Dbgap home

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dbGaP Study Submission Guide

  • Study Accession Number - Once the study config is loaded, a study accession is assigned: phs#####.v#.p#
  • The study accession is a unique, stable, and versioned identifier (ID) that can be used in publications
  • It is prefixed by "phs," indicating a phenotype study.

Ncbi.nlm.nih.gov   DA: 20 PA: 26 MOZ Rank: 47

dbGaP Data Browser

  • Download SRA data from the dbGaP Data Browser
  • Install and Configure the SRA toolkit for use with protected data from dbGaP
  • Show command line parameters; Download SRA key; Download genotype data

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The NCBI dbGaP database of genotypes and phenotypes

  • dbGaP is a general repository for studies examining the association between phenotype and genotype
  • At the time of writing, dbGaP has 12 public studies at various stages of completion
  • Several other genome-wide association studies are being processed and …

Ncbi.nlm.nih.gov   DA: 20 PA: 25 MOZ Rank: 48

Comparison of home lead dust reduction techniques on hard

  • The effectiveness of a home cleaning intervention strategy in reducing potential dust and lead exposures
  • Lanphear BP, Winter NL, Apetz L, Eberly S, Weitzman M
  • A randomized trial of the effect of dust control on children's blood lead levels

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dbGaP: Apply for Controlled Access Data

  • This video reviews the steps to request access to controlled data in dbGaP
  • It contains a minor update -- a new screen capture of the dbGaP homepage, which r

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NCBI’s Database of Genotypes and Phenotypes: dbGaP

  • The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH)-sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype.It was launched in 2006 in response to the development of NIH’s Genome Wide Association Study (GWAS) policy and provides …

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dbGaP: Apply for Controlled Access Data

This video reviews the steps to request access to controlled data in dbGaP.

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NIH Launches dbGaP, a Database of Genome Wide Association

  • "The dbGaP project marks a new milestone in data sharing," said NLM Director Donald A
  • "Researchers, students and the public will have access to a level of study detail that was not previously available and to genotype-phenotype associations that should provide a wealth of hypothesis-generating leads," he said.

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OHRS Alert: dbGaP Default GSR Setting May

  • If you have deposited genomic data into dbGaP, you received an email from the NIH with the subject line: ACTION NEEDED: Update to NIH Access Procedures for Genomic Summary Results
  • The email requested action by May 1, 2019 regarding NIH’s new plan to share genomic summary results (GSR) in an open-access fashion within dbGaP.
  • This new policy allows unrestricted access by default to GSR …

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The Database of Genotypes and Phenotypes (dbGaP) Coriell

  • Data from AREDS is publicly available in the Database of Genotypes and Phenotypes (dbGaP)
  • The AREDS phenotype data has 2 groups of data tables: Project Data Tables (11 tables): Data from all participants enrolled in AREDS (4,757) are included
  • All phenotype variables are included
  • ID number is used as the subject

Coriell.org   DA: 11 PA: 32 MOZ Rank: 53

Genotype-Tissue Expression (GTEx)

The GTEx Portal has been updated to data release V8 (dbGaP accession phs000424.v8.p2)! This release includes genotype data from approximately 948 post-mortem donors and approximately 17,382 RNA-seq samples across 54 tissue sites and 2 cell lines, with adequate power to detect Expression Quantitative Trait Loci in 48 tissues.

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NCBI GAIN in dbGaP GAIN in dbGaP 110101 Updating and

dbGaP Home - Windows Internet Explorer J File Edit Favorites Tools Help dbGaP Home NCBI search&term st, u Emba rgo July 10, 2008 Google FMC o Tools NC81 [Sian In [Reaister Type of Case- 2902 control Community- based, longitudinal GENOTYPE and PHENOTYPE Limits Preview/lndex History Clipboard Details N cal dbGaP About dbGaP Browse dbGaP Controlled

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Prefetch issue with dbGap data · Issue #328 · ncbi/sra

  • Hi, Following your suggestion 2 to rerun the same prefetch command (below) again and it will continue the download: I ran prefetch with no success once and a directory SRRXXX has been created but stayed empty
  • When I ran prefetch again I got the following: SRRXXXXX (not a file) is found locally: consider it complete.

