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DNANEXUS
View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
DNANEXUS
Come work with us! View open positions with our team.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_job_id (dxid): """:param dxid: ID of a job:type dxid: string Sets the ID of the running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment, but wish to test it outside of an actual Execution Environment. """ global JOB_ID JOB_ID = DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCT OVERVIEWBLOGCHARGE PROJECT The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.DNANEXUS
View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
DNANEXUS
Come work with us! View open positions with our team.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_job_id (dxid): """:param dxid: ID of a job:type dxid: string Sets the ID of the running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment, but wish to test it outside of an actual Execution Environment. """ global JOB_ID JOB_ID =DNANEXUS
View our products for multi-omics data exploration and NGS analysis DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform throughDNANEXUS
Come work with us! View open positions with our team.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the US DASH EXAMPLE WEB APP This is an example web app made with Dash, which in turn uses Flask underneath. View full source code on GitHub COMPARISON OF BGISEQ 500 TO ILLUMINA NOVASEQ DATA Comparison of BGISEQ 500 to Illumina NovaSeq Data. Last Thursday, BGI uploaded three WGS data sets of NA12878/HG001. Included in this was a challenge to conduct a side-by-side analysis. Albert Villela of Cambridge Epigenetix drew our attention to this dataset. Given our love of benchmarking and new technologies, we applied our evaluation SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects areLOADING PLATFORM...
Loading Platform
DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.DNANEXUS
View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine.DNANEXUS
View our products for multi-omics data exploration and NGS analysis OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products. SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
DNANEXUS
Come work with us! View open positions with our team.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in the SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_job_id (dxid): """:param dxid: ID of a job:type dxid: string Sets the ID of the running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment, but wish to test it outside of an actual Execution Environment. """ global JOB_ID JOB_ID =DNANEXUS
View our products for multi-omics data exploration and NGS analysis DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform throughDNANEXUS
Come work with us! View open positions with our team. HUMAN REFERENCE GENOMES The Human Genome Project set out to identify the sequences of these 25 distinct DNA entities (chromosomes 1 through 22, chromosomes X and Y, and the mitochondria), aka "the human genome". In February of 2009, the Genome Reference Consortium (GRC) released "build 37" of the human genome, called GRCh37.In 2013, the GRC released a newer "build 38" of the human genome, called GRCh38. GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the USLOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.ASSOCIATION BROWSER
Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation(Manhattan
DASH EXAMPLE WEB APP This is an example web app made with Dash, which in turn uses Flask underneath. View full source code on GitHub SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
LOADING PLATFORM...
Loading Platform
DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in theLOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.VCF PREPROCESSING
The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATION Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in theLOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.VCF PREPROCESSING
The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform throughDNANEXUS
We're building a world-class team of innovators to harness cutting-edge science to solve the future's most important data problems in precision medicine.DNANEXUS
Come work with us! View open positions with our team.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.EOL DOCUMENTATION
End-of-life (EOL) documentation for products and tools that are no longer supported will be linked from the menu on the left.SINGLE SIGN-ON
To use the command line with an SSO-enabled account, first create an API token on the DNAnexus Platform website. Click on the user name and navigate to the Profile, then click API Tokens and create a new token. Then specify the token on the command line using dx login --token TOKEN. How do users register their SSO accounts on DNAnexus for the GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the USASSOCIATION BROWSER
Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation(Manhattan
SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUSINCDNANEXUS REVENUE
Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in theLOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.VCF PREPROCESSING
The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUSINCDNANEXUS REVENUE
Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in theLOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.VCF PREPROCESSING
The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform throughDNANEXUS
We're building a world-class team of innovators to harness cutting-edge science to solve the future's most important data problems in precision medicine.DNANEXUS
Come work with us! View open positions with our team.LOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.EOL DOCUMENTATION
End-of-life (EOL) documentation for products and tools that are no longer supported will be linked from the menu on the left.SINGLE SIGN-ON
To use the command line with an SSO-enabled account, first create an API token on the DNAnexus Platform website. Click on the user name and navigate to the Profile, then click API Tokens and create a new token. Then specify the token on the command line using dx login --token TOKEN. How do users register their SSO accounts on DNAnexus for the GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the USASSOCIATION BROWSER
Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation(Manhattan
SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
The world’s most secure cloud platform & global network for scientific collaboration & accelerated discovery in genomic, multiomic, & precision medicine. OVERVIEW - DNANEXUS DOCUMENTATIONDNANEXUS APIDNANEXUS DRAGENDNANEXUSINCDNANEXUS REVENUE
Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in theLOADING PLATFORM...
