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{"name":"Tissue Enrichment Analysis (TEA)","tagline":"This repository holds the scripts for WormBase's tissue enrichment analysis tool (TEA).","body":"Tissue Enrichment Analysis (TEA)\r\n================================\r\n\r\nThis repository holds the scripts to calculate enrichment of a set of labels using hypergeometric statistics. Results are output to a dataframe. A standard plotting function is provided, but it is really just a thin wrapper around a seaborn plot.\r\n\r\nRequirements\r\n============\r\n\r\nThis library has been developed in Python &gt;= 3.5, using the Anaconda distribution. Requirements include `pandas`, `matplotlib`, `numpy`, `scipy` and `seaborn`.\r\n\r\nInstallation\r\n============\r\n\r\nUse `pip install tissue_enrichment_analysis`\r\n\r\nBasic Usage\r\n===========\r\n\r\nWeb usage\r\n---------\r\n\r\nGo to [www.wormbase.org/tea](http://www.wormbase.org/tea), input your gene list and enjoy the results!\r\n\r\nWithin a Python Script\r\n----------------------\r\n\r\nThere are really just two main functions that are provided in TEA: `enrichment_analysis` and `plot_enrichment_results`.\r\n\r\nA standard call to this library would be as follows:\r\n\r\n`import tissue_enrichment_analysis as tea`\r\n\r\n`gene_list= some_gene_list`\r\n\r\n`tissue_df= tea.fetch_dictionary()`\r\n\r\n`df_results= tea.enrichment_analysis(tissue_df, gene_list, aname= 'FileName')`\r\n\r\n`tea.plot_enrichment_results(df_results, title= 'FileName')`\r\n\r\nCalling from Terminal\r\n---------------------\r\n\r\nGene enrichment analysis can be generated easily by calling the program via terminal using: `tea tissue_dictionary your_gene_list -[OPTIONS]`\r\n\r\nType `tea -h` for help and full documentation.\r\n\r\nFuture Work\r\n===========\r\n\r\nWe may try to add support for other model organisms!\r\n\r\nContact\r\n=======\r\n\r\nIf you find any bugs, have suggestions or just want to say hi, feel free to contact me at <dangeles@caltech.edu>\r\n\r\nGood luck!\r\n\r\nDavid Angeles-Albores\r\n\r\nAuthor:\r\n=======\r\n\r\nDavid Angeles-Albores\r\n\r\nContributors:\r\n=============\r\n\r\nRaymond Y. Lee, Paul W. Sternberg\r\n\r\nAcknowledgements\r\n================\r\n\r\nWith special thanks to the entire worm community!\r\n","google":"UA-31223175-1","note":"Don't delete this file! It's used internally to help with page regeneration."}