# Installing and using hctsa

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