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| # *CoNekT:* Coexpression Network Toolkit | |
|  CoNekT, the **Co**expression **Net**work **T**oolkit, | |
| documentation and code. | |
| What is CoNekT ? | |
| ---------------- | |
| CoNekT is an online platform that allows users to browse expression profiles, study expression specificty, co-expression | |
| networks and more across different species. A public version including seven plant species which includes thousands of | |
| publicly available RNASeq samples (from the [SRA](https://www.ncbi.nlm.nih.gov/sra)) is available | |
| [here](http://conekt.mpimp-golm.mpg.de/pub/). | |
| Here you can find **tutorials** how to use the public version along with the **source-code** and build instructions that | |
| allow you to **host your own instance** with other species or in-house data. | |
| Tutorials | |
| --------- | |
| * [The Basics](docs/tutorials/001_basics.md) | |
| * [Expression profiles, heatmaps and specificity](docs/tutorials/002_expression_profiles.md) | |
| * [Gene Families and Phylogenetic trees](docs/tutorials/003_gene_families_trees.md) | |
| * [Comparing specificity](docs/tutorials/004_compare_specificity.md) | |
| * [Coexpression Networks and Clusters](docs/tutorials/005_coexpression_networks_clusters.md) | |
| Anything missing ? Further questions ? Don't hesitate to [contact](mailto:proost@mpimp-golm.mpg.de) us. | |
| Setting up CoNekT | |
| ----------------- | |
| Below are the instructions to set up and host your own CoNekT instance. | |
| * [Linux Installation instructions](docs/install_linux.md) | |
| * [Windows Installation instructions](docs/install_windows.md) | |
| * [Run website](docs/run_website.md) | |
| * [Build CoNekT](docs/building_conekt.md): Upload your data to the platform using the Admin interface | |
| Optional steps (recommended for production environments) | |
| * [Connecting with MySQL/MariaDB](docs/connect_mysql.md) | |
| * [Setting up CoNekT with apache and mod_wsgi](docs/apache_wsgi.md) | |
| Acknowledgements | |
| ---------------- | |
| CoNekT is based upon many open-source projects, check the full list [here](docs/acknowledgements.md). This work is | |
| supported by [ERA-CAPS](http://www.eracaps.org/) though the [EVOREPRO](http://www.evorepro.org/) project. | |
| The authors would like to thank Andreas Donath for technical support and helpful discussions. | |
| Contact | |
| ------- | |
| * [Marek Mutwil](mailto:mutwil@mpmpi-golm.mpg.de) ( mutwil@mpmpi-golm.mpg.de ) | |
| * [Sebastian Proost](mailto:proost@mpimp-golm.mpg.de) ( proost@mpimp-golm.mpg.de ) | |