Frederick, MD
Core Facility
The centrally funded Statistics team within the Advanced Biomedical Computational Science group at the Frederick National Lab provides statistical consultation and data analysis support for NCI laboratories. We have broad-range expertise in biomedically relevant areas Read More...
Bethesda, MD
Core Facility
The Pharmacogenetics Core is responsible for correlating outcome observations (toxicity, efficacy, survival, PK/PD) with genetic variants (germline or somatic) to identify key genetic determinants and biomarkers that predict response to specific treatments. We also Read More...
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Bioinformatics
In this session of the BTEP Coding Club, Duncan Donohue, PhD, Senior Programmer and Analyst with the Statistical Consulting and Scientific Programming Group (ABCS, NCI at Frederick), showed us how to use the R package Read More...
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Bioinformatics
01/15/2025 - This session of the BTEP Coding Club will demonstrate how to use the R package “survival” to conduct a survival analysis of an example dataset. Senior Programmer and Analyst, Duncan Donohue, PhD, will cover Read More...
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Bioinformatics
01/14/2025 - In this talk, we will cover the basics of survival analysis as a statistical methodology developed for censored data. Special emphasis will be on visualizing survival data, comparing survival-time distributions for subject groups, and Read More...
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Bioinformatics
09/29/2022 - An overview of the JPSurv webtool to analyze survival data by year of diagnosis and estimate calendar years when changes in survival have occurred. Covers topics such as the JPsurv model, trend survival measures Read More...
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Bioinformatics
07/09/2025 - This session of the BTEP Coding Club will demonstrate the use of R programming to perform decision tree analysis, survival tree analysis, and random forest. This event complements a Statistics for Lunch event, " Read More...
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Bioinformatics
In this session of the BTEP Coding Club, Brian Luke, PhD, Senior Principal Computational Scientist with the Advanced Biomedical Computational Science (ABCS) group, demonstrated the use of R programming to perform decision tree analysis, survival Read More...
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Bioinformatics
05/19/2022 - THIS EVENT HAS BEEN CANCELLED Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood and are subdivided into three major histomorphologic subtypes: alveolar (ARMS), embryonal (ERMS), or spindle/sclerosing (SSRMS). Patients with Read More...
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Bioinformatics
04/07/2025 - AI Club is a weekly meeting that explores various topics relating to AI and deep learning in biomedical sciences, typically in a seminar, workshop, or journal club format. AI Club is intended to be Read More...
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Bioinformatics
07/08/2025 - Thi pre entation de cribe the ba ic mechanic of con tructing a deci ion tree and interpreting the re ult . Deci ion tree will be u ed to determine factor a ociated with 2 Read More...
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Bioinformatics
For a more detailed background on survival analysis as a statistical methodology, check out this related presentation ("Introduction to Survival Analysis") by Alexander Mitrophanov, PhD.
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Bioinformatics
January 15, 2025: Survival Analysis in R Using the survival Package (Recording) February 19, 2025: Introduction to GitHub Actions for Analysts and Engineers (Recording) March 12, 2025: Clustering with R and RStudio (Recording) March 26th, 2025: Getting Started with HPC OnDemand: A Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
Add a variable to the data frame called age_cat (child = % mutate(age_cat= case_when(Age = 12 & Age = 18 ~ "adult" )) %>% ggplot() + geom_bar(aes(x=age_cat, fill=factor(Sex)), position=position_ Read More...
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Bioinformatics
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...
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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
10/12/2021 - Speaker : Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This Read More...
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Bioinformatics
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...
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Bioinformatics
For a more detailed theoretical background on these topics, check out this related presentation ("Decision Trees, Survival Trees, and Random Forest") also by Brian Luke, Ph.D.
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Bioinformatics
BAM Slicing Download Slice individual BAM files based on the variant, gene, position, or SNPs for individual cases/entities Download unmapped reads from a BAM file Clinical Data Analysis Visualize clinical data with histograms, survival Read More...
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Confocal
2024 Senatorov IS, Bowman J, Jansson KJ, Alilin AN, Capaldo BJ, Lake R, Riba M, Abbey YC, Mcknight C, Zhang X, Raj S, Beshiri ML, Shinn P, Ngyuyen H, Thomas CJ, Corey E, Kelly K. Castrate Read More...
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Bioinformatics
Let's use some other geoms. Plot the number of passengers (a simple count) that survived by ticket class and facet by sex. {{Sdet}} Possible Solution{{Esum}} ggplot(titanic) + geom_bar(aes(x=Pclass, fill= Read More...
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Bioinformatics
This data set provides information on the fate of passengers on the fatal maiden voyage of the ocean liner ‘Titanic’, summarized according to economic status (class), sex, age and survival. --- R Documentation ?Titanic data(& Read More...
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Bioinformatics
03/14/2023 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering classes geared to cover general concepts behind statistics and epidemiology. This five-part lecture series will Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
03/17/2021 - Register/Join The focus of this webinar will be on two aspects of integrative analysis and translational research in the field of estrogen receptor-positive (ER+) breast cancer research. Namely, Dr. Meenakshi Anurag will discuss Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
10/23/2012 - Learn the fundamentals in genomic data analysis of CGH and SNP arrays using BioDiscovery Nexus Copy Number software. In this hands-on training session, you will learn how to load, process, visualize, and analyze array Read More...
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Bioinformatics
ggfortify is an excellent package to consider for easily generating PCA plots. ggfortify provides "unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package Read More...
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Confocal
2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...
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Bioinformatics
04/09/2026 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering several trainings that cover general concepts behind statistics and epidemiology. These trainings will help participants Read More...
