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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://petab.readthedocs.io/en/latest/

Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology.

Proper citation: PEtab (RRID:SCR_026915) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexandrovLab/SigProfilerAssignment

Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations.

Proper citation: SigProfilerAssignment (RRID:SCR_026899) Copy   

•   Source: SciCrunch Registry

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

Software R package designed to streamline collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Used for collection and implementation of public transcriptional cancer signatures.

Proper citation: signifinder (RRID:SCR_027141) 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://health.ucdavis.edu/cancer/research/sharedresources/im.html

Clinical Laboratory Improvement Amendments certified laboratory established to provide scientific support to investigators conducting clinical studies in humans, preclinical studies in animals and/or studies in veterinary medicine. Conducts immunology based assays needed to monitor patients in clinical immunotherapy trials. Offers molecular and cellular assays for investigators in different fields, including custom assays designes.

Proper citation: University of California Davis Health Immune Modeling, Analysis and Diagnostics Shared Resource Core Facility (RRID:SCR_023587) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/ger.html

Provides expertise and comprehensive services to accomplish virtually every application of next generation sequencing based genomics research, including gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services. GSR also specializes in development of custom protocols and extensive data analysis and integrative bioinformatics support. The shared resource provides wide range of additional services for translational and clinical genomics research.

Proper citation: University of California Davis Health Genomics Shared Resource Core Facility (RRID:SCR_023586) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/specimen.html

Provides specimens with annotated data for clinical and basic science research purposes.Biorepository functions as centralized tissue bank to provide researchers access to cancer- and non-cancer-related specimens including fresh or frozen tissue, paraffin blocks,sections and fluids, procured and stored using international standards of best practices and protocols compliant with Office for Human Research Protection. Specimens can be obtained prospectively as part of clinical trials or accessed through UC Davis Health Clinical Laboratories, where over 5.5 million blood specimens are processed annually.

Proper citation: University of California Davis Health Biorepository Shared Resource Core Facility (RRID:SCR_023583) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/animalimaging.html

Provides access to in vivo imaging technologies including molecular imaging, optical imaging, quantitative physiologic and anatomic imaging, and whole body PET/CT scanning in humans and animals. Provides targeted imaging probes and tracers as well as expertise in planning, executing and analyzing in vivo imaging studies. Supports imaging studies in small animals, large animals and humans.This resource is located in three adjacent buildings in the Health Sciences district of the Davis campus:Center for Molecular and Genomic Imaging (CMGI), Genome and Biomedical Sciences Facility (small-animal imaging);Nuclear Magnetic Resonance (NMR) Facility, Tupper Hall (small-animal MRI);Center for Imaging Sciences (CIS), Veterinary School (large-animal imaging).

Proper citation: University of California Davis Health In Vivo Translational Imaging Shared Resource Core Facility (RRID:SCR_023589) Copy   

•   Source: SciCrunch Registry

https://ctl.cornell.edu/industry/mrdetect-license-request/

Software application to estimate presence of MRD in plasma cfDNA WGS through evaluation of matched tumour-derived mutations (SNVs or CNVs).

Proper citation: MRDetect (RRID:SCR_024766) Copy   

•   Source: SciCrunch Registry

https://www.minerva.im/

Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases.

Proper citation: Minerva (RRID:SCR_024750) Copy   

•   Source: SciCrunch Registry

https://scimap.xyz

Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells.

Proper citation: scimap (RRID:SCR_024751) Copy   

•   Source: SciCrunch Registry

https://reprint-apms.org/?q=chooseworkflow

Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.

Proper citation: CRAPome (RRID:SCR_025008) 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

https://umiamihealth.org/sylvester-comprehensive-cancer-center/research/research-resources/shared-resources/cancer-proteomics-shared-resource

Core provides advanced mass spectrometry-based proteomics to support basic, translational, and clinical cancer research. Delivers high quality, quantitative proteomic data using instrumentation, including Thermo Scientific Astral Zoom and Ascend Tribrid orbitrap mass spectrometers. Services include gel band protein identification, immunoprecipitation and pulldown proteomics, cleavable cross-linking mass spectrometry, and global quantitative proteomics and post‑translational modification analysis using tandem mass tag‑based multiplexing or label‑free data-independent acquisition and data-dependent acquisition approaches. The CPSR supports end-to-end proteomics pipelines—from whole cells and primary tumor organoids through quantitative analysis and data visualization—providing comprehensive “soup to nuts” analytical capability.

Proper citation: University of Miami Sylvester Cancer Proteomics Shared Resource Core Facility (RRID:SCR_028491) Copy   

•   Source: SciCrunch Registry

https://micr.med.wayne.edu/

Core provides advanced instrumentation, consultation, and support for flow cytometry, light and electron microscopy, and small-animal imaging. Services include confocal microscopy, multi-plex whole slide imaging, conventional, widefield epifluorescence microscopy, Electron Microscopy, in vivo small animal PET, SPECT, CT, X-Ray, white light, fluorescence, and bioluminescence imaging, in vitro and in vivo X-Ray irradiation, multi-parameter flow cytometry, including conventional and spectral technologies, cell sorting, imaging cytometry, and advanced data analysis support.

Proper citation: Wayne State University Microscopy Imaging and Cytometry Resources MICR Core Facility (RRID:SCR_028700) Copy   

•   Source: SciCrunch Registry

http://hlathena.tools/

Web tool and predictive model used by researchers to identify which small protein fragments (peptides) will be presented by human leukocyte antigen (HLA) proteins on the surface of cells. It is heavily used in the development of cancer immunotherapies and personalized

Proper citation: HLAthena (RRID:SCR_028691) Copy   

•   Source: SciCrunch Registry