Search Results for: 125I-GCC 3-23

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment. conda activate bioinfo The jellyfish program is dependent on a program called "gcc" which is Read More...

07/23/2025 - Harne ing the Power of Tran criptomic for cientific Di covery

01/23/2026 - In the second class of Statistical Analysis of Research Data (SARD) hosted by NCI Center for Cancer Training, participants will learn about: Inferential statistics Two sample tests of means Small versus large sample consideration Read More...

01/23/2026 - This is the second class of the Statistical Analysis of Research Data (SARD) series offered by NCI Center for Cancer Training. In this class participants will learn about: Inferential statistics  Two sample Read More...

09/23/2025 - There are many challenges associated with moving cancer AI originally developed in a research setting into a clinical setting, including into clinical trials. During this event, participants will discuss the integration of AI in Read More...

04/23/2025 - Dr. Ruppin's research is focused on multi-disciplinary, algorithmic, computationally driven analysis of large-scale biomedical omics and clinical data, with an emphasis on AI and machine / deep learning approaches. Overall, it centers on three Read More...

01/23/2025 - The NCI Rising Scholars: Cancer Research Seminar Series , hosted by the Center for Cancer Training, highlights the research and important contributions made by postdoctoral scholars and early-career investigators funded via an NCI extramural fellowship Read More...

10/23/2024 - Learn the nuts and bolts of 16S amplicon microbiome sequence analysis with DADA2. This hands-on tutorial will walk through all key steps in detail, providing understanding about each component and common pitfalls. Feel free Read More...

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...

07/23/2024 - Cancer AI Conversations are virtual events featuring timely topics related to the application of artificial intelligence (AI) in cancer research. This discussion will focus on the impact of AI on cancer health disparities.& Read More...

04/23/2024 - Join Dr. Kai Tan of the Children’s Hospital of Philadelphia as he discusses his cutting-edge technology, CytoCommunity, for the supervised and unsupervised discovery of tissue cellular neighborhoods. CytoCommunity offers a powerful Read More...

01/23/2024 - This is the first lesson of the R Introductory Series. This lesson will serve as a general introduction to R and RStudio. Attendees will explore the RStudio interactive development environment (IDE) and learn to Read More...

01/23/2024 - This class focuses on using Git and GitHub, with RStudio. Using integrated RStudio tools, participants will have a chance to experiment with this integration and understand its advantages for collaboration and managing projects. You Read More...

01/23/2024 - In this session, we will discuss the potential of GPUs, and when and why to use GPUs on the Frederick Research Computing Environment (FRCE). We will explore the possibilities of GPU-accelerated AI applications and Read More...

For the following plots, let's use the diamonds data ( ?diamonds ). The diamonds dataset comes in ggplot2 and contains information about ~54,000 diamonds, including the price, carat, color, clarity, and cut of each diamond. --- R4 Read More...

10/23/2023 - This class focuses on using Git and  GitHub , with RStudio. Using integrated RStudio tools, participants will have a chance to experiment with this integration and understand its advantages for collaboration and managing Read More...

02/23/2026 - This one and a half hour online training equips participants with powerful data wrangling techniques using R and the tidyverse ecosystem. The tidyverse is a cohesive ecosystem of R packages designed to make data Read More...

10/23/2025 - Qiagen CLC Genomics Workbench is a point-and-click software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis that is available to NCI scientists. Submit a Read More...

10/23/2025 - This one-hour online training will cover the fundamentals, applications, and ethical considerations of Artificial Intelligence (AI). Attendees will explore key topics such as machine learning, deep learning, data handling, and real-world AI applications across Read More...

09/23/2025 - This one-hour online training covers various aspects of sharing code using MATLAB community tools like File Exchange and GitHub. Well-documented methods and workflows enable reproducible research by helping scientists follow each other& Read More...

09/23/2025 - Dr. Church's clinical and research work focus on bringing molecular testing to the clinical care of children with cancer. Through institutional projects (the Profile study, GAIN consortium study) she has profiled thousands of Read More...

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...

07/23/2025 - Thi one-hour training, provided by a pre enter from A , will demon trate tip and trick to make your A code run more efficiently. There are at lea t ix way to do mo Read More...

07/23/2025 - The QIIME platform, including QIIME 1 and QIIME 2, has been extensively applied in microbiome research, repeatedly making analyses that were once challenging or impossible into routine tasks. While QIIME began as a marker gene (e. Read More...

01/23/2025 - The "Data Visualization in R" series focuses on using ggplot and the broader tidyverse ecosystem to create insightful and customizable visualizations. It covers key principles of data visualization, from basic plots to Read More...

01/23/2025 - AI in Medicine: Focus on Deep Learning in Medical Genomics This series invites Principal Investigators, Senior Scientists, and Senior Clinicians  to share cutting-edge research and developments in their fields. Each session includes a 20-30 Read More...

10/23/2024 - This one-hour online training will cover tips and tricks to run your processing against large datasets more efficiently in SAS.   By the end of this training, attendees will be able Read More...

