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moving a few things around

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e.g. software-centric tutorials join the software section
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@ -191,7 +191,8 @@ Inspired by [Awesome Deep Learning](https://github.com/ChristosChristofidis/awes
## Review Articles ## Review Articles
1. "[Biological Networks](http://algo.uni-konstanz.de/publications/bbs-bn-13.pdf)" (_Handbook of Graph Drawing and Visualization_, 2013). 1. "[Basic Notions for the Analysis of Large Two-mode Networks](http://www.sciencedirect.com/science/article/pii/S0378873307000494)" ([preprint](https://www-complexnetworks.lip6.fr/~latapy/Publis/socnet07.pdf), [related code](https://www-complexnetworks.lip6.fr/~latapy/Bip/); _Social Networks_, 2008).
- "[Biological Networks](http://algo.uni-konstanz.de/publications/bbs-bn-13.pdf)" (_Handbook of Graph Drawing and Visualization_, 2013).
- "[Graph Theory and Networks in Biology](http://dx.doi.org/10.1049/iet-syb:20060038)" ([preprint](http://arxiv.org/abs/q-bio/0604006); _IET Systems Biology_, 2007). - "[Graph Theory and Networks in Biology](http://dx.doi.org/10.1049/iet-syb:20060038)" ([preprint](http://arxiv.org/abs/q-bio/0604006); _IET Systems Biology_, 2007).
- "[Network Analysis and Political Science](http://www.annualreviews.org/doi/abs/10.1146/annurev.polisci.12.040907.115949)" (_Annual Review of Political Science_, 2011). - "[Network Analysis and Political Science](http://www.annualreviews.org/doi/abs/10.1146/annurev.polisci.12.040907.115949)" (_Annual Review of Political Science_, 2011).
- "[Networks and History](http://onlinelibrary.wiley.com/doi/10.1002/cplx.10054/abstract)" (_Complexity_, 2002). - "[Networks and History](http://onlinelibrary.wiley.com/doi/10.1002/cplx.10054/abstract)" (_Complexity_, 2002).
@ -202,13 +203,14 @@ Inspired by [Awesome Deep Learning](https://github.com/ChristosChristofidis/awes
## Software ## Software
> Several links in this section come from the [NetWiki Shared Code](http://netwiki.amath.unc.edu/SharedCode/SharedCode) page. > Several links in this section come from the [NetWiki Shared Code](http://netwiki.amath.unc.edu/SharedCode/SharedCode) page. Software-centric tutorials are listed below their program of choice: other tutorials are listed [in the next section](#tutorials).
> See also the [Social Network Analysis Project Survey](https://docs.google.com/spreadsheets/d/1Xo-ehJatzmxMek6gPG0h-d7yRSuiO6_flViTQNMAku0/edit#gid=0) ([blog post](http://pudo.org/blog/2013/12/21/sna-survey.html)), an earlier attempt to chart social network analysis tools that links to many commercial platforms not included in this list, such as [Detective.io](http://www.detective.io/). > See also the [Social Network Analysis Project Survey](https://docs.google.com/spreadsheets/d/1Xo-ehJatzmxMek6gPG0h-d7yRSuiO6_flViTQNMAku0/edit#gid=0) ([blog post](http://pudo.org/blog/2013/12/21/sna-survey.html)), an earlier attempt to chart social network analysis tools that links to many commercial platforms not included in this list, such as [Detective.io](http://www.detective.io/).
> Also note that the Wikipedia English entry on [Social Network Analysis Software](https://en.wikipedia.org/wiki/Social_network_analysis_software) links to many commercial that are often very expensive, outdated, and far from being awesome by any reasonable standard. > Also note that the Wikipedia English entry on [Social Network Analysis Software](https://en.wikipedia.org/wiki/Social_network_analysis_software) links to many commercial that are often very expensive, outdated, and far from being awesome by any reasonable standard.
1. [Cytoscape](http://www.cytoscape.org/) - Cross-platform Java program to build, analyze and visualize networks. 1. [Cytoscape](http://www.cytoscape.org/) - Cross-platform Java program to build, analyze and visualize networks.
