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Bioinformatics
06/27/2024 - In this in-person session, participants will have an opportunity to discuss their own research and use of Qiagen products with Qiagen scientists. Note on Technology Participants are expected to bring Read More...
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Bioinformatics
Introduction to Qiagen Ingenuity Pathway Analysis Lesson objective In this lesson, we will continue to le arn about pathway analysis using the Qiagen Ingenuity Pathway Analysis(IPA) package. This class will be taught by Qiagen Read More...
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QIAGEN Ingenuity Pathway Analysis (IPA) works with differential expression data (NGS, microarray, proteomics, and others) or genetic variant data to extract various biological insights. QIAGEN Ingenuity Pathway Analysis (IPA) High Impact Features and Functionality in Read More...
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Bioinformatics
10/23/2024 - Please send any questions and/or specific topic areas that you’re interested in hearing about for this presentation by Friday, 10/18 to Kayla Strauss . QIAGEN Ingenuity Pathway Analysis (IPA) is the leading Read More...
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Bioinformatics
10/23/2023 - QIAGEN Ingenuity Pathway Analysis (IPA) is the leading pathway analysis application among the life science research community and is cited in tens of thousands of articles for the analysis, integration and interpretation of data Read More...
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Bioinformatics
10/21/2021 - Announcing a FREE 30 day TRIAL to Qiagen IPA's Land Explorer (an add-on to the existing NCI Qiagen IPA license). If you are interested in access to the FREE TRIAL, please register for this Read More...
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Bioinformatics
11/19/2020 - Recording Link QIAGEN’s Ingenuity Pathway Analysis (IPA) allows for quick and easy biological interpretation using the results of your RNA-Seq differential expression analyses. IPA’s functionality is tied to an extensive, rich set Read More...
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Bioinformatics
05/28/2020 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
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Bioinformatics
QIAGEN CLC Genomics Workbench is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and next generation sequencing (NGS) analysis. CLC genomics workbench functionality includes: Analysis of your NGS data, Read More...
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Bioinformatics
QIAGEN CLC Genomics Workbench is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and next generation sequencing (NGS) analysis. CLC genomics workbench functionality includes: Analysis of your NGS data, Read More...
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QIAGEN CLC Workbench is a user-friendly solution for DNA, RNA and protein data sequence analysis. It houses tools for molecular biology and next generation sequencing (NGS) data analysis. QIAGEN CLC Genomics Workbench The CLC Genomics Read More...
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Bioinformatics
12/12/2024 - This class will introduce bulk RNA sequencing analysis using Qiagen software. Participants will learn how to process FASTQ files and obtain differential expression using CLC Genomics Workbench as well as extract biological insight using Read More...
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Bioinformatics
Notes: PANTHER DAVID Qiagen IPA - more detailed R Bioconductor clusterProfiler GSVA goseq GOexpress (for GO annotation) pathview EGSEA seqGSEA CRAN GANPA GOxploreR geneset GSEA, GSVA, ORA https://www.rna-seqblog.com/blitzgsea-efficient-computation-of-gene-set-enrichment-analysis-in-python/ https://github.com/ Read More...
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Bioinformatics
07/17/2019 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in >16,000 Read More...
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Bioinformatics
09/19/2024 - Qiagen Ingenuity Pathway Analysis (IPA) is a point-and-click software that enables scientists to discern how genomic, transcriptomic, proteomic, and metabolomic changes influence molecular biology pathways and networks. This software is available to NCI investigators, Read More...
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Bioinformatics
08/15/2024 - Qiagen’s CLC Genomics Workbench is a point-and-click software for analyzing multi-omics sequencing data including variant analysis, RNA sequencing, and ChIP sequencing. This class will demonstrate variant analysis using this software. Participants will be Read More...
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Bioinformatics
07/18/2024 - Long read sequencing holds an advantage over short read sequencing in areas such as structural variant and transcript isoform discovery. This class will demonstrate long read analysis using Qiagen’s CLC Genomics Workbench, a Read More...
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Bioinformatics
06/13/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...
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Bioinformatics
05/16/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...
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Bioinformatics
We are using the datasets below in the Qiagen IPA course. Human Brain Reference (HBR) and Univeral Human Reference (UHR) dataset Using this for the one hour lecture (from 1 - 2 pm) Find more information about Read More...
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Bioinformatics
04/20/2022 - Qiagen IPA Land Explorer links out to the OmicSoft “Land” collections of disease-relevant datasets (>500,000 samples) directly from within IPA to: Explore sample-level data expression, variation, fusions, and more from 500,000+ datasets Explore full Read More...
