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https://dmimedicalusa.com/product/aperio-at2-dx-system

400 slide scanner with Aperio ImageScope DX clinical viewing software, and high-performance viewing workstation including color-calibrated medical grade monitors. System can be used standalone, or in conjunction with Aperio Path DX case management software, for streamlined, clinical workflow. Developed from Leica Biosystems,enables to produce consistent, diagnostic quality images, enabling pathologists to diagnose with confidence.

Proper citation: Leica: Aperio AT2 DX System (RRID:SCR_027461) Copy   

•   Source: SciCrunch Registry

https://www.ers.usda.gov/data-products/rural-urban-continuum-codes

Mission of U.S. Department of Agriculture's Economic Research Service is to anticipate trends and emerging issues in agriculture, food, environment, and rural America and to conduct high-quality, objective economic research to inform and enhance public and private decision making. Rural-Urban Continuum Codes distinguish U.S. metropolitan (metro) counties by the population size of their metro area, and nonmetropolitan (nonmetro) counties by their degree of urbanization and adjacency to a metro area. The codes allow researchers, policy makers, and others to view county-level data by finer residential groups—beyond metro and nonmetro—when analyzing trends related to population density and metro influence.

Proper citation: USDA ERS Rural-Urban Continuum Codes (RRID:SCR_027474) Copy   

•   Source: SciCrunch Registry

https://www.beckman.com/landing/ppc/liquid-handlers/synthetic-biology

Non-contact liquid handler that uses Acoustic Droplet Ejection (ADE) technology to precisely transfer nanoliter-sized droplets of liquid for high-throughput applications in pharmaceutical research, drug discovery, and various areas of genomics and biology. Echo 555 / 550 Liquid Handler: 2.5 nL increment; Flow rate:0.25 – 1 µL/sec; Ideal for reactions of 0.05 – 1 µL; Supports 384 and 1536-well source plate formats; Used for transfer of small molecules for high throughput screening.

Proper citation: Bechman Coulter: Labcyte Echo 550 acoustic liquid handler (RRID:SCR_027476) Copy   

•   Source: SciCrunch Registry

https://github.com/HazyResearch/hyena-dna

Software application as long-range genomic foundation model pretrained on context lengths of up to 1 million tokens at single nucleotide resolution.

Proper citation: HyenaDNA (RRID:SCR_027471) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/create_cisTarget_databases

Code to create cisTarget databases.

Proper citation: create_cisTarget_databases (RRID:SCR_027473) Copy   

•   Source: SciCrunch Registry

https://github.com/instadeepai/nucleotide-transformer

Genomic language model trained on cross species data.

Proper citation: Nucleotide Transformer (RRID:SCR_027472) Copy   

•   Source: SciCrunch Registry

https://icahn.mssm.edu/research/resources/deans-cores/neuropathology

Provides access to collection of human postmortem brain tissues, including fresh, frozen, and formalin-fixed paraffin-embedded (FFPE) specimens, along with detailed clinical histories and neuropathological assessments. Available histology services include processing and embedding, slide sectioning for FFPE and cryosections, immunohistochemistry (IHC), immunofluorescence (IF), and advanced RNA assays such as RNAscope, BaseScope, and miRscope. High-resolution digital slide imaging is performed using the GT450 scanner. CoRE scientists also collaborate with investigators and trainees to support project development, method optimization and troubleshooting, data analysis.

Proper citation: Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility (RRID:SCR_027565) Copy   

•   Source: SciCrunch Registry

https://brain-bican.github.io/bkbit/

Software package contains tools to use the BICAN Knowledgebase Data Models.

Proper citation: bkbit (RRID:SCR_027564) Copy   

•   Source: SciCrunch Registry

https://icahn.mssm.edu/research/human-immune-monitoring-center

Core provides team of experts in the characterization of immune profiles and treatment responses across a diverse range of diseases, such as cancer, autoimmunity, allergy, and neuro-immune disorders. Offers equipment in the field for research at Genomic, cellular and proteomic analysis. Develops assays to balance innovation with protocols and operating procedures to ensure data quality and reproducibility.