- [Discourse Network Analyzer (DNA)](http://www.philipleifeld.com/discourse-network-analyzer/discourse-network-analyzer-dna.html) - Qualitative content analysis tool with network export facilities, written in Java with R integration. - [Discourse Network Analyzer (DNA)](http://www.philipleifeld.com/discourse-network-analyzer/discourse-network-analyzer-dna.html) - Qualitative content analysis tool with network export facilities, written in Java with R integration.
- [Gephi](https://gephi.github.io/) - Cross-platform, free and open source tool for network visualization. - [Gephi](https://gephi.github.io/) - Cross-platform, free and open source tool for network visualization.
- [Practical Social Network Analysis With Gephi](http://derekgreene.com/gephitutorial/) (2014).
- [GLEAMviz Simulator](http://www.gleamviz.org/) - Cross-platform tool intended for the prediction of human epidemics. - [GLEAMviz Simulator](http://www.gleamviz.org/) - Cross-platform tool intended for the prediction of human epidemics.
- [Graphviz](http://www.graphviz.org/) - Cross-platform software to draw graphs in the DOT graph drawing language. - [Graphviz](http://www.graphviz.org/) - Cross-platform software to draw graphs in the DOT graph drawing language.
- [MuxViz](http://muxviz.net/) - Cross-platform, free and open source tool to study multilayer networks, based on R and GNU Octave. - [MuxViz](http://muxviz.net/) - Cross-platform, free and open source tool to study multilayer networks, based on R and GNU Octave.
@ -216,6 +218,8 @@ Inspired by [Awesome Deep Learning](https://github.com/ChristosChristofidis/awes
- [NodeXL](http://nodexl.codeplex.com/) - Free, open-source template to explore network graphs with Microsoft Excel. - [NodeXL](http://nodexl.codeplex.com/) - Free, open-source template to explore network graphs with Microsoft Excel.
- [ORA-LITE](http://www.casos.cs.cmu.edu/projects/ora/) - Windows program for dynamic meta-network assessment and analysis. - [ORA-LITE](http://www.casos.cs.cmu.edu/projects/ora/) - Windows program for dynamic meta-network assessment and analysis.
- [Pajek](http://vlado.fmf.uni-lj.si/pub/networks/pajek/) - Windows program for large network analysis, free for noncommercial use. - [Pajek](http://vlado.fmf.uni-lj.si/pub/networks/pajek/) - Windows program for large network analysis, free for noncommercial use.
- [Analyse des réseaux : une introduction à Pajek](http://quanti.hypotheses.org/512/), in French (2011).
- [La détection de communautés avec Pajek 3.6](http://groupefmr.hypotheses.org/544), in French (2012).
- [PNet](http://www.swinburne.edu.au/fbl/research/transformative-innovation/our-research/MelNet-social-network-group/PNet-software/index.html) - Simulation and estimation of exponential random graph models (ERGMs), written in Java for Windows. - [PNet](http://www.swinburne.edu.au/fbl/research/transformative-innovation/our-research/MelNet-social-network-group/PNet-software/index.html) - Simulation and estimation of exponential random graph models (ERGMs), written in Java for Windows.
- [Radatools](http://deim.urv.cat/~sergio.gomez/radatools.php) - Set of tools intended for the analysis of complex networks, built on top of [Radalib](http://deim.urv.cat/~sergio.gomez/radalib.php), a library written in Ada. - [Radatools](http://deim.urv.cat/~sergio.gomez/radatools.php) - Set of tools intended for the analysis of complex networks, built on top of [Radalib](http://deim.urv.cat/~sergio.gomez/radalib.php), a library written in Ada.
- [Siena](http://www.stats.ox.ac.uk/~snijders/siena/) - Simulation Investigation for Empirical Network Analysis. Formerly a Windows program, now developed as the RSiena R package. - [Siena](http://www.stats.ox.ac.uk/~snijders/siena/) - Simulation Investigation for Empirical Network Analysis. Formerly a Windows program, now developed as the RSiena R package.
@ -293,6 +297,7 @@ Inspired by [Awesome Deep Learning](https://github.com/ChristosChristofidis/awes
- [ggraph](https://github.com/thomasp85/ggraph) - A grammar of graph graphics built in the spirit of ggplot2. - [ggraph](https://github.com/thomasp85/ggraph) - A grammar of graph graphics built in the spirit of ggplot2.
