Abstract: A method for identifying framework regions and complementarity-determining regions in an amino acid sequence. The amino acid sequence is received. A plurality of candidate start positions is identified within the amino acid sequence for a start position for a selected region of interest. A score is generated for each candidate start position of the plurality of candidate start positions via analysis of a motif window that begins at each candidate start position. The start position for the selected region of interest is identified based on a candidate start position of the plurality of candidate start positions having a highest score.

Abstract: Methods and systems for selecting a cell of interest based on immune cell data are disclosed. For example, a method may comprise obtaining a single cell or spatial dataset, wherein the single cell or spatial dataset comprises a dataset of immune cell receptors, antibodies, or fragments thereof from a sample; identifying a clonotype group in the single cell or spatial dataset; selecting a schema to visualize selected amino acids in the clonotype group based on positions or chemical identity of the selected amino acids; visualizing the selected amino acids in the clonotype group in a graphic representation according to the schema; and selecting a cell of interest from the clonotype group based on a pre-defined criterion using the graphic representation.

Abstract: A method is provided for identifying one or more D gene segment in a VDJ or VDDJ sequence. The method can include obtaining a B cell receptor and/or T cell receptor data set, wherein the data set includes a VDJ sequence, aligning the VDJ sequence to one or more VDJ reference sequences thereby generating a first potential alignment and a second potential alignment, determining a first score for the first potential alignment and a second score for the second potential alignment in accordance with a D gene segment alignment scoring schema, and identifying a D gene segment region associated with a highest score between the first score and the second score.

Abstract: A method for grouping immune cells within an immune cell receptor sequence dataset, is disclosed. An immune cell receptor sequence dataset is obtained from a sample. The dataset includes a plurality of full-length immune cell receptor sequences. Each full-length immune cell receptor sequence can comprise of at least one heavy chain region sequence and one light chain region sequence. Each immune cell receptor sequence is associated with an individual immune cell in the sample. The immune cell receptor sequences associated with a first immune cell and a second immune cell from the sample is compared using a comparison protocol. The first immune cell and the second immune cell are identified as members of the same clonotype if one or more immune cell receptor sequence comparison criteria is met.

Abstract: Interactive visualization systems and methods are disclosed herein. The system includes a data source, user input device, processor, and display. The data source obtains a data set comprising B cell receptor and/or T cell receptor data associated with a plurality of cells. The user input device receives a user-selected first parameter under which to analyze the data set. The processor performs the method by identifying a plurality of clonotype groups in the data set using the first parameter, identifying subclonotypes within the clonotype groups (wherein each identified subclonotype comprises cells having identical V(D)J transcripts), and processing the data to define a visualization model that can display a compressed view of the clonotype groups and of the plurality of subclonotypes. The display renders a visualization of said data set according to said visualization model.

Abstract: The disclosed computer-implemented method may include obtaining an original media data structure that comprises a plurality of layers, determining, for each layer within the plurality of layers, that at least one declarative patch within a plurality of declarative patches is applicable to the layer, generating a modified media data structure that comprises, for each layer determined to have at least one applicable declarative patch, a placeholder and a patcher function associated with the respective at least one declarative patch, rendering the modified media data structure, the rendering comprising, for each layer including a placeholder and a patcher function, executing the patcher function, the executing comprising replacing the placeholder based on user data, and providing, for display on a display device of a computing device of the user, the rendered modified media data structure. Various other methods, systems, and computer-readable media are also disclosed.