very good tools for SNA and analysis in general. I also use Gephi as well.

There are few I work with: NodeXL is Microsoft Excel template and is very useful. Get it from here: http://nodexl.codeplex.com/. The other is Social Networks Visualizer (http://socnetv.sourceforge.net/). Both are free and very ease to use.

I like NodeXL -- it works with Microsoft Excel -- an excellent book is at ... http://www.amazon.com/Analyzing-Social-Media-Networks-NodeXL/dp/0123822297

Gephi is a very good software that provides nice illustrations.

The R framework is popular with many network data analysts. http://www.r-project.org/. And these two packages provide many useful functions: http://cran.r-project.org/web/packages/sna/index.html and http://cran.r-project.org/web/packages/igraph/index.html

There is also a nice course Prof. Albert-László Barabási on the web:

somewhat higher level than Adamic

if you are asking about the biological data analysis side, then i suggest you Cell Designer and Cytoscape for data analysis

In my opinion the best software to use for network analysis will really depend on a number of factors, including: 

It's a bit of a generalization and the below is not an exhaustive list, but in my mind the available tools can be divided into four categories:

By no means an exhaustive list but rather a few of the more commonly used applications to illustrate the trade-offs. 

Dear Andrew Pitts,

Thanks for your answer and information.

I am confused with Networkx after reading slide of Prof Salvatore Scellato (Lecture slide 7, 8 - page 5)  http://www.cl.cam.ac.uk/teaching/1617/L109/materials.html 

in another place they have mentioned (see attachment): 

When should I AVOID NetworkX to perform network analysis?

• Large-scale problems that require faster approaches (i.e. massive networks

with 100M/1B edges)

• Better use of memory/threads than Python (large objects, parallel computation)

so what should I use to analyze social net with millions of nodes??? :(

Ashis that is more of a question than an answer. But for truly large networks (> 1m nodes) you should look at Pajek-XXL or Pajek-3XL: http://mrvar.fdv.uni-lj.si/pajek/PajekXXL.htm. From a development perspective (i.e. code required) Apache Spark's GraphX is also an option (not for visualisation though): http://spark.apache.org/graphx/. You can also look at neo4j but you won't find out-of-the-box algorithms going down that route. Oh, and if your network isn't that large then, depending on the resources on your computer, Gephi can be workable up to a few million nodes. 

Agreed, I would use Apache Spark, or Oracle PGX, or Apache Titan to do this. You may find advantages with a PGX approach over Spark if you don't have a lot of high-end nodes to run thing on. 

Andrew Pitts provides a great response with lots of reference systems. I'd like to add one more to the mix - although this is not an "open source" -- but rather more of an "open standards" platform -- DataWalk. https://datawalk.com/ There are a lot of foundational data representation capabilities in "link charts" and it is not simply presenting a network diagram, but rather, how the underlying representation is defined, the ability to create the objects (and links). Many of these concepts are overviewed in my books. However, to transition the theory into real-work practice is not always efficient, practical, or consistent. Therefore, how accurate, true, complete, and reliable are the results generated? There are some good videos @ https://datawalk.com/resources/

Is there any software for social media analysis similar to the SNA Software Tool NodeXL that you recommend? For academia.

Sara, you might also want to evaluate this one: https://onodo.org/locale/EN

gephi is the best for you . i think

Gephi is best because of its visual encoding and plenty of features for network statistics etc. So many builtin features.

I have used Gephi, cytoscape, Igraph and pajek.

According to me Gephi is easiest and can be used very easily. Cytoscape can also be used easily, Igraph is available in Python and R .

I found Pajek not so friendly as you need to convert the input file in . net format.

I used to be a HUGE fan of Gephi -- it was easy to use, had a pretty intuitive UI, generated all sorts of handy SNA metrics, etc. However, it has not worked properly with Windows 10 for years (check the various user forums if you don't believe me). I've tried every suggested fix (most of which have to do with making sure that the Java home path is specified correctly)--edit the config file, uninstall and reinstall, clear out the temp folder, etc., etc. Nothing has worked, and this has been an ongoing issue for at least four years if not longer. NodeXL is an *okay* workaround, but the free version is more limited in terms of metrics (won't calculate modularity class, for example) and the graphical output is nowhere near as nice as Gephi. BLERG.

We've been using Gephi, when it isn't crashing for no reason - we're looking for an alternative - might just have to go back to python & coding it all.

Hi Sara, I used Cytoscape for network analysis. Easy to use and to start with for the first time users.

Best wishes.

My favorites are Gephi (easy and beautiful graphs), iGraph (vast number of resources, good for larger networks), Statnet (great option if you want to run Exponential Random Grapho Models - ERGMs), Pajek and Ucinet (good for smaller networks, but their graphs are not as pretty as the previous options).