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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/Martin-Fahrenberger/GTestimate
Software R package for scRNA-seq normalization. Uses Simple Good-Turing estimator for the per cell relative gene expression estimation.
Proper citation: GTestimate (RRID:SCR_026562) Copy
https://github.com/SchapiroLabor/phenoimager2mc
Software tool for formatting PhenoImager TIFF/OME-TIFF metadata for compatibility with MCMICRO workflow.
Proper citation: phenoimager2mc (RRID:SCR_026561) Copy
https://github.com/higlass/higlass
Web-based visual exploration and analysis of genome interaction maps.
Proper citation: HiGlass (RRID:SCR_026687) Copy
Offers microscopy instrumentation and services. Offers support and training on variety of high-end instrumentation and advanced methodologies for both light and electron microscopy, sample preparation services for electron microscopy, training and assistance with image analysis. Provides support across variety of open-source and commercial image analysis software packages.
Proper citation: University of Michigan Medical School BRCF Microscopy Core Facility (RRID:SCR_026722) Copy
Offers full-service sample analysis to measure concentrations of small molecules in biological samples. Services include targeted and untargeted metabolomic screening, method development to explore novel metabolic pathways and systems. Staff helps with interpretation and visualization of your data, and the preparation of grants, proposals, and manuscripts.
Proper citation: University of Michigan Medical School BRCF Metabolomics Core Facility (RRID:SCR_026721) Copy
https://github.com/tabatsky/projectionpursuit
Software tool for automated projection pursuit clustering. Alternative clustering approach that alleviates the curse of dimensionality by sequentially projecting high-dimensional data into a low-dimensional representation.
Proper citation: Automated Projection Pursuit (RRID:SCR_026560) Copy
https://www.benaroyaresearch.org/our-research/core-labs/genomics-core
Core provides services for genomics analysis, from sample processing through data generation. Available technologies focus on Illumina RNA and DNA sequencing. RNA-seq can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples of 50-1000 cells), or single cells (either plate-sorted rare populations or high-throughput 10x single-cell analyses). DNA-seq pipelines can also be performed, including bulk CUT and Tag/CUT and RUN, and ATAC-seq and single cell ATACseq and multiome capture. Custom prepared libraries can also be submitted for sequencing. Core laboratory houses Illumina sequencers, NextSeq2000 instruments and Miseq, plus 10x Chromium X and 10x CytAssist. Additional equipment includes ThermoFisher Kingfisher Flex, for extracting nucleic acid from variety of sample types using magnetic bead technology with throughput of up to 96 samples. Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. Ancillary equipment for sample processing includes Formulatrix Mantis Liquid Handler, Agilent TapeStation 4200 and Tecan NanoQuant.
Proper citation: Benaroya Research Institute Genomics Core Facility (RRID:SCR_026658) Copy
https://www.ifom.eu/en/cancer-research/technological-units/imaging.php
Core Facility provides technological platforms in the field of light microscopy. A team of highly qualified and experienced professionals supports IFOM's research activities, assisting in sample preparation and acquisition, data post-processing and image analysis.
Proper citation: Cancer Research Institute IFOM ALM Advanced Light Microscopy Core Facility (RRID:SCR_026866) Copy
https://healthsurveys.ipums.org/
Integrated Public Use Microdata Series Health Surveys provide free individual-level survey data for research purposes from two leading sources of self-reported health and health care access information: the National Health Interview Survey (NHIS) and the Medical Expenditure Panel Survey (MEPS).
Proper citation: IPUMS Health Surveys (RRID:SCR_026762) Copy
https://github.com/Neural-Systems-at-UIO/WebWarp
Web application for nonlinear refinement of image registration after WebAlign.
Proper citation: WebWarp (RRID:SCR_026759) Copy
https://github.com/Neural-Systems-at-UIO/WebAlign
Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps).
Proper citation: WebAlign (RRID:SCR_026758) Copy
https://github.com/carmonalab/ProjecTILs
Software tool to project scRNA-seq data into reference single-cell atlases, enabling their direct comparison in stable, annotated system of coordinates. Predicts effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. Used for interpretation of cell states using reference single-cell maps.
Proper citation: projecTILs (RRID:SCR_026854) Copy
https://medresearch.umich.edu/office-research/about-office-research/our-units/central-biorepository
Core provides annotated biospecimens for basic, clinical, and translational research. Helps researchers access, collect, manage, and protect biospecimens using automated processes and quality control. Offers safe and monitored management of biospecimens including temperature-controlled storage, preparation of derivatives from these specimens, aliquoting, distribution, and production of specimen collection kits.
Proper citation: University of Michigan Medical School Central Biorepository Core Facility (RRID:SCR_026845) Copy
https://www.ifom.eu/en/cancer-research/technological-units/mechanomedicine.php
Core focuses on development of innovative biomedical technologies and devices for cancer research as well as biomedical applications using microfabrication and 3D printing.
Proper citation: Cancer Research Institute IFOM CERD Cancer Engineering R&D Core Facility (RRID:SCR_026862) Copy
https://www.ifom.eu/en/cancer-research/technological-units/preclinical-models.php
Specialized laboratory designed for growth, maintenance, and experimentation of living cells under controlled conditions. This facility is used in various fields such as biomedical research, drug development, and supports the culture of primary cells, immortalized cell lines, human-induced pluripotent stem cells (hiPSCs), and organoids, among others.
Proper citation: Cancer Research Institute IFOM CPM Cellular And Preclinical Models Core Facility (RRID:SCR_026864) Copy
https://github.com/BGI-shenzhen/RectChr
Software tool for multi-level visualization of genomic statistical variables on rectangular chromosomes.
Proper citation: RectChr (RRID:SCR_026859) Copy
https://dnamage.genetics.ucla.edu/
Web portal contains information on how to calculate DNA methylation (DNAm) age based on data measured using the Illumina Infinium platform.
Proper citation: DNA Methylation Age Calculator (RRID:SCR_026822) Copy
https://github.com/james-cole/brainageR
Software R tool for generating brain-predicted age value, using Gaussian Processes regression. Used for generating brain-predicted age value from raw T1-weighted MRI scan.
Proper citation: brainageR (RRID:SCR_026826) Copy
https://jnm.snmjournals.org/content/46/6/1023.long
Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models.
Proper citation: OLINDA/EXM (RRID:SCR_026835) Copy
https://github.com/DerrickWood/kraken2
Software tool as second version of Kraken taxonomic sequence classification system.
Proper citation: kraken2 (RRID:SCR_026838) Copy
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