Search Results for: TCGA

05/11/2022 - Many new studies include RNA sequencing data. In this webinar we will go through the process of downloading and importing SRA data using the SRA toolkit, how to use an aligner to convert fastq Read More...

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...

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...

Note This is not an exhaustive list. cBioPortal cBioPortal is a platform for exploratory and interactive visualization, analysis, and download of cancer genomics data. With cBioPortal You can quickly view genomic alterations across a set Read More...

Let's look at a more complicated example using the gene_expression data. We can use ggpubr to explore genes of interest. However, in cases where comparisons are more complicated and faceting is used, this Read More...

Scatter plots are useful to visually inspect similarity (correlation) between variables. For example, we can see how closely two replicates from the TCGA lung adenocarcinoma data set correlate. luad<-readr::read_csv(" Read More...

The GDC allows you to perform some analyses on cancer data spanning multiple programs and projects. You can perform similar tasks and other advanced tasks using other data platforms. However, you may want to download Read More...

09/21/2020 - Join Zoom Meeting BIO: Jean Claude Zenklusen was born 1964 in Visp, Switzerland. He earned a Master in Sciences (Biochemistry) from the University of Buenos Aires in 1990. He received his PhD in Cancer Biology & Read More...

Like many large projects, there are variations of data available. Let's clear up some confusion and define the following: Harmonized data Data aligned to GRCh38 and data further proccessed using standard pipelines featuring open-source Read More...

Learners will Discover public resources for accessing, analyzing, and downloading TCGA data. Learn about features of the NCI Genomic Data Commons Data Portal. Understand how to download TCGA data from the GDC.

Data collected for a specific case in TCGA may have differed according to sample quality and quantity, cancer type, or technology available at the time of analysis. --- https://www.cancer.gov/ccg/research/genome-sequencing/ Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

03/13/2024 - Dear Colleagues,    UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations.   Xena showcases seminal cancer genomics datasets from Read More...

08/21/2023 - Xena can help you answer questions like: •    Is over-expression of this gene associated with lower survival in these two cancer types? •    Is this gene differentially expressed in TCGA tumor vs GTEx normal? •    What are Read More...

10/31/2022 - UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as well as Read More...

09/27/2017 - UCSC Xena ( http://xena.ucsc.edu ) is a web-based, visual exploration tool for all modes of multi-omic data and associated annotations. Xena has several seminal cancer datasets pre-loaded and ready for visualization including TCGA, Read More...

06/19/2017 - Harvesting the Wealth of TCGA Data The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA Read More...

The Genomic Data Commons (GDC) is a repository and computational resource for cancer genomic data and associated clinical and related information. The GDC includes data from 22 programs (including TCGA), 83 projects, 69 primary sites, and 44,637 cases. Genomic Read More...

Navigate to the GDC Data Portal at https://portal.gdc.cancer.gov/ To select your cases of interest, you can navigate to "Projects" or "Cohort Builder" Let's use breast cancer Read More...

UCSC Xena Functional Genomics Browser is an open-source, web-based tool for analytics and visualization of viewing the public data hubs. Xena also allows securely analysis and visualization of your private functional genomics data set in Read More...

The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The cBioPortal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, Read More...

05/22/2024 - The ISB-CGC (Cancer Gateway in the Cloud) hosts data from programs such as The Cancer Genome Atlas Program (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) in Google BigQuery where it can be quickly Read More...

02/23/2023 - In this session we will go over a visual, dynamic, and interactive way to work with OMICs data using public leukemia GEO gene expression data sets. We will approach the data with confirmatory and Read More...

10/28/2021 - The Cancer Genomics Cloud (CGC) (link is external) , powered by Seven Bridges, is an NCI-funded resource that provides a unified platform for cancer data analysis by co-localizing three components within the cloud: 1) large cancer Read More...

05/26/2021 - Register Description: This webinar will highlight UCSC Xena's newest features including genome-wide differential gene expression analysis, violin plots, and a simpler way to filter and subgroup. UCSC Xena ( http://xena.ucsc.edu/ ) is Read More...

03/30/2021 - Register Presenter: Yana Stackpole, PhD (Qlucore Training and Support) Description: In this session we will go over a visual, dynamic and interactive way to work with OMICs data using public leukemia GEO gene expression Read More...

12/03/2020 - Register Registration is required to join this event. If you have not registered, please do so now. It has been established that over half of all cancer types are driven by DNA Copy Number Read More...

10/22/2020 - Register Presenter: Dr. Sam Dougaparsad Field Application Scientist It has been established that over half of all cancer types are driven by DNA Copy Number Variants (CNVs). In this presentation, we will demonstrate the Read More...

02/27/2020 - The Annotation, Visualization and Impact Analysis (AVIA) is an application developed to guide, prioritize and summarize genomic variants. AVIA maintains and aggregates dozens of publicly available variant annotation databases and predictions from impact analysis Read More...

ggpubr allows us to easily incorporate additional information into our plots (e.g., mean, individual case information, etc.). Where this package really shines is its ability to easily include the results of common statistical tests. Read More...

Correlation analysis refers to a group of statistical methods used to discover the relationship between two or more variables of interest. Common methods of correlation are included in the table below. Methods R function Description Read More...

January 24, 2024: Documenting Your Data Analysis with Quarto (Recording) February 21, 2024: Version Control Using Github (Recording) March 27, 2024: An Introduction to DAVID for Functional Enrichment Analysis (Recording) May 23, 2024: Version Control Using Git Command Line (Recording) June 18, 2024: Accessing and Read More...

If you are interested in ggpubr, you may find the following tutorials useful: http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/77-facilitating-exploratory-data-visualization-application-to-tcga-genomic-data/. https://malucalle.github.io/statistical-pills/nice-plots-with-r.html. https://documentation1458.rssing.com/chan-49683810/all_p8. Read More...

