Abstract: A facility for analyzing a sample of cells is described. The facility accesses an emphasis weight specifying a degree to which cell type is to be emphasized relative to cell constituent expression levels in determining visualization coordinates for each cell of the sample. The facility generates a cell matrix comprising a grid of values in which each row represents a cell of the sample, in which a first group of the columns correspond to constituent expression levels detected for the cell, and a second group of the columns correspond to a representation established for the cell's cell type, the values in the first group of the columns being weighted against the values in the second group of the columns in accordance with the accessed emphasis weight. The facility performs dimensionality reduction on the rows of the generated cell matrix to obtain visualization coordinates for each cell of the sample.

Abstract: A data structure relating to a sample of cells is described. The data structure includes first data elements each representing one of a number of first-degree nodes. Each of the first-degree nodes corresponds to a different one of a number of cellular constituents. Each first data element includes a quantitative indication of the portion of cells of the sample in which the constituent has positive expression. The data structure also includes second data elements each representing one of a number of greater-than-first-degree nodes, which each correspond to a different subset of the constituents of size two or more. Each second data element includes a quantitative indication of the portion of cells of the sample in which the subset of constituents all have positive expression. The contents of the data structure are usable to generate a visual co-expression graph characterizing the sample.

Abstract: The present invention provides an approach for the determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, expression markers and other criteria, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of modulators of cellular activation allows for characterization of pathways and cell populations.

Abstract: A method is disclosed in which control processes are used to maintain consistency across a research or diagnostic series of steps. Some embodiments of the processes include the use of fresh or lyophilized cell lines, beads, surface or other markers. The use of quality control processes is intended to monitor data from the underlying methods in order to detect unacceptable variations and to allow for exclusion or normalization. Overlapping control processes allows for tighter control and for redundancy in the monitoring.

Abstract: The present invention provides an approach for the determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, expression markers and other criteria, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of modulators of cellular activation allows for characterization of pathways and cell populations.