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https://pathoman.mskcc.org/

Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources.

Proper citation: PathoMAN (RRID:SCR_026552) Copy   

•   Source: SciCrunch Registry

https://github.com/QuackenbushLab/NetworkDataCompanion

Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning.

Proper citation: NetworkDataCompanion (RRID:SCR_026532) Copy   

•   Source: SciCrunch Registry

https://github.com/calico/borzoi

Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.

Proper citation: Borzoi (RRID:SCR_026619) 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://www.cshl.edu/research/cancer/flow-cytometry/

Resource provides equipment, training, and operating assistance for cell sorting and analysis. Facility staff oversees equipment maintenance, trains new users, and assists with assay development and operation of equipment.

Proper citation: Cold Spring Harbor Laboratory Flow Cytometry Shared Resource Core Facility (RRID:SCR_022164) Copy   

•   Source: SciCrunch Registry

https://pathbio.med.upenn.edu/pbr/portal/flowcyto/

Flow cytometry shared resource laboratory at the University of Pennsylvania. Facility has instruments, which include analyzers, cell sorters, small particle detectors, dual fluorescence cell counter/viability instrument, tissue dissociator for cell preparation. Provides on-site and off-site support to instrument users, including analyzer and cell sorter training. Core's Research and Development team collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis.

Proper citation: University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility (RRID:SCR_022376) Copy   

•   Source: SciCrunch Registry

http://www.sylvester.org/OGSR

Provides access to technologies and services for study of genomics and epigenomics of cancer, in addition to providing technical expertise for project design, trouble shooting and pre and post award support. Services include next generation sequencing, single cell genomics, spatial genomics, gene expression assays and molecular quantitation, services for sample extraction and QC.

Proper citation: University of Miami Sylvester Onco Genomics Shared Resource Core Facility (RRID:SCR_022502) Copy   

•   Source: SciCrunch Registry

http://igm.ucsd.edu/genomics/

Provides services including sequencing library preparation and sequencing on Illumina MiSeq and NovaSeq 6000 platforms. Supports single cell sequencing on 10X Genomics Chromium Controller. Provides Illumina Infinium Beadchips, which includes variety of whole genome genotyping arrays as well as Infinium MethylationEPIC BeadChip.

Proper citation: University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy (RRID:SCR_022740) Copy   

•   Source: SciCrunch Registry

https://redu.ucsd.edu/

Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE.

Proper citation: ReDU (RRID:SCR_025105) Copy   

•   Source: SciCrunch Registry

https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/

Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.

Proper citation: IBEX Knowledge Base (RRID:SCR_025296) Copy   

•   Source: SciCrunch Registry

https://github.com/GregorySchwartz/too-many-cells

Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades.

Proper citation: TooManyCells (RRID:SCR_025328) Copy   

•   Source: SciCrunch Registry

https://github.com/willtownes/glmpca

Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.

Proper citation: glmpca (RRID:SCR_025517) Copy   

•   Source: SciCrunch Registry

https://discover.nci.nih.gov/rsconnect/cellminercdb/

Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements.

Proper citation: CellMinerCDB (RRID:SCR_025649) Copy   

•   Source: SciCrunch Registry

https://www.borch.dev/uploads/screpertoire/

Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis.

Proper citation: scRepertoire (RRID:SCR_025691) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/research/ski/core-facilities/monoclonal-antibody-core-facility

ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University.

Proper citation: Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility (RRID:SCR_017691) Copy   

•   Source: SciCrunch Registry