Search Results for: PB-FGF8b-line 3

01/30/2025 - This lesson is part of a course,  B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

command line interactively.\ command line using a script .\ interactively through an environment. This course will demonstrate the utility of the RStudio integrated development environment (IDE). ::: notes I am also a fan of the R extension Read More...

R can be used via command line interactively, command line using a script , or interactively through an environment. This course will demonstrate the utility of the RStudio integrated development environment (IDE).

Q2studio Graphical user interface Q2cli Command line interface The classic way to use qiime2 Artifact API Python 3 application programming interface (API) for QIIME 2 Use with Jupyter notebook Recommended for advanced users Galaxy The Read More...

Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status, and enzyme activity levels. You can choose to search for a Read More...

The Protein Expression Laboratory produces proteins to help CCR investigators achieve their research goals with the lowest possible cost in the shortest time. PEL is operated by Leidos Biomedical Research Inc. on behalf of NCI Read More...

The Developmental Therapeutics Program (DTP) within NCI's Division of Cancer Treatment and Diagnostics (DCTD), has maintained a low temperature repository of transplantable in vivo-derived tumors and in vitro-established tumor cell lines from various species. This Read More...

Recently, the NIH HPC Team has provided on demand access to HPC resources via web browser through integration of Open OnDemand , an open source project supporting "nearly 400 HPC centers around the world" . This Read More...

02/11/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

02/06/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

01/28/2025 - This lesson is part of a course, B4B: Unix and Biowulf.    This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...

12/12/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...

09/19/2024 - This one hour and half online training builds on the topics covered in the Data Visualization in ggplot training. It provides an overview of options for working with dates, times, and options for customizing Read More...

09/06/2024 - This course provides an introduction to data visualization using R. Participants will learn data visualization with base R and using the R package ggplot2 to explore various types of data visualizations, including scatter plots, Read More...

08/27/2024 - This hands-on workshop will help you advance your microbiome analysis and computing skills, and help you learn new ways to leverage computing resources for your research. What you’ll learn: ● The basics of interacting Read More...

07/24/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...

05/29/2024 - This class provides an overview of options for customizing a ggplot graph. This class will focus on methods for creating small multiples, options for customizing a graph, and how to apply ggplot themes.& Read More...

Due to limits on computational resources, you may be interested in running your analysis on an HPC. Biowulf is the NIH high performance compute cluster. It has greater than 90k processors, and can easily perform Read More...

03/19/2024 - This class is designed for those who want to extend the basics covered in the Introduction to Quarto for Scholarly Publishing to Formatting class. This class uses Quarto to render formatted citations and bibliographies Read More...

A geom is the geometrical object that a plot uses to represent data. People often describe plots by the type of geom that the plot uses. --- R4DS There are multiple geom functions that Read More...

Because we build plots using layers in ggplot2. We can add multiple geoms to a plot to represent the data in unique ways. #We can combine geoms; here we combine a scatter plot with a # Read More...

You do not need to load a package to visually explore data. Rather, you can use base R graphics for plotting (from the graphics package). This plotting is fairly different from ggplot2 , which is based Read More...

Quarto® is an open-source scientific and technical publishing system built on Pandoc --- https://quarto.org/ What does this mean? Quarto allows you to combine code, commentary, and other features to tell a story about Read More...

As we learn more about R and start learning our first commands, we will keep a record of our commands using an R script. Remember, good annotation is key to reproducible data analysis. An R Read More...

What geoms would you use to draw each of the following named plots? a. Scatterplot b. Line chart c. Histogram d. Bar chart e. Pie chart (Question taken from https://ggplot2-book.org/individual-geoms.html .) {{ Read More...

Lesson 5 Exercise Questions: ggplot2 What geoms would you use to draw each of the following named plots? a. Scatterplot b. Line chart c. Histogram d. Bar chart e. Pie chart (Question taken from https://ggplot2 Read More...

Quarto helps you tell others exactly what you did and how you derived your conclusions - code, results, and conclusions wrapped up in a single document. Advantages of Quarto compared with other publishing systems: Can Read More...

02/13/2024 - This class provides an overview of options for customizing a ggplot graph. This class will focus on methods for creating small multiples, options for customizing a graph, and how to apply ggplot themes.& Read More...

01/22/2024 - This is the first lesson in the Introduction to Unix on Biowulf, January 2024 series. In this lesson, participants will learn to log onto Biowulf and receive an overview of Unix command line as well Read More...

A geom is the geometrical object that a plot uses to represent data. People often describe plots by the type of geom that the plot uses. --- R4DS There are multiple geom functions that Read More...

Once the job is running, wait about 4 minutes before clicking on the web address shown to the right of job status line. (It will look similar to this " https://job-GBb1xFQ0YKq8PqYJKx1bVv6 Read More...

As you continue to work in R, at some point you will need to incorporate regular expressions into your code. We used a regular expression escape above \\. to denote that we wanted to match a Read More...

