Table 2.

Common useful terms

Term	Definition
Alignment	The process of matching reads to a particular region of the genome.
Counts	Number of reads that map to a particular gene.
Coverage	The extent to which a genomic region of interest was sequenced.
Dimensionality reduction	The processed by which the most important features of a high-dimensional data set are extracted thus resulting in a data set with reduced dimensions.
Dropout events	Missing data values due to low transcript expression and the stochastic nature of gene expression.
Embedding	Mapping of high-dimensional features onto a low dimensional space.
Feature extraction	Transformed data set built with the most predictive features of a high-dimensional data set.
Feature selection	Selection of most predictive features in a high-dimensional data set.
Features	Variables of a particular data set (i.e. fluorescence intensity or gene counts).
Machine learning	Process of building mathematical models that allow computers to be trained to be predictive. Requires training with a “training dataset”.
Partitioning	Division of data.
Quantitation	Generation of count table that integrates that number of reads per gene that were aligned successfully.
Reads	Nucleotide sequences as a result of sequencing.
Sequencing depth	The number of reads per genomic region.