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https://github.com/ccipd/MRQy

Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data.

Proper citation: MRQy (RRID:SCR_025779) Copy   

•   Source: SciCrunch Registry

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

Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.

Proper citation: tximeta (RRID:SCR_028005) Copy   

•   Source: SciCrunch Registry

https://github.com/SalasLab/HiTIMED

Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens.

Proper citation: HiTIMED (RRID:SCR_028180) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/somalier

Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Proper citation: somalier (RRID:SCR_028167) Copy   

•   Source: SciCrunch Registry

https://oncodb.org/

Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival.

Proper citation: OncoDB (RRID:SCR_028340) Copy   

•   Source: SciCrunch Registry

https://github.com/andygxzeng/BoneMarrowMap

Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations.

Proper citation: BoneMarrowMap (RRID:SCR_028324) Copy   

•   Source: SciCrunch Registry

https://github.com/KarchinLab/mhcnuggets

Software tool that predicts how protein pieces bind to Major Histocompatibility Complex (MHC) molecules. It uses deep learning to process peptide sequences, handle variable lengths, and evaluate both common and rare alleles. Used to predicts peptide-MHC binding. Can predict binding for common or rare alleles of MHC class I or II with a single neural network architecture.

Proper citation: MHCnuggets (RRID:SCR_028674) Copy   

•   Source: SciCrunch Registry

https://biotech.wisc.edu/age/

Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications.

Proper citation: University of Wisconsin-Madison Advanced Genome Editing Laboratory (RRID:SCR_021070) Copy   

•   Source: SciCrunch Registry

https://fccf.mskcc.org/

Provides advanced instrumentation as well as high level technical and scientific expertise in multi dimensional Flow Cytometry and Cell Sorting, to facilitate science, improve the quality, and advance the scope of MSK research.

Proper citation: Memorial Sloan Kettering Cancer Center Flow Cytometry Core Facility (RRID:SCR_021105) Copy   

•   Source: SciCrunch Registry

https://cancer.dartmouth.edu/scientists-researchers/mouse-modeling

Supports generation and utilization of genetically modified mice, design and production of genetic constructs with methods including yeast and E.coli recombineering, ES cell targeting (transfection, drug selection, and expansion). Produces transgenic mice: DNA injections into oocytes, ES cell injections into blastocysts.Provides humanized immune system mouse models.Offers start to finish experiment services to assist your many needs, please ask for more info.Other services include animal husbandry, IP and IV injections, blood drawing, necropsy and surgeries- embryo transfers, ovariectomy, vasectomy, tumor removal.

Proper citation: Dartmouth Geisel School of Medicine Mouse Modeling Core Facility (RRID:SCR_021284) Copy   

•   Source: SciCrunch Registry

https://cancer.dartmouth.edu/scientists-researchers/molecular-biology-resource

Genomics Section provides services and instrumentation that enable DNA/RNA extraction and quality control, next-generation Illumina and Nanopore sequencing, epigenetic profiling, and microarray analysis on a whole-genome scale, from the level organisms to single cells. Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology.

Proper citation: Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR) (RRID:SCR_021293) Copy   

•   Source: SciCrunch Registry

https://htrc.uchicago.edu

Coordinated, centralized, and dedicated program for procuring, processing, dispersing and assessing all types of biospecimens together with downstream histology services. CAP Accredited.

Proper citation: University of Chicago Human Tissue Resource Center Core Facility (RRID:SCR_019199) Copy   

•   Source: SciCrunch Registry

https://voices.uchicago.edu/confocal/

Offers microscopy imaging, including bright field color and DIC, fluorescence multi-dimension,TIRFM including bleaching, ablation, FLIM and high resolution, highspeed, high sensitivity, confocal, and physiologic techniques, STED, GSD3D, lightsheet selective plane illumination and lattice lightsheet structured illumination super resolution microscopy.

Proper citation: University of Chicago Integrated Light Microscopy Core Facility (RRID:SCR_019197) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/cytometry-cell-sorting-laboratory

Provides access to flow cytometry and cell sorting technologies and instruments. If your research requires cytometric analysis, instruments acquire optical measurements using different lasers to detect fluorophores with high level of precision.

Proper citation: New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility (RRID:SCR_019179) Copy   

•   Source: SciCrunch Registry

https://www.unmc.edu/vcr/cores/vcr-cores/confocal-microscopy/index.html

Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.

Proper citation: University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) Copy   

•   Source: SciCrunch Registry

https://www.utsouthwestern.edu/labs/qlmc/

Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros.

Proper citation: University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility (RRID:SCR_022605) Copy   

•   Source: SciCrunch Registry

https://www.nationwidechildrens.org/research/areas-of-research/biopathology-center/about

Provides services related to biospecimen procurement, banking, processing, and distribution. Housed biospecimen collections are from biorepositories of National Cancer Institute funded Children’s Oncology Group, NRG Oncology-Columbus (formerly the GOG Tissue Bank), SWOG, Pediatric Division of Cooperative Human Tissue Network, and Biospecimen Core Resource of Center for Cancer Genomics, as well as numerous biospecimen collections sponsored by funded NCH investigators. Cooperative Human Tissue Network is one of six institutions funded by National Cancer Institutes to access to remnant human tissues for biomedical researchers throughout the United States and Canada. Offers expertise in tissue preparation and preservation to meet the research needs of basic and applied scientists.

Proper citation: Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility (RRID:SCR_023260) Copy   

•   Source: SciCrunch Registry

https://weghornlab.org/software.html

Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.

Proper citation: CBaSE (RRID:SCR_027765) Copy   

•   Source: SciCrunch Registry

https://github.com/McGranahanLab/TcellExTRECT

Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes.

Proper citation: T Cell ExTRECT (RRID:SCR_027742) Copy   

•   Source: SciCrunch Registry

https://github.com/vanallenlab/comut

Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.

Proper citation: CoMUT (RRID:SCR_027745) Copy   

•   Source: SciCrunch Registry