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https://github.com/gbouras13/pharokka

Software fast scalable bacteriophage genome annotation tool. Used to annotate bacteriophage genomes easily, rapidly and consistently with standards compliant outputs.

Proper citation: Pharokka (RRID:SCR_026017) Copy   

•   Source: SciCrunch Registry

https://github.com/oicr-gsi/ESTIMATE

Software application provides researchers with scores for tumor purity, level of stromal cells present, and infiltration level of immune cells in tumor tissues based on expression data.

Proper citation: ESTIMATE (RRID:SCR_026090) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/jrobust/

Software application for analysis of force microscopy recordings, including images and force curves. Allows for fast and reliable processing of single force curves and force maps, providing estimation of mechanical properties of sample.

Proper citation: AtomicJ (RRID:SCR_026023) Copy   

•   Source: SciCrunch Registry

https://github.com/huayc09/SeuratExtend

Software R package that streamlines single-cell RNA-seq analysis by integrating essential tools and databases with the Seurat framework. Provides comprehensive functionality for functional enrichment, trajectory inference, gene regulatory network reconstruction, and enhanced visualization.

Proper citation: SeuratExtend (RRID:SCR_026143) Copy   

•   Source: SciCrunch Registry

https://friedmanlab.weizmann.ac.il/McPAS-TCR/

Manually curated database of T cell receptor sequences associated with various pathologic conditions including pathogen infections, cancer and autoimmunity and their respective antigens in humans and in mice. Links TCR sequences to their target antigen and/or to the organ with which they are associated and subsequent pathologies. Database can be searched by source organism, disease, tissue, T cell type, antigen sequence, MHC class, etc.

Proper citation: McPAS-TCR (RRID:SCR_026024) Copy   

•   Source: SciCrunch Registry

https://mutalyzer.nl/

Software suite is designed to be of help when working with Human Genome Variation Society sequence variant nomenclature descriptions.

Proper citation: LUMC Mutalyzer 3 (RRID:SCR_026148) Copy   

•   Source: SciCrunch Registry

https://www.naaccr.org/

Professional organization that develops and promotes uniform data standards for cancer registration. Provides education and training, certifies population-based registries, aggregates and publishes data from central cancer registries and promotes the use of cancer surveillance data and systems for cancer control and epidemiologic research, public health programs, and patient care to reduce the burden of cancer in North America. Data Standards and Data Dictionary is intended for hospital and central cancer registries, programmers, and analysts. It provides detailed specifications and codes for each data item in the NAACCR data exchange record layout.

Proper citation: North American Association of Central Cancer Registries (RRID:SCR_026199) Copy   

•   Source: SciCrunch Registry

https://github.com/grubbybio/pRNASeqTools

Software integrated pipeline for plant NGS analysis.

Proper citation: pRNASeqTools (RRID:SCR_026232) Copy   

•   Source: SciCrunch Registry

https://www.wuxiapptec.com/services/

Pharmaceutical, biopharmaceutical, and medical device company founded in December 2000 in Shanghai. Contract research organization.

Proper citation: Wuxi AppTec (RRID:SCR_026235) Copy   

•   Source: SciCrunch Registry

https://www.research.uky.edu/mass-spectrometry-and-proteomics-core

Mass spectrometry core lab performing proteomics, small molecule, and lipidomic analyses. Provides access to advanced analytical equipment for quantitation and structural analysis. Offers assistance in sample preparation, method development, acquisition, and data analysis.

Proper citation: University of Kentucky Research Mass Spectrometry and Proteomics Core Facility (RRID:SCR_026359) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/cancermoonshots/research_platforms/cancer-genomics-laboratory.html

Facility for sequencing samples for the MD Anderson Cancer Center.

Proper citation: University of Texas MD Anderson Cancer Genomics Library Core Facility (RRID:SCR_026237) Copy   

•   Source: SciCrunch Registry

https://www.liverpool.ac.uk/research/facilities/egg-facility/

Through the use of fertilised hen's eggs, the Egg Facility offers researchers methods for scientific research that can reduce or replace the use of mammalian models. It provides expertise in chorioallantoic membrane assays, specialising in cancer xenograft models, including patient-derived xenografts, to translate in vitro cancer studies and test therapeutic approaches.