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The NCBI dbGaP database of genotypes and phenotypes

dbGaP home page’s list of studies (ii) the pub-1182 VOLUME 39 | NUMBER 10 | OCTOBER 2007 | NATURE GENETICS Figure 1 Accession numbers in dbGaP are created separately for a study and its subordinate objects — phenotype variables, phenotype trait tables, documents and genotype datasets – prefixed phs, phv, pht, phd and phg, respectively.

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SNP Names in dbGaP – BARU Software

  • SNP identifiers are an important means to refer to SNPs
  • The most canonical form of SNP identifier is rs-code, provided by dbSNP.
  • Unfortunately, in genotypic files provided by dbGaP, SNPs are identified by various means, and virtually none of them are convenient.To understand why it happens, one needs to learn a bit more how SNPs obtain final identifiers, and what intermediate

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dbGaP: Renew Authorized Access

This short video walks through the steps to renew authorized access for a dbGaP project.

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NCBI Insights : Database of Genotypes and Phenotypes (dbGaP)

  • The submissions made to dbGaP represent the best and latest research in topic areas such as cardiovascular diseases, diabetes, autism spectrum disorders, precision medicine and many more
  • Submitters are central to the success of dbGaP and sharing of genomic research across the broader scientific community.

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NCBI Insights : View GEO, SRA, or dbGaP data tracks in

  • Data tracks from dbGaP display significantly-associated SNPs as a scatterplot, with the color and Y-axis position of SNPs corresponding to the P-value in the selected GWAS study (Figure 4)
  • Refer to the complete Legends for the NCBI graphical viewers for more information on the visual rendering of the data in these tracks and how to configure

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fastq-dump issue after dbGaP download · Issue #510 · ncbi

Hey, I recently got access to data on dbGaP, followed the instructions for downloading and decrypting (although by the output I got it looks like decrypting wasn't necessary), I then tried to u

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Embargo dates for dbGaP datasets UCSF Office of

  • Embargo release dates are provided in several places: (1) the public dbGaP home page's list of studies; (2) the public dbGaP summary pages for each study; and (3) file download manifests that accompany each authorized-use data download
  • We strongly urge anyone working with dbGaP datasets to review the embargo dates associated with each dataset

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NCBI Insights : Nov 3 Webinar: dbGaP submission

  • 4 hours ago · Attention dbGaP submitters! Join us on November 3, 2021 at 12PM US eastern time learn about data submission and processing improvements to dbGaP, NIH's database of Genotype and Phenotype, which contains individual-level data associated with human research studies
  • You will see how we have made submission easier through the Submission Portal using automated preliminary …

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dbGaP Request Procedures to Access Individual-Level Data

dbGaP Request Procedures to Access Individual-Level Data Developed and operated by the National Library of Medicine’s National Center for Biotechnology Information (NCBI), dbGaP archives and distributes data from studies that have investigated the relationship between phenotype and genotype, such as genome-wide association studies (GWAS).

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fasterq-dump works for protected dbGaP data

  • I have been trying to download protected dbGaP data via an aws instance and am experiencing extremely slow download speeds
  • I have tried using a variety of instances (with different download speeds, the fastest reported is 25MBPS) but its taking at least 40 minutes per SRR ID (which seems really slow to me).

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We need your input: dbGaP Data Submission and Access Process

  • dbGaP is a controlled-access data repository that serves as a central portal to submit, locate and request access to genomic and associated phenotypic data
  • It is a valuable and rapidly growing resource with over 750 studies available for access, representing over 1.2 million unique research participants
  • Users of dbGaP have access to a wide

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How to Access NHLBI Data NHLBI, NIH

  • The dbGaP data request process is outlined in this video
  • NHLBI encourages exploration of the NHLBI Big Data Analysis Heart Failure Challenge Data Collection
  • The collection is a helpful list of NHLBI-funded dbGaP datasets with data use limitations fitting the scope of the Challenge.