Nexus Copy Number (BioDiscovery) is a graphical user interface (GUI) based bioinformatics software that specializes in copy number detection using array or sequence derived data. Its analysis capabilities are listed below. {{Sdet}}{{Ssum}}List of Read More...

05/07/2025 - Join Dr. Eytan Ruppin, NCI investigator in the Center for Cancer Research, as he discusses Path2Space, a new and unpublished deep learning approach that predicts spatial gene expression directly from histopathology slides. Spatial Read More...

10/24/2024 - Recent advances in artificial intelligence (AI) have revolutionized the use of hematoxylin and eosin (H&E)-stained tumor slides for precision oncology, enabling data-driven approaches to predict molecular characteristics and therapeutic outcomes. In Read More...

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...

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...

05/09/2023 - T he  C ancer  P roteome  A tlas (TCPA) : a major bioinformatics resource for cancer proteomics data using  reverse-phase protein arrays (RPPAs)   In contrast to the recent exploration of next-generation sequencing at both DNA Read More...

05/02/2023 - T he  C ancer  P roteome  A tlas (TCPA) : a major bioinformatics resource for cancer proteomics data using  reverse-phase protein arrays (RPPAs) In contrast to the recent exploration of next-generation sequencing at both DNA Read More...

01/30/2023 - Are you interested in accessing cancer data from genomics studies? If so, register for this NCI webinar to learn more about the  Genomic Data Commons  (GDC)! University of Chicago’s Dr. Bill Wysocki will Read More...

10/25/2022 - Speaker: Jill S. Barnholtz-Sloan, Ph.D. Associate Director Informatics and Data Science at the Center for Biomedical Informatics and Information Technology Senior Investigator Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, NCI Dr. Read More...

01/07/2022 - Environmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases including lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to Read More...

11/04/2021 - FireCloud (Powered by Terra (link is external) ) is a data analysis platform that contains a system of workspace functionalities centered on data sharing and analysis. Researchers can use FireCloud to perform a variety of Read More...

10/27/2021 - Wrapping up its final webinar of 2021, the NCI Cancer Research Data Commons (CRDC) Cancer Genomics Cloud (CGC) welcomes Cold Spring Harbor Laboratory fellow Dr. Pascal Belleau. He will share his findings from recent work Read More...

10/14/2021 - The  ISB Cancer Gateway in the Cloud (link is external)  (ISB-CGC) offers multiple avenues for accessing and analyzing large-scale cancer datasets, including TCGA, TARGET, CPTAC and important references such as GENCODE and COSMIC. ISB-CGC Read More...

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...

05/14/2021 - Presenter: Sai Lakshmi Subramanian Program Manager, Cancer Genomics Cloud Seven Bridges   Abstract The Cancer Genomics Cloud powered by Seven Bridges (CGC) is a NCI-funded cloud resource that provides a unified platform for Read More...

03/29/2021 - For coming Monday's CDSl webinar, we'll be hosting Dr. Yun Liu from Google Health. Abstract: This talk will briefly cover two categories of our work: deep learning to identify dermatology conditions from Read More...

03/24/2021 - Register/Join At the next Cancer Genome Cloud’s (CGC's) monthly webinar series, NCI Research Fellow, Dr. Xavier Bofill-De Ros, will share his experiences leveraging the NCI Cancer Research Data Commons (CRDC) Cloud Read More...

03/22/2021 - Join Dear NCI Staff, The NCI Cloud Resources are chief components of the NCI Cancer Research Data Commons (CRDC), helping to bring together data and computational power to advance cancer research and discovery. These Read More...

02/17/2021 - Speaker is Dr. Michal Linial from the Hebrew University of Jerusalem, Israel. Abstract: Incredible progress has also been made in the field of cancer genetics with the sequencing and molecular profiling of tens of Read More...

09/25/2020 - NCI Cancer Research Data Commons (CRDC) provides access to large-scale datasets such as The Cancer Genome Atlas (TCGA) that span multiple data types, including genomics, proteomics, imaging, and clinical data. The CRDC offers bioinformatics Read More...

05/19/2020 - UCSC Xena ( xena.ucscedu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as Read More...

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...

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...

02/08/2016 - BTEP Workshop on Data Visualization, Exploration and Analysis NOTE: This is a Bring Your Own Computer (BYOC) class, and will be simultaneously shared via GoToMeeting with attendees at the Advanced Technology Research Facility (ATRF) Read More...

06/02/2015 - This workshop will cover some basic concepts involved in the integration of different types of NGS data in order to obtain a better overall picture of the underlying biology. Specifically, the course will examine Read More...

05/28/2013 - Nexus Copy Number is a user-friendly desktop application for analysis and visualization of structural variation (copy number, allelic events, and small sequence variations) from CGH and SNP array- and NGS-generated data. The simple and Read More...

Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) based package used for -omics data anlaysis. Qlucore Omics Explorer can analyze many types of -omics data that are in tabular format (e.g., RNA Read More...

What is rstatix? rstatix is a package created by Alboukadel Kassambara, the author of ggpubr. The rstatix package includes tidyverse friendly functions for performing various statistical tests. Because functions from rstatix are tidyverse compatible, they Read More...

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...

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...

08/10/2022 - For our next CDSL webinar we will have two fellows’ talks from Dr. Zisha Zhong and Arati Rajeevan . Zisha’s talk details: Title:  Multi-task Feature Learning to train Interpretable Encoders on Histopathology Images Digital Read More...

09/01/2016 - This 2-day workshop, including a BYOD (Bring Your Own Data) exercise, will provide an introduction and hands-on training for Cytoscape, which is an open source software platform for visualizing  networks and integrating these networks Read More...

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...