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https://moai.colostate.edu/

Light and fluorescence microscopy core facility with Zeiss, Nikon, 3I, Leica and Olympus Microscopes. Distributed light microscopy core facility consisting of inverted and upright confocal microscopes (laser scanning and spinning disk) some with superresolution, atomic force microscopy, total internal fluorescence reflection (TIRF), high throughput multicolor imaging of fixed tissue sections or cells on slides, and live cell imaging in most modalities.

Proper citation: Colorado State University Microscopes for Open Access Imaging Core Facility (RRID:SCR_025891) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/seerstat/

Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population.

Proper citation: SEER*Stat (RRID:SCR_025808) Copy   

•   Source: SciCrunch Registry

https://www.rogelcancercenter.org/research/shared-resources-and-cores/experimental-irradiation

Core provides irradiation services for investigators, including those whose primary interests are not in radiation biology, but who need this tool in support of other efforts, such immunosuppression of animals prior to stem cell transplantation through total body irradiation. Facility is equipped to perform moderate dose rate gamma irradiation (0.1-4 Gy/min) of cell cultures, tissue specimens or animals as well as low dose rate irradiation (0.05-0.3 Gy/hr) of cell cultures.

Proper citation: University of Michigan Rogel Cancer Center Experimental Irradiation Core Facility (RRID:SCR_025766) Copy   

•   Source: SciCrunch Registry

https://gseapy.readthedocs.io/en/latest/

Software Python package for performing gene set enrichment analysis. Used for characterizing gene expression changes by analysis of large single-cell datasets.

Proper citation: GSEApy (RRID:SCR_025803) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/es/products-and-solutions/infrared-and-raman/opus-spectroscopy-software/release-overview.html#accordion-1e89899198-item-06b2720261

Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra.

Proper citation: Bruker OPUS (RRID:SCR_025806) Copy   

•   Source: SciCrunch Registry

https://www.cryo-em.uni-freiburg.de/

Core offers services related to cryo electron microscopy. Services include grid preparation, screening and data collection, as well as user training.

Proper citation: University of Freiburg Cryo-Electron Microscopy Core Facility (RRID:SCR_025860) Copy   

•   Source: SciCrunch Registry

https://www.biochem.mpg.de/protein_production

Facility for protein production. Provides services for protein expression and purification, assists with projects in designing strategies for high level expression of soluble proteins, provides vectors and strains. Offers clonning the gene of interest into expression vectors, rapid screening for optimal combinations of vectors, strains and expression conditions and producing protein of interest in E. coli, Pichia pastoris, mammalian and insect cells. Produces biomass at 1L to 10L scale using multiple bioreactor system for high cell density fermentation of bacteria and yeast cells and reusable bioreactor for cell culture. Proteins are then purified using standard techniques and chromatography systems. Quality control is routinely assessing protein identity, purity, stability and folding using set of different biochemical and biophysical methods.

Proper citation: Max Planck Institute of Biochemistry Protein Production and Structural Validation Core Facility (RRID:SCR_025741) Copy   

•   Source: SciCrunch Registry

https://www.biochem.mpg.de/bioinformatics

Facility for bioinformatics. Offers to assist wet-lab researchers in our institute for their bioinformatics data analysis.

Proper citation: Max Planck Institute of Biochemistry Bioinformatics Core Facility (RRID:SCR_025742) Copy   

•   Source: SciCrunch Registry

https://www.biochem.mpg.de/bioorganic_chemistry

Facility for bioorganic chemistry and biophysics. Offers services for studying protein structure and folding, protein-protein or protein-ligand interactions and protein complex formation, synthesis, purification and characterization of organic compounds, automated solid phase synthesis of peptides.

Proper citation: Max Planck Institute of Biochemistry Biochemistry Core Facility (RRID:SCR_025743) Copy   

•   Source: SciCrunch Registry

https://github.com/PeeperLab/CopywriteR

Software R package for DNA copy number detection from off-target sequence data. Used to extract DNA copy number information from targeted sequencing by utiizing off-target reads.

