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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

https://bhpc.uhnresearch.ca/

Core provides services including Basic High-Throughput Sequencing Analysis, Advanced Data Analysis, High Performance Computing.

Proper citation: University Health Network Bioinformatics and High Performance Computing HPC Core Facility (RRID:SCR_027532) Copy   

•   Source: SciCrunch Registry

https://sttarr.ca/

Offers services to support studies in medical fields across oncology, cardiology, metabolic diseases, radiotheranostics and more.Helps with study design to final data analysis, including GLP-compliant histopathology services.

Proper citation: University Health Network Spatio-Temporal Targeting and Amplification of Radiation Response Core Facility (RRID:SCR_027531) Copy   

•   Source: SciCrunch Registry

https://github.com/mjskay/ARTool

Software R package for aligned rank transform for nonparametric factorial ANOVAs.

Proper citation: ARTool (RRID:SCR_027412) Copy   

•   Source: SciCrunch Registry

http://www.aomf.ca

Core offers services in optical microscopy experiments including: confocal, multiphoton, super-resolution, FRAP, FRET, live-cell timelapse, whole-slide scanning, image analysis and more.

Proper citation: University Health Network Advanced Optical Microscopy Core Facility (RRID:SCR_027535) Copy   

•   Source: SciCrunch Registry

https://lightning.ai/

Open-source software Python library that provides high-level interface for PyTorch deep learning framework.

Proper citation: PyTorch Lightning (RRID:SCR_027468) Copy   

•   Source: SciCrunch Registry

https://github.com/wheaton5/souporcell

Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes.

Proper citation: Souporcell (RRID:SCR_027462) 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://gpspalm.biocuckoo.cn/

Software deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins.

Proper citation: GPS-Palm (RRID:SCR_027506) Copy   

•   Source: SciCrunch Registry

https://ibidi.com

German manufacturer specializing in advanced cell culture and imaging products, including µ-Slide chambers, microfluidic devices, and reagents for live-cell analysis. Ibidi’s technologies support high-resolution microscopy, cell migration assays, angiogenesis studies, and immunological research.

Proper citation: Ibidi GmbH (RRID:SCR_027508) 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://github.com/atakanekiz/CIPR-Package

Software R package for annotating cell clusters in scRNAseq data.

Proper citation: CIPR-Package (RRID:SCR_027697) Copy   

•   Source: SciCrunch Registry

https://github.com/MANO-B/U3-Nomogram

Software application for C-CAT CALICO database. Used for Germline-focUsed analysis of tUmoUr-detected variants with Nomogram for C-CAT CALICO database.

Proper citation: U3-Nomogram (RRID:SCR_027696) Copy   

•   Source: SciCrunch Registry

https://www.dnagenotek.com/row/index

Subsidiary of OraSure Technologies, Inc. focuses on providing biological sample collection products and services for human genomics, microbiome and infectious disease applications. Offers Research Use Only products to collect and preserve large amounts of DNA or RNA from multiple sample types.

Proper citation: DNA Genotek Inc (RRID:SCR_027611) Copy   

•   Source: SciCrunch Registry