Proper citation: Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility (RRID:SCR_027571) Copy   

•   Source: SciCrunch Registry

http://confocal.uconn.edu

Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation.

Proper citation: University of Connecticut Advanced Light Microscopy Core Facility (RRID:SCR_027547) Copy   

•   Source: SciCrunch Registry

https://github.com/kermitt2/grobid

Software tool for extracting information from scholarly documents.

Proper citation: Grobid (RRID:SCR_027539) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com.cn/zh-cn/product/gas-chromatography-mass-spectrometry-gc-ms/gc-ms-instruments/7000e-triple-quadrupole-gc-ms

Agilent 7000E triple quadrupole GC/MS instruments incorporate intelligent technology that reduces instrument downtime and improves run times for maximum productivity in analytical labs. Mass spectrometer is used for routine, high-sensitivity analysis of targeted compounds in complex samples, especially for trace-level detection in areas like food safety and environmental testing.

Proper citation: Agilent: 7000E Triple Quadrupole GC/MS system (RRID:SCR_027552) Copy   

•   Source: SciCrunch Registry

https://analysistools.cancer.gov/apc/

Web tool, developed by the U.S. National Cancer Institute (NCI), performs statistical modeling of cancer incidence or mortality data using age-period-cohort analysis. It allows users to examine and interpret temporal trends while disentangling the effects of age, calendar period, and birth cohort. The tool supports data import, graphical output, and model fit assessment via interactive web interface.

Proper citation: NCI Age-Period-Cohort Web Tool (RRID:SCR_027554) Copy   

•   Source: SciCrunch Registry

https://pmlivingbiobank.uhnresearch.ca/

Core provides services for the use of Xenograft (PDX) models listed in open global catalogue of PDX models for comprehensive search and attribute filtering support for clinico-pathological and molecular data. Molecular data and visualization of profiled models could be accessed through the institute's portal.

Proper citation: University Health Network Princess Margaret Living PDX Core Facility (RRID:SCR_027523) Copy   

•   Source: SciCrunch Registry

https://www.pmgenomics.ca/pmgenomics/

Core is dedicated to providing access to cost-effective and high quality genomics services including standard and custom-tailored DNA sequencing using Illumina technologies, epigenomics, panel-based profiling (Luminex and Nanostring) and functional genomics. Single cell genomics applications on variety of popular platforms.

Proper citation: University Health Network Princess Margaret Genomics Centre PMGC Core Facility (RRID:SCR_027524) Copy   

•   Source: SciCrunch Registry

https://github.com/Huang-lab/BEACON

Software application to perform Bayesian analysis on expression and gene dependency data across different cell lineages. Integrates expression as the dependent variable and gene dependency data as the independent variable. Used to identify cancer gene targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across tissue lineages.

Proper citation: BEACON (RRID:SCR_027484) Copy   

•   Source: SciCrunch Registry

https://github.com/The-Zhou-Lab/SeedGerm-VIG

Software pipeline to quantify seed vigour in wheat and other cereal crops using deep learning powered dynamic phenotypic analysis.

Proper citation: SeedGerm-VIG (RRID:SCR_027483) Copy   

•   Source: SciCrunch Registry

https://github.com/epi2me-labs/wf-pore-c

Software workflow for analysing Pore-c data for chromatin conformation capture.

Proper citation: Pore-c Workflow (RRID:SCR_027517) Copy   

•   Source: SciCrunch Registry

https://pmlivingbiobank.uhnresearch.ca/

Core provides services for the use of patient-Derived tumor Organoid (PDO) model.Organoid models are derived from patient-derived xenograft tissues, primary tumors, and metastatic patient tissues. PMLB organoid repository includes models generated from colorectal, pancreatic, and lung cancer tissues.

Proper citation: University Health Network Princess Margaret Living Biobank PDO Core Facility (RRID:SCR_027530) Copy   

•   Source: SciCrunch Registry

https://github.com/smorabit/hdWGCNA

Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics.

Proper citation: hdWGCNA (RRID:SCR_027496) Copy   

•   Source: SciCrunch Registry