- [hergm](https://cran.r-project.org/web/packages/hergm/) - Estimate and simulate hierarchical exponential-family random graph models (HERGM) with local dependence. - [hergm](https://cran.r-project.org/web/packages/hergm/) - Estimate and simulate hierarchical exponential-family random graph models (HERGM) with local dependence.
- [igraph](http://igraph.org/r/) - A collection of network analysis tools. - [igraph](http://igraph.org/r/) - A collection of network analysis tools.
- [Network Analysis and Visualization with R and igraph](http://kateto.net/networks-r-igraph) (2016).
- [influenceR](https://cran.r-project.org/web/packages/influenceR/) - Compute various node centrality network measures by Burt, Borgatti and others. - [influenceR](https://cran.r-project.org/web/packages/influenceR/) - Compute various node centrality network measures by Burt, Borgatti and others.
- [latentnet](https://cran.r-project.org/web/packages/latentnet/) - Latent position and cluster models for network objects. - [latentnet](https://cran.r-project.org/web/packages/latentnet/) - Latent position and cluster models for network objects.
- [networkD3](http://christophergandrud.github.io/networkD3/) - D3 JavaScript network graphs from R. - [networkD3](http://christophergandrud.github.io/networkD3/) - D3 JavaScript network graphs from R.
@ -306,6 +311,9 @@ Inspired by [Awesome Deep Learning](https://github.com/ChristosChristofidis/awes
- [spectralGOF](http://people.bu.edu/jccs/spectralGOF.html) - Compute the "spectral goodness of fit" (SGOF), a measure of how well a network model explains the structure of an observed network. - [spectralGOF](http://people.bu.edu/jccs/spectralGOF.html) - Compute the "spectral goodness of fit" (SGOF), a measure of how well a network model explains the structure of an observed network.
- [spnet](http://cran.r-project.org/web/packages/spnet/) - Methods for dealing with spatial social networks. - [spnet](http://cran.r-project.org/web/packages/spnet/) - Methods for dealing with spatial social networks.
- [statnet](http://statnet.org/) - The project behind many R network analysis packages ([mailing-list](https://mailman.u.washington.edu/mailman/listinfo/statnet_help)). - [statnet](http://statnet.org/) - The project behind many R network analysis packages ([mailing-list](https://mailman.u.washington.edu/mailman/listinfo/statnet_help)).
- [Exponential Random Graph Models (ERGMs) Using statnet](https://statnet.org/trac/raw-attachment/wiki/Sunbelt2015/ergm_tutorial.html) (2015).
- [Guides for Using the statnet Package](http://www.melissaclarkson.com/resources/R_guides/) (2010).
- [Modeling Valued Networks with statnet](https://statnet.org/trac/raw-attachment/wiki/Sunbelt2013/Valued.pdf) (2013).
- [tergm](https://cran.r-project.org/web/packages/tergm/) - Fit, simulate and diagnose models for temporal exponential-family random graph models (TERGM). - [tergm](https://cran.r-project.org/web/packages/tergm/) - Fit, simulate and diagnose models for temporal exponential-family random graph models (TERGM).
- [tnet](https://cran.r-project.org/web/packages/tnet/) - Network measures for weighted, two-mode and longitudinal networks. - [tnet](https://cran.r-project.org/web/packages/tnet/) - Network measures for weighted, two-mode and longitudinal networks.
- [tsna](https://cran.r-project.org/web/packages/tsna/) - Tools for temporal social network analysis. - [tsna](https://cran.r-project.org/web/packages/tsna/) - Tools for temporal social network analysis.
@ -334,27 +342,20 @@ Inspired by [Awesome Deep Learning](https://github.com/ChristosChristofidis/awes
## Tutorials ## Tutorials
1. [Analyse des réseaux : une introduction à Pajek](http://quanti.hypotheses.org/512/), in French (2011). > Tutorials that are not focused on a single specific software program.
- [Basic and Advanced Network Visualization with Gephi and R](http://kateto.net/sunbelt2016) (2016).
- [Exponential Random Graph Models (ERGMs) Using statnet](https://statnet.org/trac/raw-attachment/wiki/Sunbelt2015/ergm_tutorial.html) (2015). 1. [Basic and Advanced Network Visualization with Gephi and R](http://kateto.net/sunbelt2016) (2016).