Load in the comma separated file "./data/countB.csv" and save to an object named gcounts . {{Sdet}} Solution } gcounts `...1` colnames ( gcounts )[ 1 ] ## 1 Tspan6 703 567 867 71 970 242 ## 2 TNMD 490 482 18 342 935 469 ## 3 DPM1 921 797 622 661 8 500 ## 4 SCYL3 335 216 222 774 979 793 ## 5 FGR 574 574 515 584 941 344 ## 6 CFH 577 792 672 104 192 936 ## 7 FUCA2 798 766 995 27 756 546 ## 8 GCLC 822 874 923 705 667 522 ## 9 NFYA 622 793 918 868 334 64 {{Edet}} Plot the Read More...

To create an R object, you need a name, a value, and an assignment operator (e.g.,

11/15/2023 - This class provides an overview of options for customizing a ggplot graph. This class will focus on methods for creating small multiples, options for customizing a graph, and how to apply ggplot themes.& Read More...

09/11/2023 - We invite you to attend the Biobanking for Precision Medicine seminar series. The seminar series is brought to you by NCI’s Biorepositories and Biospecimen Research Branch (BBRB) and addresses current topics Read More...

The Center for Advanced Tissue Imaging (CAT-I) is an NIAID and NCI supported effort involving collaborative studies between experts in the Laboratory of Immune System Biology, DIR, NIAID and investigators in the DIR, NIAID and Read More...

The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...

The Genomics and Pharmacology Facility is part of the NCI's Center for Cancer Research (CCR), within the Developmental Therapeutics Branch. Its mission is to manage and assess molecular interaction data obtained through multiple platforms, increase Read More...

Mass Spectrometry Section of the Collaborative Protein Technology Resource (Bldg. 37) Core Capabilities: Identification of proteins in complexes, organelles, subcellular fractions, or fluids. Global relative protein quantitation. Quantitation by isotopic labeling of cells in culture (SILAC) Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

NCI LASP Animal Research Technology Support (ARTS) provides customized technical support for basic and translational animal-based research to the scientific community. We offer a wide array of services ranging from expert colony management to the Read More...

Molecular Cytogenetics Core Facility facilitates the assessment of structural and numerical genomic changes in pre-cancer and cancer research models. This core provides comprehensive support for the cytogenetic analysis of cells from human and research animal Read More...

The Laboratory Animal Sciences Program (LASP) of the Frederick National Laboratory operates a Gnotobiotics Facility (GF) to support research focused on the role of microbiota in cancer inflammation, pathogenesis, and treatment response. The GF can Read More...

The OSTR offers cutting-edge technology platforms to the CCR scientific community through centralized facilities. The videos accessed through this page are designed to introduce the various scientific methodologies OSTR makes available through the cores on Read More...

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at Read More...

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class Read More...

Anaconda ( https://www.anaconda.com/ ) is a package manager and distributor for a wide array of data science software. Package managers are ideal for scientists who conduct analysis on a personal computer as they eliminate 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...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

03/21/2025 - Partek Flow is a point-and-click software for analyzing multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. Input options include FASTQ, BAM, or expression tables, thus enabling scientists Read More...

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...

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...

What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...

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...

Please see https://bioinformatics.ccr.cancer.gov/btep/self-learning/ to sign up for a license. Contact ncibtep@nih.gov with any questions about obtaining a license. Did you know that CCR researchers have access to Read More...

07/24/2024 - Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is hosted on Biowulf, the NIH high performance computing Read More...

Partek Flow enables scientists to build comprehensive workflows for analyzing multi-omics high throughput sequencing data including DNA and variant calling, bulk and single cell modalities for RNA, ChIP, and ATAC, spatial transcriptomics, CITE, and immune Read More...

ALWAYS, ALWAYS, ALWAYS read the documentation. Use the help pane in the lower right of RStudio or the functions, help() and help.search() or ? and ?? . Check out package vignettes ( vignette() ). Check the Github site if Read More...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

03/06/2024 - The National Institutes of Health (NIH) promotes the use of Common Data Elements (CDEs) to standardize data collection, sharing, and interoperability in health and disease research. In line with Congressional Appropriations language, the Office Read More...

Partek Flow is a start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing sequencing Read More...

Accessing Partek Flow at NIH and tips for data transfer Learning objectives Instructions for accessing Partek Flow NCI researchers can find instructions for accessing Partek Flow at https://bioinformatics.ccr.cancer.gov/btep/partek-flow-bulk-and-single-cell-rna-seq-data-analysis/ . But Read More...

Course Overview Partek Flow is a start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with Read More...

02/21/2024 - https://cap-lab.bio (link is external) https:// (link is external) qiime2.org (link is external) The QIIME platform, including QIIME 1 and QIIME 2 ( https://qiime2.org (link is external) ), has been extensively applied in microbiome Read More...

