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https://www.uhcancercenter.org/research/shared-resources/genomics-and-bioinformatics

Core offers central service that uses genomic technologies combined with expert data analysis.Provides genomic analyses and bioinformatics as well as technical and scientific consultation,collaboration and initial data interpretation to all UH faculty with priority given to Cancer Center members with federal funding for cancer related projects. Offers expertise in molecular biology, genetics, genomics and bioinformatics, and can provide project planning, advice, and troubleshooting at all phases of the project.Genomic analysis services include DNA/RNA isolation, plating, and quality analysis, custom genotyping, Real-Time qPCR-based gene expression, copy number and methylation assays, pyrosequencing, Affymetrix and Illumina microarray based assays,Next Generation Sequencing on NextSeq500, iSeq100, NanoString nCounter analysis.

Proper citation: University of Hawaii at Manoa Cancer Center Genomics and Bioinformatics Shared Resource Core Facility (RRID:SCR_019085) Copy   

•   Source: SciCrunch Registry

http://ncore.web.unc.edu/

Core provides physicochemical characterization of nanoscale entities. Offers characterization of several classes of nanomaterials:Polymer conjugates,Polymeric micelles,Liposomes,Nanogels,Polyion complexes of small drugs and biomacromolecules (proteins, DNA, and RNA),Inorganic/metal nanoparticles,Bio-derived nanoparticles such as exosomes with protein and nucleic acid cargo.

Proper citation: North Carolina University at Chapel Hill Nanomedicines Characterization Core Facility (RRID:SCR_017951) Copy   

•   Source: SciCrunch Registry

https://www.feinberg.northwestern.edu/research/cores/units/structural-bio.html

Core provides equipment, training, technical support, and maintenance of equipment for studying structures of biological macromolecules and materials. Serves with expertise in structural and computational biology. Services offered include Macromolecular Structure Determination and Analysis,Macromolecular crystallography at LS-CAT,Robotics equipment for crystallization experiments,UV crystal imaging capabilities,Software for structure analysis,Graphics facilities for visualization/presentation of molecular structures,Computer servers specialized for structural biology calculationss,Support and Training ,X-ray crystallography, from designing crystallization experiments to structure determination and refinemen,Molecular graphics for analysis and presentation,CryoEM and EM training.Resources Available:Crystallography Art Robbins, Inc. Phoenix and Gryphon crystallization robots,TTP Labtech Dragonfly liquid handler for crystal tray setup,Jansi UVEX UV/Vis microscope/imaging system,Stereomicroscopes (camera equipped, at room temperature and 4 degrees C),Incubators for temperature-controlled crystallization,Coordination of access to LS-CAT for Northwestern University users,CryoEM,JEOL 3200FS TEM equipped with in-column energy filter (omega filter), field emission gun capable of operating at 200 or 300 kV and Gatan K2 Summit Direct Electron Detector,JEOL 1400 with Gatan 4k x 4k Ultrascan CCD camera,Solarus Plasma Cleaner and Pelco easyGlow Discharge Cleaning System,Cressington 308R carbon coater,Gatan Cryoplunge 3 and FEI Vitrobot Mark IV,Gatan 626 cryoholders with 655 Turbo pump stations.Resources available Computational:50+ node cluster running Linux including several single- and multi-GPU nodes,7 Quad-core Intel Xeon 3.4GHz workstations (3D stereo equipped for visualization and model building) 3 Dual Quad-core Intel Xeon 3.5GHz workstations with GPU computing capabilities (3D stereo equipped for visualization, model building, and GPU computing),LTO6 writers for quick data backup,45 tape LTO6 system for continuous data backup,Over 200 Tb of disk storage including RAID systems,10 Gigabit fiber Ethernet connection to APS.Software Crystallography,CCP4 suite,PHENIX,SHARP,SOLVE,HKL2000,XDS,CryoEM,CryoSparc,Relion3,Leginon,cisTEM,Appion,NMR,CNS,FELIX,Aria Modeling, graphics, and simulations,COOT,Pymol,Chimera,APBS,GROMACS,AMBER,VMD/NAMD.

Proper citation: Northwestern University School of Medicine Structural Biology Core Facility (RRID:SCR_017952) Copy   

•   Source: SciCrunch Registry

https://www.lsi.umich.edu/science/centers-technologies/center-structural-biology

Comprehensive structural biology resource.Provides high throughput protein laboratory for protein engineering, protein purification facilities for small- and large-scale protein production, macromolecular crystallization and crystallography laboratories for solving crystal structures of biological molecules, and X-ray facility with access to high energy synchrotron radiation. Provides expert guidance to researchers through every stage of project, collaborating and consulting with researchers who use the facilities. Service categories are Chemical, Material and Protein Characterization, Molecular Biology. Services include Cloning, Crystallization, Differential thermal analysis, Drug development, NMR (small molecule), PCR, Protein crystallography, Protein engineering, Protein production, Structure determination, Xray.

Proper citation: University of Michigan Center for Structural Biology Core Facility (RRID:SCR_021065) Copy   

•   Source: SciCrunch Registry

https://cami.northwestern.edu/

Provides access to range of preclinical imaging modalities and support services. These include MRI, nuclear imaging (PET, SPECT, and CT), in vivo bioluminescence and fluorescence imaging, animal housing and prep spaces, and tissue culture. Image analysis services are available, as are software packages (JIM, Amira, Matlab) and a workstation for users to perform their own data analysis. Imaging services can be provided for investigators' own animal models, or animal models can be supplied by the Developmental Therapeutics Core.

