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https://mranalysis.cn/

Web-based platform providing integrated and standardized Mendelian Randomization analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Interactive R Shiny application designed for Mendelian randomization analysis.

Proper citation: MRanalysis (RRID:SCR_027338) Copy   

•   Source: SciCrunch Registry

https://github.com/janjoy/BTE-RAG

Software application for BTE RAG implementation for DMDB QA datasets. Provides implementation of BTE-RAG framework, designed specifically for retrieval-augmented question answering (QA) in biomedical contexts. BTE-RAG leverages explicit mechanistic knowledge retrieval from BioThings Explorer (BTE) to significantly enhance the accuracy and reliability of large language models (LLMs) on biomedical benchmarks.

Proper citation: BTE-RAG (RRID:SCR_027297) Copy   

•   Source: SciCrunch Registry

https://www.merative.com/real-world-evidence/real-world-data-analytics#skiptheform-marketscan

Employer-sourced medical and drugs claims database of the under-65 working population and their dependents, as well as 65+ with Medicare supplemental insurance paid by employers.

Proper citation: MarketScan by Merative (RRID:SCR_027329) Copy   

•   Source: SciCrunch Registry

https://www.janelia.org/support-team/janelia-experimental-technology

Core team designs, builds and tests instruments, tools, and software that enable novel scientific investigation. Offers expertise in Data acquisition and analysis; Machine vision and image processing; Precision machining; Embedded systems design and programming; Laser, microscopy, and optical imaging systems engineering; Custom circuit design; Novel sensor systems; Lab automation, robotics and motion control; Mechanical design, machined and/or fabricated components and assemblies; Process automation.

Proper citation: Howard Hughes Medical Institute at Janelia Research Campus Janelia Experimental Technology jET Core Facility (RRID:SCR_027301) Copy   

•   Source: SciCrunch Registry

https://github.com/calebclayreagor/DELAY

Software application as convolutional neural network for inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. Used for depicting pseudotime-lagged causality for accurate gene-regulatory inference.

Proper citation: DELAY (RRID:SCR_027302) Copy   

•   Source: SciCrunch Registry

https://github.com/NikolayOskolkov/MCWorkflow

Software application as computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes.

Proper citation: MCWorkflow (RRID:SCR_027305) Copy   

•   Source: SciCrunch Registry

https://wertheim.scripps.ufl.edu/cores-and-technologies/flow-cytometry/

Core provides flow cytometry and cell sorting services.

Proper citation: University of Florida Scripps Institute for Biomedical Innovation and Technology Flow Cytometry Core Facility (RRID:SCR_027278) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/cancer/research/shared-resources/biorepository/

Core provides collection, annotation, and storage solutions. This Biorepository is also home to a state-wide resource, the Biorepository Alliance of Georgia for Oncology (BRAG-Onc), which functions to collect samples from 6 participating sites across the State to represent the diversity of cancer patients within the State and to enhance cancer research in Georgia.Tissue specimens are fast-frozen in vapor phase liquid nitrogen to preserve their integrity and stored in large cryofreezers at -170 to -190°C. Blood is routinely separated into serum or plasma and buffy coats prior to freezing. Blood derivatives are stored at -70 to -80°C. The freezers are monitored constantly and are connected to an alarm system to ensure that the low temperatures are maintained.

Proper citation: Augusta University Georgia Cancer Center Biorepository Core Facility (RRID:SCR_027271) Copy   

•   Source: SciCrunch Registry

https://github.com/Kataoka-K-Lab/Celline

Software Python pipeline for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

Proper citation: Celline (RRID:SCR_027273) Copy   

•   Source: SciCrunch Registry

https://www.crukscotlandinstitute.ac.uk/advanced-technologies/molecular-technology.html

Core provides Next Generation Sequencing (NGS) services and Single Cell services predominantly focussing on single cell RNAseq. Processes samples for variety of cancer associated projects, in both mouse and human derived materials. Offers full end-to-end service, from initial study design and planning, through sample QC, full library preparation, sequencing and data return. Offers range of standard molecular tests covering, plasmid purifications, Sanger sequencing and mycoplasma screening.

Proper citation: Cancer Research UK Scotland Institute Molecular Technology Service Core Facility (RRID:SCR_027368) Copy   

•   Source: SciCrunch Registry

https://rfxplot.sourceforge.net/

Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications.

Proper citation: rfxplot (RRID:SCR_027375) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.cn/order/catalog/product/BRE725531?query=mass%20spectrometry%20instruments%20&%20equipment

Orbitrap Exploris 120 LC-MS spectrometry instruments

Proper citation: Thermo Fisher: Orbitrap Exploris 120 high-resolution mass spectrometer (RRID:SCR_027370) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.sdstate.edu/idep/

Integrated web application for differential expression and pathway analysis of RNA-Seq data.

Proper citation: iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) Copy   

•   Source: SciCrunch Registry

https://github.com/songlabcodes/MSC

Software R package for multi-scale clustering to perform single-cell transcriptome clustering.

Proper citation: Multi Scale Clustering (RRID:SCR_027342) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/lifesciences-faculty/laboratory-molecular-cell-biology/research/platforms-and-facilities/electron-microscopy

Electron microscopy facility specialising in cell biological electron microscopy for basic and medical research applications.

Proper citation: University College London LMCB Electron Microscopy Core Facility (RRID:SCR_027340) Copy   

•   Source: SciCrunch Registry

https://github.com/wenmm/EssSubgraph/tree/main

A model algorithm that integrates omics data and network data to predict essential genes.

Proper citation: EssSubgraph (RRID:SCR_027354) Copy   

•   Source: SciCrunch Registry

https://microscopecentral.com/products/olympus-bx41-microscope

Olympus BX41 is clinical and research grade microscope. Can be customized. Offered as pre-configured with your choice of viewing head - binocular, ergo binocular, or trinocular. This has Plan N 4x, 10x, 40x, 100x oil objectives but others can be provided if needed. Comes with XY mechanical stage with slide holder and focusable condenser.

Proper citation: Olympus: BX41 Clinical Microscope (RRID:SCR_027355) Copy   

•   Source: SciCrunch Registry

https://github.com/rnajena/dynamont

Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals.

Proper citation: Dynamont (RRID:SCR_027357) Copy   

•   Source: SciCrunch Registry

https://github.com/Baohua-Chen/GFFx

Software Rust-Based suite of utilities for ultra-fast genomic feature extraction. Used for ultra-fast and scalable genome annotation access. Can be used both as a command-line tool and as a Rust library.

Proper citation: GFFx (RRID:SCR_027445) Copy   

•   Source: SciCrunch Registry

https://www.toyobo-global.com/

Japanese company that began as a textile manufacturer in 1882 and has expanded to become a global provider of high-function products, including films, functional polymers, industrial materials, and biotechnology products such as enzymes and diagnostic reagents. The company's business is organized around its core technologies in polymerization, modification, processing, and biotechnology, allowing it to contribute to fields like healthcare, environment, and electronics.

Proper citation: TOYOBO (RRID:SCR_027440) Copy   

•   Source: SciCrunch Registry