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https://research.utk.edu/oried/core-facilities/advanced-microscopy-and-imaging-center/

Multi-user, multi-disciplinary facility that provides microscopy and imaging services. It houses instrumentation for optical microscopy including laser scanning confocal microscopy and total internal reflection microscopy (TIRF), scanning as well as transmission electron microscopy, MALDI mass spectrometry imaging, and an X-ray MicroCT. Offers complete technical support, individual training and courses that cover both the practical applications and physical principles of microscopy. Provides consultations for development of microscopy projects for inclusion in grant proposals.

Proper citation: University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility (RRID:SCR_028273) Copy   

•   Source: SciCrunch Registry

https://ycmd.yale.edu/

Full-service core facility specializing in high throughput assay development and screening of chemical and genomic probes.

Proper citation: Yale Center for Molecular Discovery YCMD Core Facility (RRID:SCR_028309) 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/GangCaoLab/CoolBox

Software Jupyter notebook based genomic data visualization toolkit.

Proper citation: CoolBox (RRID:SCR_028427) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/data/experiment/html/scRNAseq.html

Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

Proper citation: scRNAseq (RRID:SCR_028417) Copy   

•   Source: SciCrunch Registry

https://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling

Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.

Proper citation: SCANDAN-DICOM-labelling (RRID:SCR_028365) Copy   

•   Source: SciCrunch Registry

https://uwhistologyandimaging.org/

Core provides histology, immunohistochemistry, imaging, quantitative image analysis, and pathology consultation services. Offers experience, expertise and instrumentation across all platforms. Through the partnership with the Comparative Pathology Program (CPP), we have board certifies veterinary pathologists on staff who are available for research consultation and collaboration.

Proper citation: University of Washington Histology and Imaging Core Facility (RRID:SCR_028435) Copy   

•   Source: SciCrunch Registry

https://bokeh.org/

Software Python package for interactive and static data visualization.Interactive visualization library for modern web browsers. Provides concise construction of graphics and affords high-performance interactivity across large or streaming datasets.

Proper citation: Bokeh (RRID:SCR_028392) Copy   

•   Source: SciCrunch Registry

https://glycoshape.org/

Database of glycans 3D structural data and information that can be downloaded or used with Re-Glyco to rebuild glycoproteins from the RCSB PDB or EMBL-EBI AlphaFold repositories. Glycan structure database and toolbox designed to restore glycoproteins to their native and functional form.

Proper citation: GlycoShape (RRID:SCR_028443) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration

Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible

Proper citation: GATK VariantFiltration (RRID:SCR_028441) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/goldenpath/help/bigWig.html

Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser.

Proper citation: bedGraphToBigWig (RRID:SCR_028439) Copy   

•   Source: SciCrunch Registry

https://github.com/maxconway/SNFtool

Software R package for constructing networks of samples (e.g., patients) for each available data type and then efficiently fuses these into one network that represents the full spectrum of underlying data. Used to taking multiple views of a network and merging them into a combined view.

Proper citation: SNFtool (RRID:SCR_028497) Copy   

•   Source: SciCrunch Registry

https://ccic.osu.edu/nuclear-magnetic-resonance/nmr-instruments#:~:text=Bruker%20Avance%20Neo%20Ascend%20800%20MHz

Spectrometer used for advanced chemical, biological, and materials research. It allows scientists to determine the atomic-level structure, dynamics, and interactions of molecules. Console: Avance Neo; Magnet: Ascend; Field Strength: 800 MHz; software:TopSpin 4.4.1 on CentOS 7; Probe: 5mm QXI-F solution; 5mm TXI solution; 4.0mm gradient hr-MAS; 3.2mm Efree; 2.5mm Tri-gamma MAS; 1.9mm MAS; 1.3mm MAS; 0.7mm ultra-fast MAS.

Proper citation: Bruker: Avance Neo Ascend 800 MHz NMR Spectrometer (RRID:SCR_028511) Copy   

•   Source: SciCrunch Registry

https://github.com/bioFAM/MOFA2

Software statistical framework for comprehensive integration of multi-modal single-cell data. Used for integration of multi-omic data sets in unsupervised fashion.

Proper citation: MOFA2 (RRID:SCR_028488) Copy   

•   Source: SciCrunch Registry

https://github.com/palombom/SANDI-Matlab-Toolbox-Latest-Release

Software toolbox for estimation of MR signal fraction of brain cell bodies (of all cell types, from neurons to glia, namely soma) and cell projections (of all cell types, from dentrites and myelinated axons to glial processes, namely neurties ) as well as apparent MR cell body radius and intraneurite and extracellular apparent diffusivities from a suitable diffusion-weighted MRI acquisition using Machine Learning.

Proper citation: SANDI Matlab Toolbox (RRID:SCR_028525) Copy   

•   Source: SciCrunch Registry

https://github.com/BioinfoUninaScala/MoNETA

Software R package to compress multi-omic data into a single matrix of reduced size. Used for fast and scalable identification of relevant multi-omics relationships between biological entities at the bulk and single-cells level.

Proper citation: MoNETA (RRID:SCR_028485) Copy   

•   Source: SciCrunch Registry

https://openslide.org/

Software C library that provides a simple interface to read whole-slide images (also known as virtual slides).

Proper citation: OpenSlide (RRID:SCR_028483) Copy   

•   Source: SciCrunch Registry

https://github.com/asalavaty/influential

Software R package for identifying and ranking influential nodes in biological and other complex networks. Implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. Provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures. Used for identification and classification of the most influential nodes.

Proper citation: influential (RRID:SCR_028517) Copy   

•   Source: SciCrunch Registry

https://github.com/msraredon/Connectome

Software R package for calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Used to explore cell-cell connectivity patterns based on ligand and receptor data in heterogeneous single-cell datasets.

Proper citation: Connectome (RRID:SCR_028632) Copy   

•   Source: SciCrunch Registry

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

Software tool to infer and map cell-to-cell communication networks using single-cell RNA sequencing (scRNA-seq) or proteomics data. Used for inference of intercellular networks from single-cell transcriptomics.

Proper citation: SingleCellSignalR (RRID:SCR_028633) Copy   

•   Source: SciCrunch Registry