Curator Dashboard

Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples.

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• RRID-Legacy
• 5 years ago - submitted by Thomas Emmanuel

Software tool as framework querying ontology terms within SciCrunch and SciCrunch SciGraph endpoints.

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• RRID-Legacy
• 5 years ago - submitted by Monique Surles-Zeigler

High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically.

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• RRID-Legacy
• 5 years ago - submitted by Thomas Emmanuel

Software tool for improved long read mapping and structural variant calling via dual mode alignment.

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• SciCrunch
• 5 years ago - submitted by Yilei Fu

System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.

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• RRID-Legacy
• 5 years ago - submitted by Timothy Errington

Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.

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• RRID-Legacy
• 5 years ago - submitted by Edyta Vieth

MultiVision AP and HRP polymers are innovative, patented technologies consisting of smaller amino acid polymer subunits that minimize conflicts in binding the target protein. The smaller polymer allows for decreased binding conflicts, resulting in more consistent staining and better signal amplification. A primary antibody cocktail of choice may be used in conjunction with ready-to-use MultiVision polymer cocktail, composed of anti-mouse/ horseradish peroxidase (HRP) plus anti-rabbit/alkaline phosphatase (AP) Cocktail is specially formulated from MultiVision polymers that provide increased sensitivity, time-savings, and detection simplicity Yields higher sensitivity and antibody efficiency as well as better signal-to-noise ratios Biotin-free, eliminating background staining Antigen Specificity: anti-Mouse IgG (H+L) and anti-Rabbit IgG (H+L) Enzyme: Peroxidase and Phosphatase Chromogen/Substrate: LVBlue/ LVRe

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• RRID-Legacy
• 5 years ago - submitted by Thomas Emmanuel

Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.

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• RRID-Legacy
• 5 years ago - by Anonymous

Open source data management system for mass spectrometry data processed with Skyline targeted mass spectrometry environment. System includes Repository Server application for targeted mass spectrometry assays that integrates into Skyline mass spec workflow and has been implemented as module within LabKey Server data management platform; Panorama Web application facilitates viewing, sharing, and disseminating results contained in Skyline documents via web browser; Panorama Public repository employs full data visualization capabilities of Panorama which facilitates sharing results with reviewers during manuscript review.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.

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• dkNET
• 5 years ago - submitted by Ko-Wei Lin

Interactive portal provides datasets, across variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. Provides comprehensive picture of genes and pathways affecting lipid droplet biology, including gene expression, proteomics, and LD morphology phenotypes, by integrating multiple relevant data types.

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• dkNET
• 5 years ago - submitted by Ko-Wei Lin

Curates and compiles genome wide QTL summary statistics for many human molecular traits across tissues and cell types. Comprises tens of millions significant genotype molecular trait associations under different conditions. Users can visualize QTL results in phenome wide and tissue wide levels, and annotate their biological functions through comprehensive genomic features and functional evidence. QTLbase provides one stop shop of QTLs retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and it will greatly help researchers interrogate biological mechanism of causal variants and guide direction of functional validation.

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• RRID-Legacy
• 5 years ago - by Anonymous

Open ecosystem of data repositories hosted by various partner organizations, who work together to ensure that their data can be federated across participating platforms. Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy.

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• RRID-Legacy
• 5 years ago - submitted by Edyta Vieth

Joint effort with Brain Architecture Portal and Single Cell Portal to visually combine anatomic and molecular brain data in. Users can search for neuroscience data using natural language and faceted search, and then this portal retrieves molecular data housed in the Single Cell Portal and anatomical data in the Brain Architecture Portal. Each study includes information on cell types, gene expression, related genes, and spatial transcriptomics. You can also download a study’s data to explore further and build on your science.

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• RRID-Legacy
• 5 years ago - submitted by Edyta Vieth

Web interactive visualization tool for large scale single cell genomics data.Interactive web application for exploring million scale single cell datasets. Can be hosted on Google App Engine application for collaborative use or can be run in standalone mode on personal computer. Consists of client side component implemented in JavaScript and server component implemented in Python. Client uses React to manage state and WebGL to visualize variables on 2D/3D embeddings in performant manner. Server component consists of functions to manage datasets, slice variables from dataset stored in PARQUET, Zarr or H5AD formats.

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• RRID-Legacy
• 5 years ago - submitted by Edyta Vieth

Software package for massive single cell data processing. Enables analysis of million scale single cell RNA-seq data and is functionally comparable to Seurat and SCANPY. Command line tool, Python package and base for Cloud based analysis workflows. Supports variety of analysis tasks, such as cell and gene level quality control, highly variable gene selection, dimension reduction, kNN graph building, data integration, clustering, differential expression analysis and putative cell type annotation.

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• RRID-Legacy
• 5 years ago - submitted by Edyta Vieth

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

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• RRID-Legacy
• 5 years ago - submitted by Edyta Vieth

Repository of gene phenotype associations for phenotypes derived from electronic health records, questionnaire data, and continuous traits computed on exomes released by UK Biobank. Repository was made available by AstraZeneca for public research.

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• dkNET
• 5 years ago - submitted by Ko-Wei Lin

Software tool for generating imzML. Allows conversion to imzML mass spectrometry imaging standard utilising mzML mass spectrometry standard as intermediary format.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

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• RRID-Legacy
• 5 years ago - by Anonymous