Cookies allow us to enable third-party services and analytics to deliver essential site functionalities and improve our products.VCF PREPROCESSING
The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP SPARK CLUSTER ENABLED DXJUPYTERLAB The Spark cluster app is a Docker-based app which runs the JupyterLab server in a Docker container. The JupyterLab instance runs on port 443. Because it is an HTTPS app, you can bring up the JupyterLab environment in a web browser using the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the job that runs the app.. The script run at the instantiation of thecontainer, /opt
SAIGE GWAS WALKTHROUGH SAIGE is a Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016) implemented as an R package. It accounts for sample relatedness, provides accurate P-values even when case-control ratios are extremely unbalanced, and can be used for genetic association tests in large cohorts with more than 400,000individuals.
COHORT BROWSER (LEGACY) Researchers can bring their data to the Platform and leverage DNAnexus apps to ingest the data into queryable databases. These databases can then be explored using the Cohort Browser. Scientists can filter the set of samples by any field within the dataset and save these filtered samples as cohort objects. SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DNANEXUSLOADING PLATFORMDEVELOPER RESOURCESSIGN UPPRODUCTOVERVIEWBLOGCAREERS
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Create and share reusable pipelines, applications for analyzing data, custom viewers, and workflows. This section is targeted towards organizational leads who have the permission to enable others to use DNAnexus for scientific purposes. Operations include managing organization permissions, billing, and authentication to the platform.AUTHENTICATION
Authentication. DNAnexus uses OAuth2 authentication, and (unless otherwise noted) API calls are considered protected resources to which requests need to be authenticated. Clients must make authenticated requests with a "bearer token" using the "Authorization" request header field with the "Bearer" HTTP authorization scheme, like in theLOADING PLATFORM...
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The VCF loader annotation step annotates the pVCF in a distributed, massively parallel way. Note that the VCF loader does not persist the intermediate, annotated pVCF as a file, so if you want to have access to the annotated file up front, you should annotate it yourself. DASH EXAMPLE WEB APP DOWNLOADS - DNANEXUS DOCUMENTATION The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform. Our SDK is released under the Apache v2.0 license.. Note: If you plan to do most of your interaction with the platform throughDNANEXUS
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To use the command line with an SSO-enabled account, first create an API token on the DNAnexus Platform website. Click on the user name and navigate to the Profile, then click API Tokens and create a new token. Then specify the token on the command line using dx login --token TOKEN. How do users register their SSO accounts on DNAnexus for the GXP - DNANEXUS DOCUMENTATION GxP offering. The GxP offering provides the “people, process and technology” of the DNAnexus managed components for our Customers to participate in regulated research (GLP), clinical trials (GCP), machine learning (GMLP) and manufacturing processes (GMP) with the regulators in their target countries. While “GxP” refers to the USASSOCIATION BROWSER
Using the Association Browser, you can view results from genome- or phenome-wide association studies (GWAS and PheWAS) as well as associations at the gene level. More specifically, you can do all of the following: Interactively browse through results by Phenotype, Variant location (or RSID), or gene. Explore a visual representation(Manhattan
SQL RUNNER - DNANEXUS DOCUMENTATION The Spark SQL Runner application brings up a Spark cluster and executes your provided list of SQL queries. This is especially useful if you need to perform a sequence repeatedly or if you need to run a complex set of queries. You can vary the size of your cluster to speedup your tasks.
DXPY — DNANEXUS PYTHON BINDINGS DOCUMENTATION def set_project_context (dxid): """:param dxid: Project ID:type dxid: string Sets the project context for a running job warning:: This function is only really useful if you are developing code that will run in and interact with the Execution Environment but wish to test it outside of an actual Execution Environment. It does not change the default data container in which new objects are ; WE'RE SORRY BUT DNA-NEXUS DOESN'T WORK PROPERLY WITHOUT JAVASCRIPT ENABLED. PLEASE ENABLE IT TO CONTINUE.* PRODUCTS
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Case StudyDNAnexus Supports Data Management & Genomic Analysis for a Global Research Consortium Case StudyHow One Pharma Company Advanced Their Drug Discovery &Development Process
Case StudyRapid Whole-Genome Sequencing Decreases Infant Morbidity and Cost of Hospitalization VideoPipeline Evolution at Regeneron Genetics Center ENABLING COLLABORATIVE SCIENCE In collaboration with Microsoft, DNAnexus Portals™forms the
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