Abstract: Provided herein are methods and systems for analysis of one or more single cells. The disclosed methods may comprise barcoding analytes from cell types of interest, while eliminating undesired cell types from analysis. Barcoding may comprise the use of a targeting agent. A targeting agent may be attached to an inhibitor or an activator, thereby inhibiting or activating analyte barcoding.

Abstract: Methods and systems may be provided for distinguishing cell populations from non-cell populations within a data set, the method comprising receiving a data set at least associated with a plurality of cells, wherein the data set comprises molecule counts of at least two genomic features for each cell; identifying duplicate subsets of data points from the data set; generating deduplicated data by condensing data points from each duplicate subset into a single data point; applying a pre-set threshold to divide the deduplicated data into an initial cell population and a non-cell population, wherein the pre-set threshold is determined using the molecule counts; and generating a refined cell population and a non-cell population by adjusting boundaries of the initial cell population and non-cell population using clustering.

Abstract: Systems and methods for visualizing patterns in discrete attribute value datasets are provided. A dataset comprises a discrete attribute value for each gene in a plurality of genes, for each cell in a plurality of cells. The dataset further comprises ATAC counts for each ATAC peak in a plurality of peaks, for each of the cells. Cells are assigned cluster groups in a first plurality of cluster groups based on a first clustering of discrete attribute values for the genes across the cells. Cell are also assigned cluster groups in a second plurality of cluster groups based on a second clustering of ATAC fragment count values for the ATAC peaks across the cells. A projection of the cells uses one of the first or second cluster group assignments. There is indicated, for each cell within the projection, membership in the other of the first or second cluster group assignments.