Curator Dashboard

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

Offers services in fragment based screening and drug discovery, characterization and QC of biologics and biosimilar drugs, metabolomics, protein NMR, small molecule NMR, and NMR of natural products. Offers 400-700MHz systems, many with cryogenic probes.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software adaptable and reusable analysis pipeline for multi scale, multi methodology analysis of cortical wave activity. Pipeline ingests data from multiple measurements types of spatially organized neuronal activity, such as ECoG or calcium imaging recordings. Pipeline returns statistical measures to quantify dynamic wave like activity patterns found in data.

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• RRID
• 4 years ago - by Anonymous

Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.

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• RRID
• 4 years ago - by Anonymous

Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.

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• RRID
• 4 years ago - by Anonymous

Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes.

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• RRID
• 4 years ago - by Anonymous

Software suite for ultra fast and sensitive sequence search and clustering. Used to search and cluster huge protein and nucleotide sequence sets. Designed to run on multiple cores and servers.

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• RRID
• 4 years ago - by Anonymous

Software pipeline for generating Circos based genome assembly consistency plot given set of contigs relative to reference genome. Intended to visualize large scale translocations or missassemblies in draft assemblies, but it can also be useful when trying to show synteny between whole genomes.Circos based tool to visualize genome assembly consistency

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• RRID
• 4 years ago - by Anonymous

Database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species. Includes 1) curated, user created Study datasets, extensively analyzed neuroimaging data associated with published figures/manuscripts, 2) Reference datasets mapped to brain atlas surfaces and volumes in human and nonhuman primates for use as general resources (e.g., published cortical parcellations), and 3) ConnectomeDB powered by BALSA for distributing HCP-Young Adult and related HCP-style processed imaging and phenotypic datasets. Datasets in BALSA may include PMID and/or DOI that links them directly to relevant publications.

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• RRID
• 4 years ago - submitted by Anita Bandrowski

Frontier (Ver 4.1) is used to estimate stochastic frontier models. Frontier Version 4.1 Resource URL https://scicrunch.org/resources/about/registry/SCR_022959 Description FRONTIER is used to obtain maximum likelihood estimates of the parameters of a variety of stochastic production and cost frontiers, and estimates of mean and individual technical or cost efficiencies. Defining Citation SCR_022958 Community resources Status pending Submitter Email czunigagonzales@gmail.com

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• RRID
• 4 years ago - submitted by Carlos Alberto Zuniga Gonzalez

Software tool to estimate stochastic frontier models. Used to obtain maximum likelihood estimates of parameters of variety of stochastic production and cost frontiers, and estimates of mean and individual technical or cost efficiencies.

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• RRID
• 4 years ago - submitted by Carlos Alberto Zuniga Gonzalez