Some of the following terms are industry-standard, and some have meanings specific to SeqGeq.

Analytical Gene Set

A list of genes created in Gene view, and which also has a geometric/threshold definition in Gene view. See Gene View.


Additional descriptive data about a gene set, input data to SeqGeq, or output data from SeqGeq.

Cell View

A mode in the graph window. In Cell view, cells are “dots,” while genes and gene sets are on the axes. A gate drawn in this mode creates a cell population.

Color Map Axis

The third axis of the Graph window overlaying colors based on a statistic of a gene set and operation used to color the events in the graph.

Derived Parameter

Parameters derived within SeqGeq from original data, for example by dimensionality reduction algorithms. (Parameters imported to SeqGeq are not considered derived parameters even if they may have been calculated from original data in BaseSpace.)

Gene View

A mode in the Graph window wherein genes are the “dots,” and cell populations are on the axes. A gate in this view creates a gene set.

Gene Collection

An organizational element for grouping gene sets. A gene collection may not contain another gene set collection, only gene sets.

Gene Set

A list of genes, along with six new parameters (mean, geom mean, median, %+, max, IQR), which summarize that list. Comes in two varieties, static and analytical (see Static Gene Set and Analytical Gene Set). See also Synthetic Parameter.

Graph Window

The primary analysis tool in SeqGeq, through which either cells or genes can be visualized for further analysis. For information about Graph window modes see Cell View, Gene-View, and Color Map Axis.

Static Gene Set

A list of genes which is purely in list form, either within the application or coming from the file system or from a database.

Synthetic Parameter

This is a summary parameter of the genes in a gene set (typically mean of expressions). As such, it is a synthesis of multiple parameters and distinguished from a derived parameter. See Derived Parameter.


This term refers to both the ‘lab bench’ within SeqGeq, which organizes an analysis carried out on samples, and to the .geq file format, which allows that workspace to be saved and opened.