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Bioinformatics
10/12/2018 - QIAGEN’s Ingenuity Variant Analysis (IVA) combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based on published Read More...
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Bioinformatics
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Bioinformatics
12/08/2022 - Learn how to leverage Activity Plot, Pattern Search, Comparison Analysis, Analysis Match and Land Explorer. Speaker: Shawn Prince Field Application Scientist
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Bioinformatics
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Bioinformatics
08/31/2022 - Users will learn how to: • Upload their dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) and perform interactive core/pathway analysis in IPA • Understand the different result types produced (pathways, key regulators, impact on biological Read More...
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Bioinformatics
Web Page
Bioinformatics
License type: CCR wide you must submit a request through service.cancer.gov to obtain access to CLC Genomics Workbench. This software requires access to a floating license server (three simultaneous users), and so care Read More...
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Bioinformatics
In this lesson, we will continue to le arn about pathway analysis using the Qiagen Ingenuity Pathway Analysis(IPA) package. This class will be taught by Qiagen field application scientist.
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Bioinformatics
Check out additional information on QIAGEN CLC Genomics Workbench, including useful links, in the BTEP Resource pages. For technical support questions, feel free to contact the Qiagen technical support team directly.
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Bioinformatics
Check out additional information on QIAGEN CLC Genomics Workbench, including useful links, in the BTEP Resource pages. For technical support questions, feel free to contact the Qiagen technical support team directly.
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Bioinformatics
10/25/2022 - Qiagen Ingenuity Pathway Analysis (IPA) For modeling, analyzing, and understanding complex 'omics data. During this workshop you will learn how to: • Upload data, run an IPA core analysis and interpret the results • Use IPA Read More...
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Bioinformatics
01/22/2025 - This three hour online training covers QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression. Read More...
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Bioinformatics
Gene Set Enrichment Analysis (GSEA) EnrichmentMap REVIGO (reducing and visualizing gene ontology) Pathview iPathwayGuide (proprietary) Qiagen IPA (proprietary, CCR license) Qlucore (proprietary, CCR license) GeneMANIA CellNetAnalyzer PARADIGM
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Bioinformatics
Module 3: Pathway Analysis Lesson #: Intro to Gene ontology and pathway analysis Discuss what this is Where can we find descriptors geneontology.org organism specific databases What is KEGG? Lesson #: More on ORA, GSEA, GSVA pros Read More...
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Bioinformatics
02/11/2021 - Register QIAGEN’s Ingenuity Variant Analysis (IVA) has been replaced by QIAGEN Clinical Insight Interpret – Translational (QCII-T), which combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling 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
Below is a list of licensed software available for use by CCR Researchers. Linked software pages include a brief description of each software, recommendations, things to know, input data types, output data types, access information, Read More...
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Bioinformatics
IPA and CLC Genomics Workbench are both Qiagen products, which allows us to more easily extract biological insight from analysis. For this reason, it is beneficial to use these two packages together.
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Bioinformatics
Qiagen IPA comes with extensive help documentations, tutorials, and video tutorials.
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Bioinformatics
Qlucore Omics Explorer does not perform upstream tasks in Next Generation Sequencing such as quality control, read mapping, or deriving gene expression counts. Use Partek Flow, Qiagen CLC Genomics Workbench, or Geneious Prime.
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Bioinformatics
Slides: QIAGEN CLC Genomics Workbench
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Bioinformatics
Slides: QIAGEN CLC Genomics Workbench
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Bioinformatics
Announcements are in the form of "news", including updated information about online learning resource licenses (Coursera, Dataquest) and available NGS analysis software packages (Partek Flow, Qlucore, Qiagen, etc.), and "bulletins". The Read More...
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Bioinformatics
Documentation for the CLC Genomics Workbench is available under the Help tab in the software. For the CLC Genomics Workbench manual, click here. Additionally, there are tutorials available for different workflows. Finally, Qiagen hosts webinars Read More...
Bethesda, MD
Collaborative
The goals of the Bioinformatics Training and Education Program within NCI/CCR are: To make researchers aware of the bioinformatics resources available to them, To provide training and guidance on these resources regularly and at Read More...
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NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, Read More...
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Bioinformatics
02/22/2024 - Join us for an introduction to bioinformatics resources for NCI CCR researchers. Featuring: NIH Bioinformatics Calendar Programming Classes (R, Unix, Python) Class documentation Website resources working on high performance compute cluster (Biowulf/Helix) Next-Gen Read More...