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dbGaP Job Submission

  • Group membership for dbgap, dbg_PiLastName, dbg_import, dbg_export along with SLURM associations are required for working with dbGaP.
  • Step 2: Understand the dbGaP Data Hierarchy The native GPFS file system (Home, Scratch, Data, Runtime) will be read-only access
  • All dbGaP related work must be done in the /dbGaP root directory
  • The /dbGaP directory has two sub-directories data & …

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The NCBI dbGaP database of genotypes and phenotypes

  • dbGaP is a general repository for studies examining the association between phenotype and genotype
  • At the time of writing, dbGaP has 12 public studies at various stages of completion

Nature.com   DA: 14 PA: 21 MOZ Rank: 62

Epigenomics Data Access Policies National Institute on

  • Requesters should access the data via the dbGaP home page (dbGaP - NCBI site)
  • Although dbGaP was primarily created for genome-wide association study data (phenotype and genotype), it is readily adaptable to handling phenotype and sequence data as well.

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ATA SE ERTIFICATION AGREEMENT (April 19, 2019, version)

  • Genotypes and Phenotypes (dbGaP) is subject to the requirements of section 301(d) of the Public Health Service Act (42 U.S.C
  • Moreover, as of October 1, 2017 dbGaP is required to adhere to the NIH Policy for Issuing Certificates of Confidentiality (NOT-OD-17-109)
  • Therefore, Approved Users of dbGaP,

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Overlap for CU607082.17 and CU611050.13

  • CU607082.17 : - : 2000..1 CU611050.13 : - : 36933..34934 Mismatches = 0, Gaps = 0, Length = 2000 Percent identity = 100% Score = 3965 bits (2000), Expect = 0 4 BAC and 4 Fosmid bridging clones
  • 4 BAC and 4 Fosmid concordant clones
  • 0 BAC and 0 Fosmid discordant clones.

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Submission Portal NCBI NLM NIH

  • Submit nucleotide sequences from any organism, including mRNA, genomic DNA, organelle, ncRNA, plasmids, other viruses, phages and synthetic constructs
  • Microarray data from clinical studies that require controlled access
  • Information on human sequence variation and relationship to human health

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Barbara Thomas, Ph.D.

  • Barbara Thomas is the Scientific Review Officer and Executive Director of the NIH Center for Inherited Disease Research (CIDR), a trans-NIH program that provides access to high throughput genotyping and next-generation sequencing services to NIH funded investigators through a contract with Johns Hopkins University.Dr
  • Thomas is involved with all aspects of the program, …

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Register in eRA Commons eRA

  • A university or organization is required to register in eRA Commons to electronically submit a grant application
  • Only individuals with legal signing authority at the university or organization (e.g., CEO, Dean)—known as signing officials (SOs)—can register their organizations.

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HCP Releases SNP Genotypes collected for HCP-Young Adult

The dbGaP data comprises array and imputed genotyping and a limited number of phenotypic variables (self reported sex, age, twin status, and family IDs) collected for 1142 of our 1206 released HCP-YA participants, including 149 pairs of genetically-confirmed monozygotic twins (298 participants) and 94 pairs of genetically-confirmed dizygotic

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dbGaP Access Instructions NHLBI Grand Opportunity Exome

  • Please see instructions and reference materials below for accessing ESP data in dbGaP: Step-by-step instructions for modifying an existing data access request (DAR) to include ESP datasets released to dbGaP proper (dbGaP DAR Modification 112211.ppt).

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Analysis Commons

  • The Analysis Commons is a cloud-computing environment that combines data from multiple sources and provides analysis access to a wide-range of analysts and developers
  • Each study uploads phenotype, genotype or other -omics data
  • Both genetic data and phenotypic data are harmonized and pooled into joint data sets.

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Domain Expiry Date Updated

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Spheris.com 314 days leftCSC Corporate Domains, Inc.A2 Hosting, Inc.
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