Alavi et al., 2018 - Google Patents
A web server for comparative analysis of single-cell RNA-seq dataAlavi et al., 2018
View HTML- Document ID
- 6286676821246466756
- Author
- Alavi A
- Ruffalo M
- Parvangada A
- Huang Z
- Bar-Joseph Z
- Publication year
- Publication venue
- Nature communications
External Links
Snippet
Abstract Single cell RNA-Seq (scRNA-seq) studies profile thousands of cells in heterogeneous environments. Current methods for characterizing cells perform unsupervised analysis followed by assignment using a small set of known marker genes …
- 229920001186 RNA-Seq 0 title abstract description 14
Classifications
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30386—Retrieval requests
- G06F17/30424—Query processing
- G06F17/30533—Other types of queries
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30386—Retrieval requests
- G06F17/30424—Query processing
- G06F17/30522—Query processing with adaptation to user needs
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30289—Database design, administration or maintenance
- G06F17/30303—Improving data quality; Data cleansing
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/3061—Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
- G06F17/30705—Clustering or classification
- G06F17/3071—Clustering or classification including class or cluster creation or modification
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30587—Details of specialised database models
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
- G06F17/30312—Storage and indexing structures; Management thereof
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/20—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
- G06F17/30861—Retrieval from the Internet, e.g. browsers
- G06F17/30864—Retrieval from the Internet, e.g. browsers by querying, e.g. search engines or meta-search engines, crawling techniques, push systems
- G06F17/30867—Retrieval from the Internet, e.g. browsers by querying, e.g. search engines or meta-search engines, crawling techniques, push systems with filtering and personalisation
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N99/00—Subject matter not provided for in other groups of this subclass
- G06N99/005—Learning machines, i.e. computer in which a programme is changed according to experience gained by the machine itself during a complete run
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computer systems based on biological models
- G06N3/12—Computer systems based on biological models using genetic models
- G06N3/126—Genetic algorithms, i.e. information processing using digital simulations of the genetic system
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
- G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
- G06K9/62—Methods or arrangements for recognition using electronic means
- G06K9/6217—Design or setup of recognition systems and techniques; Extraction of features in feature space; Clustering techniques; Blind source separation
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F15/00—Digital computers in general; Data processing equipment in general
- G06F15/18—Digital computers in general; Data processing equipment in general in which a programme is changed according to experience gained by the computer itself during a complete run; Learning machines
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N5/00—Computer systems utilising knowledge based models
- G06N5/02—Knowledge representation
- G06N5/022—Knowledge engineering, knowledge acquisition
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06Q—DATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
- G06Q50/00—Systems or methods specially adapted for a specific business sector, e.g. utilities or tourism
- G06Q50/01—Social networking
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Alavi et al. | A web server for comparative analysis of single-cell RNA-seq data | |
Liu et al. | Simultaneous deep generative modelling and clustering of single-cell genomic data | |
Qiu | Embracing the dropouts in single-cell RNA-seq analysis | |
Hao et al. | Dictionary learning for integrative, multimodal and scalable single-cell analysis | |
Zhao et al. | Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data | |
Chen et al. | Transformer for one stop interpretable cell type annotation | |
Bravo González-Blas et al. | cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data | |
Ding et al. | Interpretable dimensionality reduction of single cell transcriptome data with deep generative models | |
Duan et al. | Model-based understanding of single-cell CRISPR screening | |
Crow et al. | Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor | |
Li et al. | An accurate and robust imputation method scImpute for single-cell RNA-seq data | |
Townes et al. | Nonnegative spatial factorization applied to spatial genomics | |
Li et al. | PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks | |
Chen et al. | RA3 is a reference-guided approach for epigenetic characterization of single cells | |
Wang et al. | Single-cell classification using graph convolutional networks | |
Öztürk et al. | A novel methodology on distributed representations of proteins using their interacting ligands | |
Du et al. | A feature selection method based on multiple kernel learning with expression profiles of different types | |
Ma et al. | Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction | |
Yu et al. | Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA | |
Liu et al. | Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes | |
Kopp et al. | Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning | |
Luo et al. | Identifying disease-gene associations with graph-regularized manifold learning | |
Chen et al. | CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data | |
Li et al. | A comprehensive evaluation of disease phenotype networks for gene prioritization | |
He et al. | Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS |