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on page 1 showing 20 out of 73 results

Cite this (AbundantOTU+, RRID:SCR_016527)

URL: http://omics.informatics.indiana.edu/AbundantOTU/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

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    ACCORD

Cite this ( ACCORD , RRID:SCR_009015)

URL: https://www.accordtrial.org/public

Resource Type: Resource, resource, clinical trial

Study testing whether strict glucose control lowers the risk of heart disease and stroke in adults with type 2 diabetes. In addition the study is exploring: 1) Whether in the context of good glycemic control the use of different lowering lipid drugs will further improve these outcomes and 2) If strict control of blood pressure will also have additional beneficial effects on reducing cardiovascular disease. The design was a randomized, multicenter, double 2 X 2 factorial trial in 10,251 patients with type 2 diabetes mellitus. It was designed to test the effects on major CVD events of intensive glycemia control, of fibrate treatment to increase HDL-cholesterol and lower triglycerides (in the context of good LDL-C and glycemia control), and of intensive blood pressure control (in the context of good glycemia control), each compared to an appropriate control. All 10,251 participants were in an overarching glycemia trial. In addition, one 2 X 2 trial addressed the lipid question in 5,518 of the participants and the other 2 X 2 trial addressed the blood pressure question in 4,733 of the participants. The glycemia trial was terminated early due to higher mortality in the intensive compared with the standard glycemia treatment strategies. The results were published in June 2008 (N Eng J Med 2008;358:2545-59). Study-delivered treatment for all ACCORD participants was stopped on June 30, 2009, and the participants were assisted as needed in transferring their care to a personal physician. The lipid and blood pressure results (as well as the microvascular outcomes and eye substudy results) were published in 2010. All participants are continuing to be followed in a non-treatment observational study.

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Cite this (Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION), RRID:SCR_014373)

URL: https://www.accordionstudy.org/public/dspHome.cfm

Resource Type: Resource, data set, topical portal, portal, data or information resource

A prospective, observational follow-up study of at least 8000 participants who were treated and followed in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) Trial. Treatment in ACCORD ended in 2009 and ACCORDION is designed to further elucidate the long-term effects of the ACCORD treatment strategies and provide additional data on the relationships among various cardiovascular and diabetic risk factors.

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Cite this (Apnea, Bariatric surgery, and CPAP study, RRID:SCR_016575)

URL: https://sleepdata.org/datasets/abc

Resource Type: Resource, disease-related portal, topical portal, portal, data or information resource

Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore.

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Cite this (Best Apnea Interventions for Research (BestAIR) sleep study, RRID:SCR_016583)

URL: https://sleepdata.org/datasets/bestair/

Resource Type: Resource, disease-related portal, topical portal, portal, data or information resource

Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.

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Cite this (BioDepot-workflow-builder, RRID:SCR_017402)

URL: https://github.com/BioDepot/BioDepot-workflow-builder

Resource Type: Resource, software resource, software application, workflow software, data processing software

Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.

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Cite this (Bio-eagle, RRID:SCR_015991)

URL: https://data.broadinstitute.org/alkesgroup/Eagle/

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

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    BioJS

Cite this (BioJS, RRID:SCR_003119)

URL: https://github.com/biojs

Resource Type: Resource, data processing software, software library, software application, data visualization software, software resource, software toolkit

An open source JavaScript library of components for visualisation of biological data on the web.

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Cite this (Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC), RRID:SCR_013142)

URL: https://biolincc.nhlbi.nih.gov/home/

Resource Type: Resource, data or information resource, database, biomaterial supply resource, biospecimen repository, service resource, storage service resource, data repository, material resource, material storage repository

Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process.

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Cite this (Body Mass Index Calculator, RRID:SCR_000122)

URL: http://www.nhlbi.nih.gov/guidelines/obesity/BMI/bmicalc.htm

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women.

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Cite this (Cardiovascular Proteomics Center, RRID:SCR_000603)

URL: http://www.bumc.bu.edu/cardiovascularproteomics/

Resource Type: Resource, topical portal, portal, data or information resource

The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered.

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Cite this (CardioVascular Research Grid (CVRG), RRID:SCR_004472)

URL: http://www.cvrgrid.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resource

Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.

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Cite this (Cleveland Family Study, RRID:SCR_016585)

URL: https://sleepdata.org/datasets/cfs

Resource Type: Resource, disease-related portal, topical portal, portal, data or information resource

Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.

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Cite this (CRowd Extracted Expression of Differential Signatures, RRID:SCR_015680)

URL: http://amp.pharm.mssm.edu/CREEDS/

Resource Type: Resource, data processing software, database, software application, web application, data visualization software, software resource, data or information resource

Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.

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Cite this (Drug Target Ontology, RRID:SCR_015581)

URL: http://drugtargetontology.org/

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families.

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    Eagle

Cite this (Eagle, RRID:SCR_017262)

URL: https://github.com/poruloh/Eagle

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Open source software tool for haplotype phasing. Estimates haplotype phase either within genotyped cohort or using phased reference panel.

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Cite this (exRNA Atlas, RRID:SCR_017221)

URL: https://exrna-atlas.org

Resource Type: Resource, expression atlas, organization portal, data repository, application programming interface, data access protocol, production service resource, analysis service resource, database, consortium, atlas, service resource, portal, data analysis service, storage service resource, software resource, ontology, controlled vocabulary, data or information resource

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

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    FMA

Cite this (FMA, RRID:SCR_003379)

URL: http://sig.biostr.washington.edu/projects/fm/

Resource Type: Resource, data analysis software, data processing software, database, software application, software resource, ontology, controlled vocabulary, data or information resource

A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.

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Cite this (FuncAssociate: The Gene Set Functionator, RRID:SCR_005768)

URL: http://llama.mshri.on.ca/funcassociate/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

  • From Current Category

Cite this (GenomicFeatures, RRID:SCR_016960)

URL: http://bioconductor.org/packages/GenomicFeatures/

Resource Type: Resource, software resource, software toolkit, data analysis software, data processing software, software application

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

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