Internal Workflow

High Level Overview of Data Flow Between Modules

Module 1: Load Data

In mod_01_load_data(), users can either upload their own data or use demo data. Users then select the appropriate species, data type, and optionally load an experimental design file. The data is then processed with a function to retrieve detailed gene information from the data base. Gene labels are converted to Ensembl (unless otherwise stated). Module receives idep_data() as input and returns load_data().

Module 2: Pre process Data

In mod_02_pre_procces(), the data from the load data tab is passed in. Depending on the type of data, users have several choices. If the expression data is read counts, users specify the minimum CPM in at least n libraries and select a transformation for visualization. If the expression data is normalized values, the user can select to log transform (Y/N) and the value of an added psuedo-count. There are no additional choices for fold-change data. All data types have a choice for how to impute missing values. Data is then converted based on user input and available for EDA. The processed data is passed out for later analysis.