#Setting a theme my_theme

Now we are ready to work with some of our first R commands. We are going to run commands directly from our R script rather than typing into the R console. Our first command will Read More...

Let's explore how piping streamlines this. Piping (using |> ) allows you to employ multiple functions consecutively, while improving readability. The output of one function is passed directly to another without storing the intermediate steps Read More...

Let's explore how piping streamlines this. Piping (using |> ) allows you to employ multiple functions consecutively, while improving readability. The output of one function is passed directly to another without storing the intermediate steps Read More...

There are data sets available in R to practice with or showcase different packages. For today's lesson and the remainder of this course, we will use data from the Bioconductor package airway to showcase Read More...

Let's look a bit into our RStudio layout. Source : This pane is where you will write/view R scripts. Some outputs (such as if you view a dataset using View() ) will appear as a Read More...

Welcome! Welcome to the R Introductory Series! Who: Novices and beginners\ What: A course series introducing R and RStudio. This course will introduce the foundational skills necessary to begin to analyze and visualize data in Read More...

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of class here . The diffexp_ Read More...

Lesson 2 Exercise Questions: Part 2 (Tidyverse) The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside Read More...

The following represents the basic ggplot2 template: ggplot(data = ) + (mapping = aes()) We need three basic components to create a plot: the data we want to plot , geom function(s) , and mapping aesthetics . Notice the + symbol Read More...

Data visualization with ggplot2 Objectives To learn how to create publishable figures using the ggplot2 package in R. By the end of this lesson, learners should be able to create simple, pretty, and effective figures. 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...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...

Objectives Review the grammar of graphics template. Learn about the statistical transformations inherent to geoms. Learn more about fine tuning figures with labels, legends, scales, and themes. Learn how to save plots with ggsave() . Review Read More...

In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...

In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...

Learning Objectives Learn about data structures including factors, lists, data frames, and matrices. Load, explore, and access data in a tabular format (data frames) Learn to write out (export) data from the R environment Data Read More...

R is both a computational language and open-source environment for statistical computing and graphics. While R programming was ranked 20 th in popularity when compared with other programming languages in December 2023, it remains a favorite among Read More...

The QIIME platform, including QIIME 1 and QIIME 2, has been extensively applied in microbiome research, repeatedly making analyses that were challenging or impossible into routine tasks. While QIIME began as a marker gene (e.g., 16S, Read More...

Step 1 : Login to DNAnexus Step 2 : Once you login, you should see the Projects page. If you have used DNAnexus previously, you may see more than one project listed. If this is your first time using Read More...

In lesson 3, we learned how to read and save excel spreadsheet data to a R object using the tidyverse package readxl . Today we will use some example data from an excel spreadsheet to learn the Read More...

Lesson 1: Toward fully reproducible microbiome multi-omics bioinformatics with QIIME 2 Lesson 1 does not include a hands on component, but rather includes an introduction to QIIME2 by guest speaker, Dr. Greg Caporaso, a leading developer of the Read More...

The following represents the basic ggplot2 template. ggplot(data = ) + (mapping = aes()) The only required components to begin plotting are the data we want to plot, geom function(s), and mapping aesthetics. Notice the + symbol following Read More...

DNAnexus Basics Setting up the R-Studio environment outside of Class hours These instructions should be followed if you are setting up the R-Studio Web environment outside the normal class hours. Log into DNAnexus Each student Read More...

Often we will apply multiple functions to wrangle a data frame into the state that we need it. For example, maybe you want to select and filter. What are our options? We could run one 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...

In tab delimited files, data columns are separated by tabs. To import tab-delimited files there are several options. There are base R functions such as read.delim() and read.table() as well as the readr Read More...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

Introduction to ggplot2 Objectives 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 figures. Data Visualization in the tidyverse Read More...

Lesson 7: Course Wrap-Up Learning Objectives Introduce the QIIME2 microbiome workflow for Biowulf Review key concepts Showcase additional plugins QIIME 2 on Biowulf As mentioned previously, QIIME 2 is installed on Biowulf. To see available versions use module Read More...

Data import and reshape Objectives 1. Learn to import multiple data types 2. Data reshape with tidyr : pivot_longer() , pivot_wider() , separate() , and unite() Installing and loading packages So far we have only worked with objects that Read More...

R Crash Course: A few things to know before diving into wrangling Learning the Basics Objectives 1. Learn about R objects 3. Learn how to recognize and use R functions 4. Learn about data types and accessors Console Read More...

Introduction to dplyr and the %>% Objectives Today we will begin to wrangle data using the tidyverse package, dplyr . To this end, you will learn: how to filter data frames using dplyr how to employ Read More...

11/06/2023 - UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. The database is regularly augmented with additional data and is globally accessible Read More...

10/25/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

10/11/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

09/27/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

09/13/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

09/06/2023 - With the advancements in single cell and spatial profiling technologies and methods, some of us thought it would be helpful to re-establish a community of end users on campus. We invite those that are Read More...