Proper citation: CopywriteR (RRID:SCR_025864) Copy   

•   Source: SciCrunch Registry

https://github.com/suhrig/arriba/

Software tool for gene fusion detection from RNA-Seq data. Fusion detection algorithm specifically designed to meet demanding requirements of HTS-assisted precision oncology. Capable of detecting aberrant transcripts that are not called by most fusion detection methods but may be clinically relevant. This includes tumor suppressor genes that are occasionally inactivated by rearrangements within the gene or by translocations to introns or intergenic regions.

Proper citation: Arriba (RRID:SCR_025854) Copy   

•   Source: SciCrunch Registry

https://github.com/Nanostring-Biostats/InSituType

Software R package for performing cell typing in SMI and other single cell data.

Proper citation: InSituType (RRID:SCR_025976) Copy   

•   Source: SciCrunch Registry

https://www.biochem.mpg.de/cryoem

Facility for cryo-electron microscopy. Provides microscope access, training as well as scientific and technical support for MPIB-internal users wishing to perform cryo-EM experiments, from sample preparation to data processing.

Proper citation: Max Planck Institute of Biochemistry Cryo-EM Core Facility (RRID:SCR_025744) Copy   

•   Source: SciCrunch Registry

https://www.biochem.mpg.de/mass_spectrometry

Mass spectrometry core facility. Facility uses chromatography systems, mass spectrometers and workflows for in-depth analysis of biomolecules.

Proper citation: Max Planck Institute of Biochemistry Mass Spectrometry Core Facility (RRID:SCR_025745) Copy   

•   Source: SciCrunch Registry

https://www.biochem.mpg.de/ngs

Facility for high-throughput sequencing. Provides Next-Generation Sequencing services, supports library preparation and quality control for various applications including RNA-Seq: rRNA depletion-total RNA, mRNAseq; DNA-Seq: ChIP-Seq, Cut andTag seq, Hi-Cseq, Micro-Cseq, WGS; Single Cell: scRNAseq, scATACseq, snRNAseq, seRNAseq.

Proper citation: Max Planck Institute of Biochemistry NGS Core Facility (RRID:SCR_025746) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/cancer/research/shared-resources/flow-and-mass/index.php

Core provides access to flow and mass cytometers, support equipment, and associated software and services. Our instrumentation affords the ability to perform almost every published flow and mass cytometry protocol.

Proper citation: Augusta University Georgia Cancer Center Flow and Mass Cytometry Core Facility (RRID:SCR_025747) Copy   

•   Source: SciCrunch Registry

https://pythonvideoannotator.readthedocs.io/en/master/index.html

Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video.

Proper citation: PythonVideoAnnotator (RRID:SCR_025868) Copy   

•   Source: SciCrunch Registry

https://www.petermac.org/research/research-technologies/bioinformatics

Provides services for data analysis, pipeline management, and artificial intelligence research and operations. Data types analysed by the core include whole-genome and whole-exome sequencing, targeted re-sequencing, radiological images, RNA-sequencing, single-cell RNA sequencing, ChIP-sequencing, NanoString and various types of microarray data. Core also develops and maintains software infrastructure required for bioinformatics processing, including pipelines and cloud provision systems.

Proper citation: Peter MacCallum Cancer Centre Bioinformatics Core Facility (RRID:SCR_025901) Copy   

•   Source: SciCrunch Registry

https://subtiwiki.uni-goettingen.de/

Comprehensive database about Gram-positive model bacterium Bacillus subtilis. Provides curated information about its genes and proteins, as well as intricate protein–protein interactions, regulatory elements, expression data and metabolic pathways.

Proper citation: SubtiWiki (RRID:SCR_025748) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/devel/bioc/html/EnrichDO.html

Software R package as global weighted model for disease ontology enrichment analysis. Used for annotating and enrichment analysis with disease ontology.

Proper citation: EnrichDO (RRID:SCR_025840) Copy   

•   Source: SciCrunch Registry