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公开(公告)号：US20240347137A1
公开(公告)日：2024-10-17
申请号：US18752522
申请日：2024-06-24
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
Abstract: A visualization system comprising processing cores, memory, and a display performs a visualization method by obtaining a block of data. The data represents a single-cell characteristic of cells in a plurality of cells across each bin in a plurality of bins. Each bin maps to a different portion of a reference genome. The cells are clustered based upon the single-cell characteristic across the plurality of bins, thereby forming a tree structure that includes a current root node, a plurality of intermediate nodes, and the plurality of cells. Th plurality of cells constitute terminal nodes in the tree structure and each respective intermediate node has a corresponding plurality of daughter nodes, each daughter node being an intermediate node or a cell. The single-cell characteristic is plotted for the current root node of the tree on the screen using the dataset, across all or the portion of the plurality of bins.
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公开(公告)号：US12062418B2
公开(公告)日：2024-08-13
申请号：US18165133
申请日：2023-02-06
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
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.
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公开(公告)号：US20200005902A1
公开(公告)日：2020-01-02
申请号：US16454485
申请日：2019-06-27
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
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.
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公开(公告)号：US12125260B2
公开(公告)日：2024-10-22
申请号：US18355963
申请日：2023-07-20
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Clark Mellen , Jasper Staab , Kevin J. Wu , Neil Ira Weisenfeld , Florian Baumgartner , Brynn Claypoole
IPC: G06V10/762 , G01N1/30 , G06T7/00 , G16B15/00
CPC classification number: G06V10/762 , G01N1/30 , G06T7/0012 , G16B15/00 , G01N2001/302 , G06T2207/30024
Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.
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公开(公告)号：US11574706B2
公开(公告)日：2023-02-07
申请号：US16454485
申请日：2019-06-27
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
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.
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Patent Agency Ranking
公开(公告)号：US11756286B2
公开(公告)日：2023-09-12
申请号：US18047620
申请日：2022-10-18
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Clark Mellen , Jasper Staab , Kevin J. Wu , Neil Ira Weisenfeld , Florian Baumgartner , Brynn Claypoole
IPC: G06V10/762 , G16B15/00 , G01N1/30 , G06T7/00
CPC classification number: G06V10/762 , G01N1/30 , G06T7/0012 , G16B15/00 , G01N2001/302 , G06T2207/30024
Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.
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公开(公告)号：US11514575B2
公开(公告)日：2022-11-29
申请号：US17039935
申请日：2020-09-30
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Clark Mellen , Jasper Staab , Kevin J. Wu , Neil Ira Weisenfeld , Florian Baumgartner , Brynn Claypoole
Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.
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公开(公告)号：US20230368869A1
公开(公告)日：2023-11-16
申请号：US18165133
申请日：2023-02-06
Applicant: 10X Genomics, Inc.
Inventor： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
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.
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公开(公告)号：US20230140008A1
公开(公告)日：2023-05-04
申请号：US17960037
申请日：2022-10-04
Applicant: 10x Genomics, Inc.
Inventor： Eric Siegel , Guy Joseph , Jasper Staab , Jessica Hamel
Abstract: Systems and methods for evaluating one or more biological samples are provided. A dataset is obtained from nucleic acid sequencing of the biological samples. The dataset comprises a discrete attribute value for each of a plurality of reference sequences for each entity in a plurality of entities in the biological samples. A two-dimensional spatial arrangement of the plurality of entities is indexed, each entity independently assigned a unique two-dimensional position in a k-dimensional binary search tree, and the spatial arrangement is displayed. A user selection of a subset of the displayed arrangement is received. Each entity that is a member of the subset is determined using the k-dimensional binary search tree, thus identifying a subset of entities. Each entity in the subset of entities is assigned to a user-provided category, and the dataset is modified to store an association of each entity in the subset to the category.
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10.发明申请公开(公告)号：US20210381056A1
公开(公告)日：2021-12-09
申请号：US17175577
申请日：2021-02-12
Applicant: 10X Genomics, Inc.
Inventor： Jessica Hamel , Vijay Kumar Sreenivasa Gopalan , Li Wang , Arundhati Shamoni Maheshwari , Jasper Staab
IPC: C12Q1/6886 , G16B40/00 , G16B15/00 , G16B5/20
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.
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