10/23/2024 - CellMinerCDB is an interactive public web application ( https://discover.nci.nih.gov/cellminercdb/ ) that simplifies access and exploration of cancer cell line pharmacogenomic data across different sources such as the National Cancer Institute (NCI), Read More...

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...

09/23/2024 - Come to the Fair!  In the morning session, several different groups will speak about their training and education programs. The afternoon session will be devoted to learning about research using AI across Read More...

08/23/2024 - In this webinar, Dr. Carey will provide an introduction to Bioconductor for genomic data science.   Bioconductor.org enters its third decade as an NHGRI/NCI-funded resource for many aspects of genomic data Read More...

05/23/2024 - An exciting opportunity at the intersection of the biomedical sciences and machine learning stems from the growing availability of large-scale multi-modal data (imaging-based and sequencing-based, observational and perturbational, at the single-cell level, tissue-level, and Read More...

05/23/2024 - During this virtual conversation of the Cancer Moonshot Seminar Series, Dr. Kai Tan, an investigator with the Human Tumor Atlas Network , and Liz Salmi, a co-investigator and patient advocate with the Participant Engagement and Read More...

05/23/2024 - Versioning enables researchers to track changes in coding projects. This Coding Club introduces Git (https://git-scm.com), an open-source software used to perform versioning on a personal computer. At the end of this class, Read More...

04/23/2024 - Crunching of large data requires large resources. Exploration of holobiont metagenomes is considered a “big data” project and here I’ll be describing how I used the FRCE Read More...

04/23/2024 - What’s the difference between “regular” statistics (i.e., what you may have been using in the past several years) and the “new” Bayesian Read More...

04/23/2024 - Dr. Stephanie Harmon obtained her Ph.D. in medical physics at the University of Wisconsin–Madison and did her postgraduate training at Leidos Biomedical Research where she worked within the Molecular Imaging Read More...

02/23/2024 - Register for this presentation on recent efforts in developing methodologies and software tailored for important clinical natural language processing (NLP) tasks such as information extraction and question answering.   Advancements in large language Read More...

As mentioned, an object's mode can be used to understand the methods that can be applied to it. Objects of mode numeric can be treated as such, meaning mathematical operators can be used directly Read More...

Let's use some functions. a. Use sum() to add the numbers from 1 to 10. {{Sdet}} Solution{{Esum}} sum ( 1 : 10 ) {{Edet}} b. Compute the base 10 logarithm of the elements in the following vector and save to an Read More...

Lesson 2 Exercise Questions: Base R syntax, objects, and data types Let's use some functions. a. Use sum() to add the numbers from 1 to 10. {{Sdet}} Solution{{Esum}} sum ( 1 : 10 ) {{Edet}} b. Compute the base 10 logarithm of Read More...

Given the following R code: fruit 678] c. Total_subjects(Total_subjects < 678) d. Total_subjects[Total_subjects < 678] {{Sdet}} Solution{{Esum}} D {{Edet}}

A function in R (or any computing language) is a short program that takes some input and returns some output. An R function has three key properties: Functions have a name (e.g. dir, getwd); Read More...

Try googling your problem or using some other search engine. rseek is an R specific search engine that searches several R related sites. If using google directly, make sure you use R to tag your Read More...

01/24/2024 - Dear colleagues,   Please join us on Wed., Jan. 24 when Dr. Avi Ma’ayan from the Icahn School of Medicine at Mount Sinai will demonstrate how to use these tools to access hundreds of thousands Read More...

01/23/2024 - Looking for&nbsp; data sharing &nbsp;platforms to enhance your research and advance communal knowledge of childhood cancers? Join the first NCI Childhood Cancer Data Initiative (CCDI) webinar of the new year! Read More...

01/23/2024 - NCI is launching the virtual Cancer AI Conversations series featuring multiple perspectives on timely topics and themes in artificial intelligence for cancer research!&nbsp; Each event features short talks from 2-4 subject matter Read More...

Which of the following will throw an error and why? 4 _ chr :1:2: unexpected input ## 1: 4_ ## ^ . 4 chr :1:3: unexpected symbol ## 1: .4chr ## ^ {{Edet}} Create the following objects; give each object an appropriate name (your best guess at what name to Read More...

This is our first coding help session. We have designed some practice problems to get you acquainted with using R before beginning to wrangle in our next lesson. Practice problems Which of the following will Read More...

Help Session Lesson 4 Plotting with ggplot2 For the following plots, let's use the diamonds data ( ?diamonds ). The diamonds dataset comes in ggplot2 and contains information about ~54,000 diamonds, including the price, carat, color, clarity, and Read More...

S4 objects store complex information that isn't necessarily simple to save. If you intend to work with the object further, try using saveRDS . saveRDS(se, "airways.rds") #save the object Note saveRDS() Read More...

10/23/2023 - Do you use the Cancer Research Data Commons&rsquo; (CRDC&rsquo;s) Genomic Data Commons (GDC) for downloading molecular, clinical, and/or imaging data? Do you download large quantities of data? Attend Read More...

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...