Proper citation: Northwestern University Center for Advanced Molecular Imaging Core Facility (RRID:SCR_021192) Copy   

•   Source: SciCrunch Registry

https://www.feinberg.northwestern.edu/sites/cam/

Core offers instrumentation and services for study of biological processes at whole animal, tissue, cellular and subcellular levels. This includes light microscopy, electron microscopy and image analysis. Light microscopy offerings include super resolution microscopy (MINFLUX, STED, NSPARC, SORA), fluorescent laser scanning and spinning disk microscopy, fluorescent lifetime imaging, automated high throughput tissue cytometry, atomic force microscopy, laser capture microdissection, mutliphoton imaging, and whole animal bioluminescent and fluorescent imaging. Electron microscopy includes sample prep and imaging for TEM, SEM, platinum replicas, immuno gold and CLEM. We also provide microinjection equipment, chambers for stable live cell observation, and anesthesia equipment. CAM provides training on numerous different instrument platforms, consultation on experiment design, as well as digital image processing and image analysis.CAM is one of two Nikon Imaging Centers in the US, allowing us access and excellent support from Nikon to develop innovative solutions for the cutting edge imaging needs of users.

Proper citation: Northwestern University Feinberg School of Medicine Center for Advanced Microscopy and Nikon Imaging Center Core Facility (RRID:SCR_020996) Copy   

•   Source: SciCrunch Registry

https://fgf.uchicago.edu/

Facility offers Next-Gen Illumina and Pacific Biosciences Sequencing and Library prep services, Micro-array Illumina genotyping and EPIC arrays services, Sanger DNA Sequencing, and Bioanalyzer/Fragment analyzer sample QC services. For Single Cell sequencing project Facility operates DROP-SEQ and 10X Genomics instrument., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: University of Chicago Functional Genomics Core Facility (RRID:SCR_019196) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/applied-bioinformatics-laboratories

Core provides computational analysis for high throughput genomic data, including but not limited to, next generation sequencing data. Our mission is to accelerate scientific discoveries by guiding experimental design, performing robust data quality assessment, and carrying out comprehensive computational analyses. Registration to iLab required.

Proper citation: New York University Grossman School of Medicine Applied Bioinformatics Laboratories Facility (RRID:SCR_019178) Copy   

•   Source: SciCrunch Registry

https://medschool.cuanschutz.edu/colorado-cancer-center/research/shared-resources/biostatistics-and-bioinformatics/biostatistics

Biostatistics provides quantitative support for planning, design, analysis, and presentation of basic science, clinical, and epidemiological investigations. We are dedicated to delivering high quality, methodically developed results to improve patient outcomes and clinical care.

Proper citation: University of Colorado Anschutz Medical Campus Cancer Center Biostatistics Core Facility (RRID:SCR_021981) Copy   

•   Source: SciCrunch Registry

https://github.com/rbundschuh/CLEAR

Software workflow that identifies reliably quantifiable transcripts in limiting-cell RNA-seq (lcRNA-seq) data for differentially expressed genes (DEG) analysis. Coverage-based Limiting-cell Experiment Analysis for RNA-seq.

Proper citation: CLEAR (RRID:SCR_027171) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/RAIDS/

Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

Proper citation: RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) Copy   

•   Source: SciCrunch Registry

https://seahorse.networkmedicine.org

Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes.

Proper citation: SEAHORSE (RRID:SCR_027399) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/GenVisR.html

Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest.

Proper citation: GenVisR (RRID:SCR_027559) Copy   

•   Source: SciCrunch Registry

https://github.com/Danko-Lab/BayesPrism

Software R package for fully Bayesian inference of tumor microenvironment composition and gene expression deconvolution. Used to analyze bulk RNA-seq data and estimate cell type-specific expression profiles.

Proper citation: BayesPrism (RRID:SCR_027499) Copy   

•   Source: SciCrunch Registry

https://cytospace.stanford.edu/

Software tool for assigning single cells from scRNA-seq to spatial transcriptomics coordinates via optimization framework. Supports high-resolution cell/spot alignment, capacity-constrained/domain-aware placement, and outputs per-cell/per-spot assignments and probabilities for downstream visualization and analysis. Used for optimal mapping of scRNA-seq data to spatial transcriptomics data.

Proper citation: CytoSPACE (RRID:SCR_027634) Copy   

•   Source: SciCrunch Registry

https://github.com/KChen-lab/METAFlux?tab=readme-ov-file

Software tool that predicts cancer metabolic fluxes from bulk RNA-seq and scRNA-seq data to address these analytic gaps. Used for characterizing metabolic circuits and output non-degenerative fluxes using cancer gene expression data.

Proper citation: METAFlux (RRID:SCR_028022) Copy   

•   Source: SciCrunch Registry

https://github.com/huishenlab/biscuit

Software application for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Used to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data. Analyzing sodium bisulfite conversion-based DNA methylation/modification data.

Proper citation: BISCUIT (RRID:SCR_028006) Copy   

•   Source: SciCrunch Registry

https://CivicDb.org

Open-access, community-driven knowledgebase designed to crowdsource and curate evidence on the clinical significance of cancer-related genomic variants. It helps researchers and clinicians interpret tumor DNA mutations to guide precision medicine.

Proper citation: CivicDb (RRID:SCR_028055) Copy   

•   Source: SciCrunch Registry

https://github.com/zfyuan/EpiProfile2.0_Family

Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis.

Proper citation: EpiProfile (RRID:SCR_028224) Copy   

•   Source: SciCrunch Registry

https://hitaic.herokuapp.com/

Web-based application to trace tumor tissue of origin in primary and metastasized cancers.

Proper citation: HiTAIC (RRID:SCR_028181) Copy   

•   Source: SciCrunch Registry