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Bioinformatics
Work through DNAnexus? Find a nice cancer data set for 16S and shotgun Divide into two workshops or courses? Course structure or workshop structure? Amplicon processing and analysis (5 week course) (4 weeks) 1. Talk by Greg Caparaso? 1. Read More...
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Bioinformatics
Microbiome Course Course Outline Work through DNAnexus? Find a nice cancer data set for 16S and shotgun Divide into two workshops or courses? Course structure or workshop structure? Amplicon processing and analysis (5 week course) (4 weeks) 1. Read More...
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Bioinformatics
12/07/2023 - This hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA) and CLC Genomics Workbench tools, which are available to access from the NIH Library. IPA can be used identify biological relationships, mechanisms, pathways, functions, Read More...
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Bioinformatics
NCI scientists have many choices available to them for bioinformatic analyses of Next Generation Sequencing (NGS) data. While some require expertise in programming, others provide a more user-friendly, point-and-click interface. These options include programs for Read More...
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Bioinformatics
on the front page is the NIH Bioinformatics Calendar (search by topic, or organizer, info on current, future and past events) Licenses are available to online learning platforms (Dataquest and Coursera), where you can learn Read More...
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Bioinformatics
statistically evaluates the fraction of genes in a particular pathway found among the set of genes showing changes in expression --- Khatri et al. 2012 From this, ORA determines which pathways are over or under represented Read More...
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Bioinformatics
Lessons focus on gene ontology and pathway analysis. Lesson 17: Introduction to gene ontology and pathway analysis ( Recording ) Lesson 18: Functional enrichment with DAVID ( Recording ) Lesson 19: Pathway analysis with Qiagen IPA ( Recording ) Lesson 20: Review and Course Wrap-up ( Read More...
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Bioinformatics
Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr https://maayanlab.cloud/Enrichr/ Other Types Read More...
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Bioinformatics
Thus far we have: Learned how to interact with our computer via command line. Downloaded raw RNA-Seq data (.fastq files). Examined raw data quality using fastqc and multiqc . Performed adapter and quality trimming using Trimmomatic . Read More...
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Bioinformatics
06/15/2023 - Are you interested in analyzing your own data, but you lack coding experience? No problem. There are several proprietary -omics solutions available to researchers within the Center for Cancer Research (CCR). If you have Read More...
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Bioinformatics
02/28/2023 - This class, hosted by the Center for Biomedical Informatics & Information Technology (CBIIT) will provide refresher training for the Qiagen Ingenuity Pathway Analysis (IPA) package. The class is two hours long Read More...
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Bioinformatics
01/12/2023 - Join us for an introduction to bioinformatics resources for NCI CCR researchers. We will look at the information available on the BTEP website, such as the: NIH Bioinformatics Calendar Training opportunities Upcoming events New Read More...
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Bioinformatics
11/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
Web Page
Bioinformatics
09/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
Web Page
Bioinformatics
09/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
Web Page
Bioinformatics
06/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
Web Page
Bioinformatics
02/07/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
Web Page
Bioinformatics
09/01/2021 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...
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Bioinformatics
05/19/2021 - Register Description: IPA’s Analysis Match Explorer was launched in March 2020 and this upgrade is being evaluated for purchase by NCI. NCI scientists will have no-charge access to Analysis Match Explorer for a limited Read More...
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Bioinformatics
04/28/2021 - Register Session Description QIAGEN’s CLC Genomics Workbench enables researchers to analyze Next Generation Sequencing (NGS) data without the use of command line and is a powerful tool for processing microbial data. In this Read More...
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Bioinformatics
04/21/2021 - Registration Session Description QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression and for variant calling. In Read More...
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Bioinformatics
04/14/2021 - Register Session Description Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited Read More...
Web Page
Bioinformatics
11/05/2020 - Register Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens Read More...
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Bioinformatics
10/07/2020 - QIAGEN’s Ingenuity Variant Analysis (IVA) combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based on published Read More...
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Bioinformatics
06/03/2020 - QIAGEN’s CLC Biomedical Genomics Workbench enables researchers to analyze NGS data without the use of command line. In this workshop, we will cover RNA-Seq and variant calling as applicable to human and other Read More...
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Bioinformatics
You must submit a request through service.cancer.gov to obtain access to Qiagen IPA. This software requires access to a floating license server, and so care should be taken to return licenses when the Read More...