For this class, we are going to work with data from and associated with two commercially available sets of RNA samples, Universal Human Reference (UHR) and Human Brain Reference (HBR). UHR - bulk RNA from 10 Read More...

This data set is from the Griffith lab RNA sequencing tutorial and are kept at http://genomedata.org/rnaseq-tutorial/practical.tar. This dataset is derived from a study that profiled the transcriptome of HCC1395 breast Read More...

The Human Brain Reference (HBR) RNA sequencing data are derived from RNA extracted from 23 human brains brains are from both males and females, age ranging from 60 to 80 years The Universal Human Reference data used RNA Read More...

The Human Brain Reference (HBR) RNA sequencing data are derived from RNA extracted from 23 human brains brains are from both males and females, age ranging from 60 to 80 years The Universal Human Reference data used RNA Read More...

Two commercially available RNA samples. Universal Human Reference (UHR) is total RNA isolated from a diverse set of 10 cancer cell lines. Human Brain Reference (HBR) is total RNA isolated from the brains of 23 Caucasians, male Read More...

Two commercially available RNA samples. Universal Human Reference (UHR) is total RNA isolated from a diverse set of 10 cancer cell lines. Human Brain Reference (HBR) is total RNA isolated from the brains of 23 Caucasians, male Read More...

Two commercially available RNA samples. Universal Human Reference (UHR) is total RNA isolated from a diverse set of 10 cancer cell lines. Human Brain Reference (HBR) is total RNA isolated from the brains of 23 Caucasians, male Read More...

Recall that the Golden Snidget data resides in ~/biostar_class/snidget folder. Can you change into the folder and find where the sequencing reads are (ie. in which folder they are located)? {{Sdet}} Solution{{Esum}} Read More...

Lesson 10 Practice Objectives In this lesson, we introduced the structure of the FASTQ file and learned to assess quality of raw sequencing data using FASTQC. Here, we will practice what we learned using the Golden Read More...

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...

Before we start, remember to change into the ~/biostar_class/snidget folder and then list the content to review what is available. cd ~/biostar_class/snidget ls -l QC total 117384 drwxrwxr-x 1 joe joe 1188 Oct 31 23:29 QC Read More...

Lesson 12 Practice Objectives In this practice session, we will work with something new, which is a dataset from the Griffith lab RNA sequencing tutorial. Here, we will have a chance to practice what we have Read More...

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...

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...

Objectives To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By the end Read More...

Learning Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help how R can enhance data Read More...

Why did we focus so heavily on the tidyverse if it can't be used to manipulate Bioconductor objects? Well, for one, regardless of whether you are a user of Bioconductor packages, you will often Read More...

All solutions should use the pipe. Import the file "./data/filtlowabund_scaledcounts_airways.txt" and save to an object named sc . Create a subset data frame from sc that only includes the columns Read More...

Help Session Lesson 5 All solutions should use the pipe. Import the file "./data/filtlowabund_scaledcounts_airways.txt" and save to an object named sc . Create a subset data frame from sc that only Read More...

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...

Prior to differential expression analysis, we need to generate a design.csv file that contains the samples and their corresponding treatment conditions. Note that csv stands for comma separated value so the columns in these Read More...

The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR Read More...

The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

BBDuk is another tool that can be used for adapter and quality trimming. In addition, BBDuk can be used to filter out contaminations, perform GC filtering, filter for length, etc. (see https://jgi.doe.gov/ Read More...

The SRA (Sequence Read Archive) at NCBI is a large, public database of DNA sequencing data. The repository holds "short reads" generated by high-throughput next-generation sequencing, usually less than 1,000 bp. We will download Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Let's now take a look at our final differential analysis results table (results_with_gene_names_labeled.txt), using the SLC2A11 gene as an example and below we use the column command to Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

fastq-dump and fasterq-dump can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. fastq-dump SRR1553607 creates the file: SRR1553607.fastq Check the file to make Read More...

fastq-dump and fasterq-dump can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. fastq-dump SRR1553607 creates the file: SRR1553607.fastq Check the file to make Read More...

Let's use the tool Trimmomatic to clean up the adapters and the poor quality reads for SRR1553606. For help with Trimmomatic type trimmomatic --help at the command line. Before getting started with using trimmomatic, Read More...

This page contains content directly from The Biostar Handbook . Always remember to start the bioinformatics environment. conda activate bioinfo Pseudoalignment-based methods identify locations in the genome using patterns rather than via alignment type algorithms. It Read More...

This page contains content directly from The Biostar Handbook . Always remember to start the bioinformatics environment. conda activate bioinfo Pseudoalignment-based methods identify locations in the genome using patterns rather than via alignment type algorithms. It Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: using trimmomatic to remove low-quality bases from a sequence Always remember to activate the bioinformatics environment. conda activate bioinfo We will be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: using trimmomatic to remove low-quality bases from a sequence Always remember to activate the bioinformatics environment. conda activate bioinfo We will be Read More...

Lesson 13 Practice Objectives In this lesson we learned how to align raw sequencing reads to reference and to process alignment results for downstream analysis. Here, we will test our knowledge by continuing with the Golden Read More...