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Bioinformatics
09/18/2024 - Frederick National Laboratory Science and Technology Group: Work in Progress Seminar Series presents: “Modernization of Next Generation Sequencing Big Data Analysis Pipelines Leveraging NIH’s on-prem High Performance Computing Cluster … and Cloud.” Meeting ID: 225 592 603 654 Read More...
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Bioinformatics
04/16/2024 - GitHub is a powerful platform for tracking, sharing, and collaborating on software projects of all kinds. Whether you’re a bioinformatics analyst, a software engineer, or a biologist who sometimes codes, GitHub Read More...
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Bioinformatics
04/29/2021 - BTEP_April29_2021 Slides Recording Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external Read More...
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Bioinformatics
CCBR has created (and continues to improve) Bulk-RNAseq, Single Cell RNAseq and DSP Pipelines (see LINKS section) that can be used by users with no coding experience: Use the “Support” link to get access to Read More...
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Bioinformatics
03/13/2020 - Dr. Rommie Amaro from University of California, San Diego covers what scientific workflows and pipeline are, how they can be useful or even critical to science and big data management and presents relevant examples Read More...
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Bioinformatics
03/12/2020 - Dr. Rommie Amaro from University of California, San Diego covers what scientific workflows and pipeline are, how they can be useful or even critical to science and big data management and presents relevant examples Read More...
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Bioinformatics
03/10/2020 - Dr. Rommie Amaro from University of California, San Diego covers what scientific workflows and pipeline are, how they can be useful or even critical to science and big data management and presents relevant examples Read More...
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Bioinformatics
03/09/2020 - Dr. Rommie Amaro from University of California, San Diego covers what scientific workflows and pipeline are, how they can be useful or even critical to science and big data management and presents relevant examples Read More...
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Bioinformatics
04/10/2019 - BTEP Wednesday, April 10, 2019 9:00 am | Eastern Daylight Time (New York, GMT-04:00) | 2 hrs Meeting number (access code): 738 427 711 Meeting password: zPJpWP$6 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked Read More...
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Bioinformatics
12/05/2018 - THIS EVENT HAS BEEN CANCELLED 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked reads works SNVs, copy number variations, structural variants and phasing of the variants from linked read data Read More...
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Bioinformatics
10/26/2018 - 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked reads works SNVs, copy number variations, structural variants and phasing of the variants from linked read data Walk through of 10x Genomics Read More...
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Bioinformatics
This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic Read More...
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Bioinformatics
nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the Read More...
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Bioinformatics
What they forgot to teach you about R usethis package reference Controlling R Startup with .Rprofile, .Renviron, etc. Workflow:projects from R 4 Data Science Introduction to renv Happy Git and GitHub for the useR Building Read More...
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Bioinformatics
Bioconductor is a repository for R packages related to biological data analysis, primarily bioinformatics and computational biology, and as such it is a great place to search for -omics packages and pipelines.
Bethesda, MD
Repositories
Trans NIH Facility
The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...
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Bioinformatics
04/09/2025 - Please note: Registration is required to get the Meeting Link for this event. Please pre-register. The Human Tumor Atlas Network (HTAN) is a National Cancer Institute (NCI)-funded initiative to construct 3-dimensional atlases of Read More...
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Bioinformatics
12/17/2024 - In this one-hour session we will describe resources available to NIH researchers for performing bioinformatics data analysis. These include trainings by specific groups or institutes (NCI, NIH Library, ODSS), licenses available for online learning ( Read More...
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Bioinformatics
12/11/2024 - This session of the BTEP Coding Club introduces NIH CloudLab, a free 90-day sandbox environment partnered with AWS, Google Cloud, and Azure, and demonstrates how to run Nextflow pipelines, a powerful workflow management system Read More...
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Bioinformatics
07/23/2024 - In this presentation, we will demonstrate how to use enterprise data science platform to configure, run, share, and scale downstream bioinformatics and image analysis pipelines using cloud and HPC resources. This session is geared Read More...
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Bioinformatics
The Bioinformatics Training and Education Program is happy to announce open office hours. The BTEP team will be available virtually via Microsoft Teams to help you with your bioinformatics questions / problems from 1 PM to 3 PM , Read More...
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Bioinformatics
Bioconductor is both an open source project and repository for R packages related to the analysis of biological data, primarily bioinformatics and computational biology, and as such it is a great place to search for Read More...
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Bioinformatics
Bioconductor is a repository for R packages related to biological data analysis, primarily bioinformatics and computational biology, and as such it is a great place to search for -omics packages and pipelines. Bioconductor packages fit Read More...
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Bioinformatics
Again, rarefaction is used to eliminate issues due to differences in library size prior to beta diversity. This method is built-in to QIIME 2 core metrics pipelines. We can examine the stability of a beta diversity Read More...
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Bioinformatics
Additional Resources HPC Biowulf Resources Biowulf User Guide R/Bioconductor on Biowulf R on Biowulf Training by the HPC team Other Resources What they forgot to teach you about R usethis package reference Controlling R Read More...
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Bioinformatics
A repository for R packages related to biological data analysis , primarily bioinformatics and computational biology. a great place to search for -omics packages and pipelines. Released every 6 months and work with a specific version of Read More...
Web Page
Bioinformatics
A repository for R packages related to biological data analysis , primarily bioinformatics and computational biology. a great place to search for -omics packages and pipelines. Released every 6 months and work with a specific version of Read More...
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Bioinformatics
Bash Most of bioinformatics can be done by understanding specific software applications and running those applications in a pipeline, usually using some form of bash scripting. Bash as a scripting language is fairly important for Read More...
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Bioinformatics
Bash Most of bioinformatics can be done by understanding specific software applications and running those applications in a pipeline, usually using some form of bash scripting. Bash as a scripting language is fairly important for Read More...
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Bioinformatics
01/31/2023 - WebMeV was designed to address the hurdles present for wet lab scientists using Bioinformatics tools. RNASeq tools and pipelines have become robust and standardized. WebMeV leverages this fact to provide a simple, fully graphical, Read More...
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Bioinformatics
11/14/2022 - During this webinar, the Genomic Data Commons ’ (GDC’s) Drs. Zhenyu Zhang and Bill Wysocki will review the different types of harmonized data that the GDC makes available for the cancer research community. The Read More...
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Bioinformatics
11/10/2022 - Join Google’s Marcos Novaes, Ph.D., as he presents on the design of large-scale solutions for high-performance computing, machine learning, and the internet of things using the Google Cloud Platform. Dr. Norvaes will Read More...
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Bioinformatics
06/24/2022 - RStudio Team is a data science platform that allows data scientists to develop and share data science pipelines with collaborators. In this presentation, RStudio will highlight the basic functionalities of the platform to provide Read More...
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Bioinformatics
06/10/2022 - Join the upcoming NCI Containers and Workflows Interest Group (CWIG) webinar to learn about the research and functionality available through the University of California, San Francisco’s (UCSF) Information Commons. As an open-source platform, Read More...
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Bioinformatics
06/06/2022 - Are you a cancer researcher or bioinformatician wanting to learn more about how the experts at NCI’s Genomic Data Commons (GDC) process a variety of molecular data types? This month’s GDC support Read More...
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Bioinformatics
04/28/2022 - This webinar will provide a foundation on NCI’s Imaging Data Commons (IDC) and NCI Cloud Resources, components of the cloud-based Cancer Research Data Commons (CRDC). All American Association of Physicists in Medicine (AAPM) Read More...
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Bioinformatics
02/11/2022 - Dr. Jeremy Goecks will share how cancer researchers are using the machine learning capabilities of the Galaxy project, one of the largest and most widely used open-source platforms for biomedical data science , to predict Read More...
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Bioinformatics
10/08/2021 - Dr. Pjotr Prins and Arun Isaac will present their Concise Common Workflow Language (CCWL). CCWL makes code reusable and adaptable across a variety of software and hardware environment while following FAIR+ (Findable, Accessible, Interoperable, Read More...
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Bioinformatics
09/11/2020 - By Avi Ma'ayan, Director of the Mount Sinai Center for Bioinformatics Daniel Clarke, Senior Data Scientist and Nicole Moiseyev, Summer Scholar Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Read More...
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Bioinformatics
08/21/2020 - Abstract: Machine learning (ML) has emerged as an essential tool for building models which can be used to predict clinical outcomes for age-related diseases. A significant challenge of ML is knowing which algorithms and Read More...
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Bioinformatics
06/03/2020 - The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Single-cell analysis of healthy- and SARS-CoV-2-infected tissues offers Read More...
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Bioinformatics
11/04/2019 - This is a hands-on demo, please bring your laptop or let us know if you need to borrow one. The field of genomics has matured to a stage where organizations are sequencing DNA at Read More...
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Bioinformatics
05/24/2019 - BTEP personnel will be available to help answer any questions you might have from our RNA-Seq lectures earlier this week. Check out RNA-Seq pipelines available to CCR researchers Also - Get help working at Read More...
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Bioinformatics
04/12/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...
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Bioinformatics
04/11/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...
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Bioinformatics
04/09/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...
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Bioinformatics
11/14/2018 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...
Web Page
Bioinformatics
10/12/2018 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...
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Bioinformatics
06/26/2018 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. A point-and-click web environment provides ready access to powerful tools for the analysis, integration Read More...
Web Page
Bioinformatics
DNAnexus provides a secure cloud based platform for the analysis and sharing of next generation sequencing data. This resource allows simplified, secure access to the vast compute resources available via Amazon Web Services (AWS) and Read More...
Rockville, MD
Collaborative
Repositories
The NCI Cloud Resources are components of the NCI Cancer Research Data Commons (CRDC) that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers Read More...
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Confocal
2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...
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Bioinformatics
07/23/2025 - This presentation will explore the next emerging stage where biobanking is characterised by being part of system - Biobanking 4.0. Biobanking has always been about data generation with tissue specimens providing the biological and genomic Read More...
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Bioinformatics
05/19/2025 - Immunotherapy has the potential to revolutionize the way we treat cancer, but a key challenge has been finding ways to tailor that therapy to the right patient at the right time. Attend this webinar, Read More...
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Bioinformatics
12/05/2024 - This one and a half hour online training will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be Read More...
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Bioinformatics
12/03/2024 - This one and a half hour online training will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek Flow Read More...
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Bioinformatics
What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...
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Bioinformatics
07/11/2024 - Please join us for this special event featuring three speakers on the topic of Single-Cell Spatial Transcriptomics. George Zaki, Ph.D., Director, Applied Scientific Computing, BACS, The Frederick National Lab for Cancer Research, NCI/ Read More...
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Bioinformatics
Now that we have loaded the package, we can import our data. Generally, in R programming, functions that involve data import begin with "read / Read". Seurat includes a number of read functions for Read More...
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Bioinformatics
03/05/2024 - This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell Read More...
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Bioinformatics
12/06/2023 - NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform. The NIDAP platform hosts user-friendly bioinformatics workflows (Bulk RNA-Seq, scRNA-Seq, Digital Spatial Profiling) and other component analysis Read More...
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Bioinformatics
11/16/2023 - This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Read More...
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Bioinformatics
06/29/2023 - Please join us for a special presentation about the Fred Hutchinson’s data journal to the cloud, including an innovative cloud platform (Cirro: https://cirro.bio/ ) to streamline data collection, Read More...
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Bioinformatics
Unix, what is it, and why should biologists take the time to learn it? The Unix operating system forms the basis of many bioinformatics analyses resources, such as the NIH High Performance Cluster (HPC) Biowulf/ Read More...
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Bioinformatics
07/08/2022 - In this presentation, Drs. Hutson and Liu will provide a high-level overview of the data, software and model sharing capabilities and strategies developed as part of the Cancer Moonshot Immuno-Oncology Translational Network (IOTN) Data Read More...
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Bioinformatics
05/02/2022 - Federated Learning (FL) has emerged as a potential solution due to its capability in training models without sharing data. To enable effective FL in real applications, a robust communication framework is crucial. Join Drs. Read More...
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Bioinformatics
11/16/2021 - The NCI HALO cloud deployment provides NCI researchers with powerful image management and analysis tools for digital pathology and numerous other 2D imaging applications. Key capabilities include expert user assessment, image archiving, and advanced Read More...
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Bioinformatics
10/15/2021 - This course will introduce you to Google Cloud's big data and machine learning functions. You'll begin with a quick overview of Google Cloud and then dive deeper into its data processing capabilities. Read More...
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Bioinformatics
09/19/2021 - At the Conference on Machine Intelligence in Medical Imaging, NCI Imaging Data Commons (IDC) lead, Dr. Keyvan Farahani, will present NCl's cancer data science resources that support the imaging informatics community. As the Read More...
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Bioinformatics
09/14/2021 - OpenCRAVAT is an open source variant annotation and decision support software to support cancer variant and gene prioritization. It offers both command line functionality and a dynamic biologist-friendly GUI, allowing users to install with Read More...
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Bioinformatics
05/26/2021 - Register This month’s Cancer Genomics Cloud (CGC) webinar welcomes Dr. Wenming Xiao, a lead bioinformatics scientist at the U.S. Food and Drug Administration. Dr. Xiao specializes in researching how computational, technical, and Read More...
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Bioinformatics
03/29/2021 - Register/Join The NCI Genomic Data Commons' (GDC's) upcoming webinar will introduce new users to its portal and library of computational resources. GDC experts will also answer questions about the GDC and genomic Read More...
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Bioinformatics
03/24/2021 - WebEx: Register Accurate detection of somatic mutations is challenging but critical to understanding how cancer forms and progresses. Such detection is also critical for targeting more effective treatments. In this seminar, Dr. Mohammad Sahraeian, Read More...
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Bioinformatics
11/13/2020 - https://ncihub.org/resources/2404 Abstract: In many applications in genomics, large data sets are created and lightly used before being shared with other researchers (ideally) or simply tossed away on hard drives. The Cancer Read More...