- [Guides for Using the statnet Package](http://www.melissaclarkson.com/resources/R_guides/) (2010).
- [Implementing an ERGM From Scratch in Python](http://davidmasad.com/blog/ergms-from-scratch/) (2014). - [Implementing an ERGM From Scratch in Python](http://davidmasad.com/blog/ergms-from-scratch/) (2014).
- [L'analyse des graphes bipartis](https://halshs.archives-ouvertes.fr/FMR/halshs-00794976), in French (2013). - [L'analyse des graphes bipartis](https://halshs.archives-ouvertes.fr/FMR/halshs-00794976), in French (2013).
- [La détection de communautés avec Pajek 3.6](http://groupefmr.hypotheses.org/544), in French (2012). - [Static and Dynamic Network Visualization with R](http://kateto.net/network-visualization) - Covers the igraph, network, networkD3 and ndtv packages (2015).
- [Modeling Valued Networks with statnet](https://statnet.org/trac/raw-attachment/wiki/Sunbelt2013/Valued.pdf) (2013).
- [Network Analysis and Visualization with R and igraph](http://kateto.net/networks-r-igraph) (2016).
- [Practical Social Network Analysis With Gephi](http://derekgreene.com/gephitutorial/) (2014).
- [Static and Dynamic Network Visualization with R](http://kateto.net/network-visualization) (2015).
- [Working with Bipartite/Affiliation Network Data in R](https://solomonmessing.wordpress.com/2012/09/30/working-with-bipartiteaffiliation-network-data-in-r/) (2012). - [Working with Bipartite/Affiliation Network Data in R](https://solomonmessing.wordpress.com/2012/09/30/working-with-bipartiteaffiliation-network-data-in-r/) (2012).
## Varia ## Varia
> This section is for blog posts, videos, wikis and everything else that does not fit in other categories. > Resources that does not fit in other categories.
1. [A Sociology Citation Network](http://nealcaren.web.unc.edu/a-sociology-citation-network/) and [A Co-citation Network for Philosophy](https://kieranhealy.org/blog/archives/2013/06/18/a-co-citation-network-for-philosophy/) - Examples of scientific co-citation networks. 1. [A Sociology Citation Network](http://nealcaren.web.unc.edu/a-sociology-citation-network/) and [A Co-citation Network for Philosophy](https://kieranhealy.org/blog/archives/2013/06/18/a-co-citation-network-for-philosophy/) - Examples of scientific co-citation networks.
- [Basic Notions for the Analysis of Large Two-mode Networks](https://www-complexnetworks.lip6.fr/~latapy/Publis/socnet07.pdf) - Introduction to bipartite network analysis ([related code](https://www-complexnetworks.lip6.fr/~latapy/Bip/)).
- [David Knoke on Network Analysis](https://thesocietypages.org/methods/2015/01/30/david-knoke-on-network-analysis/) - A 20-minute interview that discusses the uses and benefits of network analysis, drawing upon Knoke's research on terrorist networks. - [David Knoke on Network Analysis](https://thesocietypages.org/methods/2015/01/30/david-knoke-on-network-analysis/) - A 20-minute interview that discusses the uses and benefits of network analysis, drawing upon Knoke's research on terrorist networks.
- [NetWiki](http://netwiki.amath.unc.edu/Main/HomePage) - Wiki of various network analysis resources.
- [Network Fact](https://twitter.com/networkfact) - Twitter account about networks, graph theory, and related topics. - [Network Fact](https://twitter.com/networkfact) - Twitter account about networks, graph theory, and related topics.
- [Tarot Cards for Principles of Complex Systems and Complex Networks](https://www.uvm.edu/~pdodds/teaching/courses/2016-01UVM-303/tarotcards/) - Part of a course by Peter Sheridan Dodds. - [Tarot Cards for Principles of Complex Systems and Complex Networks](https://www.uvm.edu/~pdodds/teaching/courses/2016-01UVM-303/tarotcards/) - Part of a course by Peter Sheridan Dodds.
- [The Performativity of Networks](http://kieranhealy.org/files/papers/performativity.pdf) - A paper that connects network theory to the sociology of science. - [The Performativity of Networks](http://kieranhealy.org/files/papers/performativity.pdf) - A paper that connects network theory to the sociology of science.