Curator Dashboard

Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ .

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• RRID
• 4 years ago - by Anonymous

Center coordinates ideas and investments to advance and democratize access to Stanford cores, instrumentation, scientific and technical staff, allowing users to perform innovative, rigorous experiments.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Computerized, non invasive system for measuring mouse and rat blood pressure. Blood pressure analyzer is standard in transgenic and knockout mouse research.

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• RRID
• 4 years ago - by Anonymous

Software is part of MouseOx Plus pulse oximeter system.

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• RRID
• 4 years ago - by Anonymous

Component of Accelerating Medicines Partnership Common Metabolic Diseases being developed at University of California San Diego as part of larger consortium of academic, industry and non-profit institutions worldwide. Resource is based on software developed by ENCODE DCC at Stanford University. Atlas provides epigenomics and other functional genomics data to promote understanding of genetic basis of common metabolic diseases.

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• dkNET
• 4 years ago - submitted by Maryann Martone

Software R package for quality check of HTG EdgeSeq datasets.

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• SciCrunch
• 4 years ago - by Anonymous

Tecnai T12 microscope combines all imaging, diffraction, and analytical techniques at good spatial resolution and detection efficiency. Transmission electron microscope with operating voltage range of 20 to 120 kV. FEI Tecnai T12 120kV TEM and 2k TVIPS camera.

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• SciCrunch
• 4 years ago - by Anonymous

Reichert Jung Ultracut E, article number 131-960, is used to cut ultrathin and semithin sections of resin embedded samples for electron microscopy.

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• SciCrunch
• 4 years ago - by Anonymous

The Precellys 24 homogenizer with automatic tube locking system with the ability to process up to 24 tubes simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 4 years ago - by Anonymous

Software R package to conduct signal deconvolution for general omics data. Can estimate individual specific and cell type specific reference panels, when there are multiple samples observed from each subject. Can solve for reference panel on individual basis. Can conduct test to identify cell type specific differential expression genes.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.

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• RRID
• 4 years ago - by Anonymous

Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible.

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• RRID
• 4 years ago - submitted by Yaroslav Halchenko

Core is involved in procurement and processing of human tissue and other biospecimens for basic, translational, and clinical research.Provides laboratory support services for clinical trials, tissue samples from remnant surgical resection and autopsy specimens linked to clinicopathologic data while maintaining patient confidentiality. Provides biorepository of human specimens.Offers advanced histology services including multi color immunohistochemistry, in situ hybridization, tissue microarrays, slide scanning, computerized image analysis, NanoString spatial profiling.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Brain tissue repository and provider. Brain tissue is obtained postmortem from individuals after donation is made by family members. Blood is also obtained to perform genetic analysis, test for viral infection(s), and/or other substances pertinent to psychiatric disorders research. As part of clinical information, we also perform detailed Psychological Autopsy about aspects of subject’s personality, well being and mental health.

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• RRID
• 4 years ago - by Anonymous

Provides support to NIDA-IRP researchers by facilitating studies of brain function under physiological and pathological conditions through developing and producing genetic tools capable of modulating and monitoring molecules, cells and circuits in nervous system.Provided services include custom design and/or production of viral vectors/nanoparticles;in vitro molecular and cell biology services; consultation and training.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core research facilities include BioImaging Research Node which houses commercial and custom imaging systems and is focused on optical imaging; Tissue Engineering and Biomaterials Testing Research Node equipped with microfluidics 3D bioprinter and mechanical testers, which facilitate development of artificial 3D biological tissue models and biomechanical testing of different biomaterials and biomedical samples; Biochemistry and Molecular Biology Research Node which houses hypoxia chamber and systems for characterization and quantification of proteins, peptides, and nucleic acids; Cellular Biology Research Node to support development and use of 3D tissue models.It houses instruments including flow cytometer for phenotyping and performing functional testing of cells and bacteria, Seahorse Analyzer for evaluation of metabolic activity of cells, and Incucyte for live cell imaging of cells and tissues in culture.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth