TABLE OF CONTENTS

• 1. Data upload
• 2. Data pretreatment
• 3. Clustering

In general, the columns you see in the metadata of your datset are either present from the dataset upload, or where were manually added by user. However, in certain cases the UniApp can also write in their results into the metadata. This happens once per dataset once after upload and whenever data pretreatment and clustering algorithms are performed.

1. Data upload

At data upload, the UniApp adds the following columns to your metadata:

• nbr_features - the number of detected genes in the observation.
• nbr_counts - the number of detected UMIs in the observation.
• In the data pretreatment module thresholds are places on these two variables in order to subset your data according to quality control metrics.

2. Data pretreatment

Every time a data pretreatment step is performed the following columns are added to the metadata:

• S_score - estimates how much the observation is enriched for the markers of the S phase of the cell cycle.
• G2M_score  - estimates how much the observation  is enriched for the markers of the G2M phase of the cell cycle. 
• Phase - estimates in which phase of the cell cycle the observation is in.
• Hypoxia - estimates how much the observation is enriched for the markers of hypoxia.
• Stress  - estimates how much the observation is enriched for the markers of cellular stress. 
• Interferon - estimates how much the observation is enriched for the markers of interferon stimulation. 
• HVG - estimates how much the observation is enriched for the highly variable genes.

These scores can be plotted on the dimension reduction plot and used to better asses your data.

3. Clustering

Every time a clustering step is performed the following column is added to the metadata:

• AutomaticClustering - states to which automated cluster the observation belongs to

Columns that are added to the metadata by data pretreatment or clustering have in their suffix the ID of the analysis step which added them. For example, the automatic clusters added by the analysis step 13355 are written in the column titled: "AutomaticClustering_13355".

To ensure reproducibility, all columns added by the UniApp are locked by default. You can modify the content of these columns by copying them and then editing the copy.