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Bioinformatics
09/28/2020 - Register/Join This webinar is intended for cancer researchers and bioinformaticians who are interested in learning more about the NCI Genomic Data Commons’ (GDC’s) bioinformatics pipelines for data harmonization. The GDC DNA-Seq analysis Read More...
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Bioinformatics
09/04/2020 - Speakers: Dave Clements, Galaxy Community Manager, Johns Hopkins University, Steven Weaver, Senior Programmer Analyst, Temple University Galaxy is an open web-based platform for data integration and analysis in the life sciences. Galaxy makes sophisticated Read More...
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Bioinformatics
06/05/2020 - OpenCRAVAT is a an open source, scalable decision support system to support cancer variant and gene prioritization. It offers both command line functionality and a dynamic biologist-friendly GUI, allowing users to install with a Read More...
Web Page
Bioinformatics
01/23/2020 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...
Web Page
Bioinformatics
10/03/2019 - Overview of single cell technologies, analysis workflows, scRNA-seq preprocessing and QC 10:00 – 10:30 AM Introduction to single cell technologies and applications (Mike Kelly) 10:30 – 11:00 AM Overview of single cell transcriptomic analysis workflow and pipelines (Yongmei Zhao) 11:05 – 12:00 PM Read More...
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Bioinformatics
09/26/2019 - Qlucore Omics Explorer is an interactive analysis and visualization tool that helps the user to find groups, structures, variable networks and discriminating variables. You can use your own data and analyze public data. Omics Read More...
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Bioinformatics
11/05/2018 - RNA-seq, expression microarrays, and other omics profiling platforms are powerful tools for discovery, and analytical pipelines often return large numbers of significant genes or other markers. This presents a challenge when trying to understand Read More...
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Bioinformatics
06/27/2017 - NGS Series Open Forum: Meet the Bioinformatics Experts You are invited to a Q & A session with a panel of bioinformatics analysts, most of whom were presenters at the BTEP NGS Workshop Read More...
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Bioinformatics
03/08/2016 - BTEP Workshop on Exome-Seq Data Analysis and Variant Annotation (2-day) This workshop will cover the basics and best practices of exome-seq analysis including downstream interpretation of variants using a variety of in-house, open-source and Read More...
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Bioinformatics
05/07/2013 - This 2 hour seminar will be an interactive discussion and demonstration of the types of applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies ( Read More...
Bethesda, MD
Trans NIH Facility
The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...
Bethesda, MD
Collaborative
Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...
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Confocal
A typical HTI screening project at HiTIF can be subdivided in 5 phases: Pre-Development The investigator contacts the Facility Head to inquire about the current availability of instrumentation time and manpower for the project to be Read More...
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Bioinformatics
General questions or comments about the BTEP program or classes should be addressed to: NCIBTEP@nih.gov Desiree Tillo, Ph.D . Staff Scientist desiree.tillo@nih.gov I have a broad research background in bioinformatics Read More...
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Bioinformatics
Cancer research is a complex and data-intensive field. Cloud computing offers a powerful solution for researchers to store, analyze, and share large datasets efficiently. In this month’s topic spotlight, we will explore cloud resources Read More...
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Bioinformatics
Congratulations, your experiments have been completed and you have a large amount of data. Now, it’s time to analyze these data. But where do you begin? How can you gain the most meaning from Read More...
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Bioinformatics
This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...
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Bioinformatics
Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...
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Bioinformatics
Lesson 6 . Learning Objectives Introduce several beta diversity metrics Discover different ordination methods Learn about statistical methods that are applicable Beta diversity Beta diversity is between sample diversity. This is useful for answering the question, how Read More...
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Bioinformatics
Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To better understand S4 objects as they relate to the Bioconductor core infrastructure. To learn more about a popular Bioconductor S4 Read More...
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Bioinformatics
Below, you will find questions and answers brought up in the course polls for the BTEP Bioinformatics for Beginners course series that took place from September 13th, 2022 to December 13th, 2022. Question 1 : Normalization - when to Read More...
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Bioinformatics
BTEP Bioinformatics for Beginners (September 13th, 2022 - December 13th, 2022) Questions and Answers Below, you will find questions and answers brought up in the course polls for the BTEP Bioinformatics for Beginners course series that took Read More...
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Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
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Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
Web Page
Bioinformatics
Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To generate high quality data reports using R Markdown to make data analysis more reproducible. Reminder: Uploading files from RStudio Server Read More...
Web Page
Bioinformatics
02/20/2020 - Learn how to easily analyze your gene expression data yourself - using Qlucore Omics Explorer NCI/CCR:To get access to Qlucore, put a request into NCI at Your Service under Get Help https:// Read More...
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Bioinformatics
02/21/2017 - This BTEP Workshop will cover the fundamentals and best practices of Exome-Seq analysis, including downstream interpretation of variants using a variety of in-house and NCI-licensed software solutions. There will be hands-on training on CCBR Read More...