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Bioinformatics
12/02/2025 - The SeqSPACE Planning Committee is pleased to announce a two-part webinar series highlighting the work of four junior investigators selected through our recent call for abstracts. Part 1 will feature presentations by Dr. Jing Dong Read More...
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Bioinformatics
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...
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Bioinformatics
03/26/2025 - Developing artificial intelligence (AI) schemes to assist the clinician towards enabling precision medicine approaches requires development of objective markers that are predictive of disease response to treatment or prognostic of longer-term patient survival. The Read More...
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Bioinformatics
03/17/2025 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a several trainings that cover general concepts behind statistics and epidemiology. These trainings will help Read More...
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Bioinformatics
12/03/2024 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering classes geared to cover general concepts behind statistics and epidemiology. This four-part lecture series will Read More...
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Bioinformatics
The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...
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Bioinformatics
12/12/2023 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering classes geared to cover general concepts behind statistics and epidemiology. This four-part lecture series will Read More...
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Bioinformatics
07/24/2023 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering classes geared to cover general concepts behind statistics and epidemiology. This four-part lecture series will Read More...
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Bioinformatics
When you have a lot of colors and you want to keep these colors consistent, you can use the following convenient functions to set a name attribute for a vector of colors. Let's do Read More...
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Bioinformatics
Load the data For these exercises, you will explore the titanic data from kaggle.com , which was downloaded from here . You will need to download the data and load into R. As this is a Read More...
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Bioinformatics
09/07/2022 - In this session of the University of Alabama at Birmingham’s O’Neal Research Seminar Series, CBIIT’s Dr. Jill Barnholtz-Sloan will share how big data has provided insight on brain and central nervous Read More...
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Bioinformatics
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...
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Bioinformatics
08/03/2022 - Abstract: Liver cancer, comprising mainly hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), is one of the deadliest cancers in the world, with a five-year survival rate less than 20%. Immunotherapy has emerged as a promising Read More...
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Bioinformatics
02/16/2022 - For our next CDSL webinar we will have a guest lecture by Dr. Leng Han from the Center for Epigenetics and Disease Prevention at Texas A&M University. Abstract: Despite advancements in 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
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
12/13/2017 - PLEASE NOTE: This workshop is a BYOC ( Bring Your Own LapTop Computer ) class, and requires installation of Partek Genomics Suite on your laptop ahead of the workshop. Government issued or personal computers are permitted. Read More...
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Bioinformatics
11/09/2015 - A Short Course in R for Biologists "A Short Course in R for Biologists" is a two-day course given in four three-hour sessions entitled: Introduction to R, Introduction to Bioconductor, Introduction to Read More...
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Bioinformatics
10/16/2012 - Fundamentals of DNA copy number analysis using Nexus Learn the basics of copy number analysis and its application to genomic research. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/ Read More...
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Bioinformatics
Partek Genomics Suite (Partek) is a graphical user interface (GUI) based bioinformatics package. It hosts a range of work flows that allow for gene expression, epigenetic, and association analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{ Read More...
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Bioinformatics
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...
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Bioinformatics
The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: Subject matter expertise in genomics, proteomics, and imaging. Machine learning/ Read More...
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Bioinformatics
The main function in ggpubr to compare means between two or more groups is compare_means(). This function includes methods for each of the tests listed in the above table. Let's see how this Read More...
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Confocal
Stephen Lockett, Ph.D. Director, OMAC locketts@nih.gov 301-846-5515 Valentin Magidson, Ph.D. Scientist magidsonv@mail.nih.gov 301-846-6092 Will Heinz, Ph.D. Scientist heinzwf@nih.gov 301-846-1239 OMAC Read More...
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Confocal
Research Mission The goal of OMAC’s research is to understand molecular mechanisms driving carcinogenesis and the reversal of this process through treatment, by utilization and advancement of optical microscopy techniques. These techniques include 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
Introduction to ggplot2 Objectives Learn how to import spreadsheet data. Learn the ggplot2 syntax. Build a ggplot2 general template. By the end of the course, students should be able to create simple, pretty, and effective Read More...
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Bioinformatics
Scatter plots and plot customization Objectives Learn to customize your ggplot with labels, axes, text annotations, and themes. Learn how to make and modify scatter plots to make fairly different overall plot representations. Load a Read More...
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Bioinformatics
06/22/2022 - Cancer origination and progression is a complex process that can be viewed as a somatic evolutionary progression with clonal cellular expansion(s) driven by accumulation of survival-/evasion-beneficial genomic mutations, alongside constantly changing selective Read More...
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Bioinformatics
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...
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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...
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Bioinformatics
10/03/2016 - The maximum number of registrations (25) allowed has been reached for this workshop. You will be put on the waitlist and informed if any cancellations do occur. You are welcome to come on the morning Read More...
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Bioinformatics
01/07/2016 - REGISTRATION IS FULL FOR THIS WORKSHOP (25 ATTENDEES; 6 WAITLIST) The Cancer Genome Atlas (TCGA) is a large-scale study that has cataloged genomic data accumulated for many different types of cancers, and includes mutations, copy number Read More...
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Bioinformatics
10/22/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...
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Bioinformatics
01/29/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...
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Bioinformatics
10/27/2014 - PLEASE NOTE: This 2 day workshop is a BYOC (Bring your own Laptop Computer) class. In order to provide more flexibility with room scheduling we are experimenting with a new format that involves students brining Read More...
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Bioinformatics
03/18/2014 - 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 and miRNA gene expression, and DNA Read More...
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Bioinformatics
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...