Curator Dashboard

Core for spatial and single cell technologies provides expertise, training, education and equipment. Supports projects, starting from consultation with matching right technologies to project needs, budget, and timeline. Provided services include single cell and spatial assays, tissue preparations, staining, sequencing, bioinformatic analyses.Equipment include 10x Genomics Visium,10x Genomics Xenium,Akoya PhenoImager HT whole slide scanner, Akoya Phenocycler Fusion,Bruker Vutara VXL,Nanostring GeoMX DSP, Vizgen MERSCOPE, Epredia TMA Grandmaster and more.

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• SciCrunch
• 4 months ago - submitted by Edyta Vieth

Core for proteomics technology development and service. Provides mass spectrometry analytical services to academic, industrial, and government laboratories.

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• SciCrunch
• 4 months ago - submitted by Edyta Vieth

Core is committed to developing scientific partnerships with research labs to develop and deploy LC/MS and GC/MS methods specifically tailored to meet the needs of every project. Provides suite of technologies, experimental design support and staff expertise to deliver metabolomics, lipidomics, and proteomics capabilities to VARI scientists and collaborators. Analytical capabilities are combined with custom informatics and statistics solutions.Specific capabilities include: Metabolomics and Lipidomics liquid chromatography mass spectrometry (LC/MS) systems (Thermo Orbitrap ID-X, Thermo Orbitrap Exploris 240, and Agilent 6470 QQQ) and gas chromatography (GC)/MS systems (Agilent 5977b (2), Thermo 7610 ISQ) dedicated to small molecule analysis;Proteomics nano LC/MS systems (Orbitrap Eclipse and Orbitrap Exploris 480) for protein analysis; Bioinformatics for developing and maintaining informatics pipelines for mass spectrometry data analysis and visualization.Major equipment in the facility includes Thermo Scientific Orbitrap ID-X LC/MS,Thermo Scientific Orbitrap Exploris 240 LC/MS,Thermo Scientific Orbitrap Eclipse nanoLC/MS,Thermo Scientific Orbitrap Exploris 4800 LC/MS,Agilent 6470 Triple Quadrupole LC/MS ,Agilent Infinity 1290II UPLC,Agilent 5977B GC/MS,Thermo Scientific ISQ7610 EI/CI enabled GC/M.

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• SciCrunch
• 4 months ago - submitted by Edyta Vieth

Core offers scientists variety of advanced plant growth spaces and expert horticultural services.This includes Greenhouse Complex,Growth Chamber facility and Headhouse space. Greenhouses are designed for cultivation and containment of research crops, including regulated and protected plant materials.All greenhouses are environmentally controlled for temperature, humidity and light levels, and have automated irrigation and nutrient delivery capability using Argus Control Systems. Many houses have 14 to 20 ft sidewalls for growing taller crops, as well as in-floor heating, height-adjustable light canopies and automated irrigation capabilities. Over 95% of the greenhouse complex utilizes high intensity, energy-efficient horticultural LED lighting. Plant Growth Facility has multiple special-use work spaces including potting areas, seed processing, seed storage coolers, plant dry-down and soil handling rooms, autoclave, fertigation/utility rooms, as well as general storage space.Core is also responsible for managing Seed Storage coolers housing Danforth Center Institutional Seed Collection.

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• SciCrunch
• 4 months ago - submitted by Edyta Vieth

Software R package for differential abundance of microbiome. Used for performing differential abundance analysis of microbiome count data. Microbiome differential abudance and correlation analyses with bias correction.

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• RRID
• 4 months ago - by Anonymous

Software R package to create HTML tables of descriptive statistics, as one would expect to see as the first table in medical epidemiological journal article. Used for generating tables of descriptive statistics in HTML.

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• RRID
• 4 months ago - by Anonymous

Software survival analysis library written in Python.

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• RRID
• 4 months ago - by Anonymous

Software Snakemake workflow for bacterial genome assembly plus polishing for Oxford Nanopore sequencing using multiple tools.

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• RRID
• 4 months ago - by Anonymous

Software Snakemake workflow for scoring and comparing multiple bacterial genome assemblies from Illumina and Nanopore to reference genomes.

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• RRID
• 4 months ago - by Anonymous

United States Cancer Statistics public information data provided by Centers for Disease Control and Prevention.

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• RRID
• 4 months ago - by Anonymous

Web application to link single-cell epigenomes and cell types.

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• RRID
• 4 months ago - submitted by Edyta Vieth

Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer.

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• RRID
• 4 months ago - submitted by Edyta Vieth

Web application for automated cell type annotation for scRNA-seq datasets. Allows for cell prediction using either built-in or custom models, in order to assist in accurate classification of different cell types and subtypes.

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• RRID
• 4 months ago - by Anonymous

Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end.

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• RRID
• 4 months ago - submitted by Nathan LeRoy

Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.

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• RRID
• 4 months ago - by Anonymous

Software tool as mapping based variant caller that implements several calling models within unified haplotype aware framework. Variant caller that uses polymorphic Bayesian genotyping model capable of modeling sequencing data from range of experimental designs within unified haplotype aware framework. Bayesian haplotype based mutation calling.

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• RRID
• 4 months ago - by Anonymous

Software R package to integrate popular Bayesian modeling methods into tidy data plus ggplot workflow.

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• RRID
• 4 months ago - by Anonymous

Software tool as unified interface to visualize statistical results of popular R packages. Provides unified interface that enables users to use one line of code to visualize statistical results of many R packages using ggplot2 idioms. Allows ggplot2 to handle some popular R packages.

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• RRID
• 4 months ago - by Anonymous

Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support.

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• RRID
• 4 months ago - by Anonymous

ZEN is the universal user interface you will see on every imaging system from ZEISS. For simple and routine works, ZEN leads you straight to result. For complex research experiments, ZEN offers the flexibility to design multi-dimensional workflows the way you wanted.

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• RRID
• 4 months ago - submitted by Farzaneh Tamnanloo