Abstract: A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.

Abstract: A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.

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: Methods for index hopping sequence read filtering are provided. Each read in a plurality of reads from a multiplexed reaction comprises an insert portion, and first (molecular identifier) and second (sample index) non-insert portions. For each of a plurality of hashes, a hash data structure is formed with a representation of each read. Each representation comprises a hash of the first non-insert portion of the corresponding read. Read pairs are identified in the hash data structures. Each pair includes a first and second read sharing a common hash value but differing index values. An entry is added into a heterogeneous data structure, for each such pair, that includes the first and second non-insert portions of the first and second reads of the pair. Reads with first non-insert portion values appearing more than a threshold number of times in the heterogeneous data structure are removed from the plurality of reads.

Abstract: A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.