> For the complete documentation index, see [llms.txt](https://time-series-features.gitbook.io/hctsa-manual/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa.md).

# Installing and using hctsa

- [General advice and common pitfalls](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/advice-and-common-pitfalls.md): Thinking about running an hctsa analysis? Read this first.
- [Installing and setting up](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/setup.md)
- [Structure of the hctsa framework](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/setup/hctsa_structure.md)
- [Overview of an hctsa analysis](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/setup/within_matlab.md)
- [Compiling binaries](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/setup/compiling_binaries.md)
- [Running hctsa computations](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/calculating.md)
- [Input files](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/calculating/input_files.md)
- [Performing calculations](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/calculating/running_computations.md)
- [Inspecting errors](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/calculating/dealing_with_errors.md)
- [Working with hctsa files](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/calculating/working_with_hctsa_files.md)
- [Analyzing and visualizing results](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing.md)
- [Assigning group labels to data](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/grouping.md)
- [Filtering and normalizing](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/filtering_and_normalizing.md)
- [Clustering rows and columns](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/clustering_rows_and_columns.md)
- [Visualizing the data matrix](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/visualizing_the_data_matrix.md)
- [Plotting the time series](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/plotting_the_time_series.md)
- [Low dimensional representation](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/low_dim.md)
- [Finding nearest neighbors](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/sim_search.md)
- [Investigating specific operations](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/feature_summary.md)
- [Exploring classification accuracy](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/ts_classify.md)
- [Finding informative features](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/ts_topfeatures.md)
- [Interpreting features](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/interpreting-features.md)
- [Comparing to existing features](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/feature-comparison.md)
- [Working with short time series](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing/working-with-short-time-series.md)
- [Working with a mySQL database](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database.md)
- [Setting up the mySQL database](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/setup_mysql_database.md)
- [The database structure](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/database_structure.md)
- [Populating the database with time series and operations](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/populating.md)
- [Adding time series](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/adding_time_series.md)
- [Retrieving from the database](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/retrieving_to_compute.md)
- [Computing operations and writing back to the database](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/computing_and_writing_back.md)
- [Cycling through computations using runscripts](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/computing_runscripts.md)
- [Clearing or removing data](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/clearing_or_removing_data.md)
- [Retrieving data from the database](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/retrieving.md)
- [Error handling and maintenance](https://time-series-features.gitbook.io/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/maintenance.md)


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