Proper citation: University of Liverpool Egg Facility (LIV-SRF) (RRID:SCR_026195) Copy   

•   Source: SciCrunch Registry

http://tide.dfci.harvard.edu/login/

Web platform for large-scale public data reuse to model immunotherapy response and resistance. Provides integrated large-scale omics data and biomarkers on published ICB trials, non-immunotherapy tumor profiles, and CRISPR screens.

Proper citation: TIDE (RRID:SCR_026350) Copy   

•   Source: SciCrunch Registry

https://www.montana.edu/uit/rci/

Core provides centralized support, systems, and services for IT specific to research. Systems and services include areas of high-performance computing, virtual machine hosting, large scale storage, and high-performance networking and data transfer.Provides MSU researchers with consulting on technology budgets and implementation for grants and support for IT components of major research instrumentation, software, and specialized or unique research technology needs.

Proper citation: Montana State University Research Cyberinfrastructure Core Facility (RRID:SCR_026229) Copy   

•   Source: SciCrunch Registry

https://www.nuance.northwestern.edu/facilities/keck-ii/index.html

Core facilitates research, collaboration, education and outreach in all science from soft biological matter to hard physical matter, specializing in surface analysis and nano-scale characterization. Instruments include Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), X-ray Photoelectron Spectroscopy (XPS), Fourier Transform Infrared Spectroscopy (FT-IR), Confocal Raman System, High Resolution Stylus Profilometer, 3D Optical Microscope, Spectroscopic Ellipsometer, and Zetasizer.Staff provides hand-on training, collaboration and assistance.

Proper citation: Northwestern University Keck Interdisciplinary Surface Science Core Facility (RRID:SCR_026360) Copy   

•   Source: SciCrunch Registry

https://www.protectedplanet.net/

Provides data on protected areas and other effective area-based conservation measures, updated monthly with submissions from governments, non-governmental organizations, landowners and communities.Through Protected Planet website, users can explore World Database on Protected Areas (WDPA), World Database on OECMs, Global Database on Protected Area Management Effectiveness (GD-PAME), and associated information.

Proper citation: Protected Planet (RRID:SCR_026240) Copy   

•   Source: SciCrunch Registry

https://www.montana.edu/nmrcorefacility/

Core provides open access availability to NMR spectroscopy instrumentation, training and sample preparation. Facility can be accessed individually or as full service center. NMR Facility has a total space of ~2,500 sq ft. divided among 3 rooms fully constructed with considerations for cooling, in-place floor dampening infrastructure and space for wet lab/sample preparation. Facility specializes in small molecule structure determination, small molecule characterization, biomolecular/protein structure determination, qualitative and quantitative NMR analysis, and small molecule purification from wide variety of sample sources.

Proper citation: Montana State University Nuclear Magnetic Resonance Core Facility (RRID:SCR_026334) Copy   

•   Source: SciCrunch Registry

https://github.com/j-rub/scVital

Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data.

Proper citation: scVital (RRID:SCR_026215) Copy   

•   Source: SciCrunch Registry

https://www.benaroyaresearch.org/our-research/core-labs/cell-and-tissue-analysis-group

Core offers flow cytometry, imaging, and histology resources.Provides expertise in the fields of imaging, histology, and flow cytometry, physical space and instruments, critical support through the whole process, from hands-on training to experiment design and data analysis.

Proper citation: Benaroya Research Institute Cell and Tissue Analysis Group Core Facility (RRID:SCR_026327) Copy   

•   Source: SciCrunch Registry

https://github.com/ly4dsg/SpatialSNV

Software tool for calling and analyzing SNVs from spatial transcriptomics data.

Proper citation: spatialSNV (RRID:SCR_026221) Copy   

•   Source: SciCrunch Registry