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Bioinformatics
CLC Genomics Workbench and Ingenuity Pathway Analysis (IPA) are developed by Qiagen. Results from CLC Genomics can be imported to IPA for pathways analysis. The combination of CLC Genomics Workbench and IPA allows us to Read More...
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Bioinformatics
Gene Set Enrichment Analysis (GSEA) EnrichmentMap REVIGO (reducing and visualizing gene ontology) Pathview iPathwayGuide (proprietary) Qiagen IPA (proprietary, CCR license) Qlucore (proprietary, CCR license) GeneMANIA CellNetAnalyzer PARADIGM
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Bioinformatics
Geneious Prime can not be used for epigenetic analysis. Please see Partek Flow or CLC Genomics Workbench for this functionality. This package does not support pathway or gene ontology analyses. Please see Partek Flow, Partek Read More...
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Bioinformatics
Ingenuity Pathway Analysis (IPA) (Qiagen) IPA works with differential expression data (derived from RNA sequencing, miRNA sequencing, microarray, proteomics, phosphoproteomics, or metabolomics) or genetic variant data to extract various biological insights. {{Sdet}}{{Ssum}}Listing of Read More...
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Bioinformatics
CLC Genomics Workbench (Qiagen) is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and Next Generation Sequencing (NGS) analysis (see Listing of Analysis Functions below). {{Sdet}}{{Ssum}}Listing of Read More...
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Bioinformatics
Analyzing your data WITHOUT coding experience: Bioinformatics Licensed Software is a two-hour event featuring four guest speakers from popular commercial software accessible by individuals affiliated with the Center for Cancer Research (CCR). Guest speakers will Read More...
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Bioinformatics
{{Sdet}}{{Ssum}}Pathway, network, and gene ontology{{Esum}} Partek Flow What file types can I start my analysis with? FASTQ BAM TXT Partek Genomics Suite What file types can I start my analysis with? BAM Read More...
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Bioinformatics
statistically evaluates the fraction of genes in a particular pathway found among the set of genes showing changes in expression --- Khatri et al. 2012 From this, ORA determines which pathways are over or under represented Read More...
Frederick, MD
Core Facility
The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...
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The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management Read More...
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Bioinformatics
01/08/2025 - This three hour online training will focus on getting started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) . IPA enables you to quickly identify biological relationships, mechanisms, pathways, functions and Read More...
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Bioinformatics
Resources Tertiary Analysis - Biological Meaning Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr Read More...
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Bioinformatics
Bioinformatics for Beginners: RNA-Seq Course Description: This course was designed to teach the basic skills needed for bioinformatics, including working on the Unix command line. This course primarily focuses on RNA-Seq analysis. All steps of Read More...
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Bioinformatics
Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...
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Bioinformatics
A common question posed to the Bioinformatics Training and Education Program (BTEP) is “How can I learn R and Python to analyze my data?”. First, it’s important to state that learning any programming language Read More...
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Bioinformatics
07/26/2022 - Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m62ed494c9292a59c0f158b2c60f08263 Join us for an introduction to bioinformatics resources for NCI CCR researchers. We will look Read More...
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Bioinformatics
05/20/2020 - Advances in technology have reduced the cost of single cell sequencing, opening the doors to many new areas of study including transcriptome, DNA genomics, epigenomics and microbial systems. This workshop, provided by experts from Read More...
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Bioinformatics
NIH Bioinformatics Calendar, sponsored by the NCI CCR Bioinformatics Training and Education Program (BTEP), contains information on all bioinformatics (and some data science) trainings/ presentations/ classes offered on the NIH campus. BTEP Distinguished Speakers Seminar Read More...
Frederick, Maryland
Core Facility
CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...
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Bioinformatics
Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...
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Bioinformatics
Gene ontology and pathway analysis Objectives Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway Read More...
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Bioinformatics
Syllabus for “Bioinformatics for Beginners" Instructors: Co-Instructors: To participate in these courses, you need a computer, reliable internet connection and a web browser. All classes and help sessions will be held online. This class Read More...
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Bioinformatics
Course Wrap-up This lesson concludes the Bioinformatics for Beginners course series. Please email us any time at ncibtep@nih.gov for help with your bioinformatics questions or concerns. Lesson Objectives Short course overview. Review BTEP 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
03/18/2015 - This workshop will cover basics of exome-seq analysis including downstream interpretation of variants using a variety of open-source and commercial webtools (Golden Helix, IGV, Ingenuity Variant Analysis, GeneGrid (Genomatix), MuPit/Cravat). Day 1 - AM (9:30 Read More...