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Bioinformatics
Because we are now creating different folders that stores results from various stages in our data analysis, we could set up some environmental variables for these so we can more easily reference these folders while Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
We are returning to the core grammar of graphics concept introduced in Lesson 2. Remember, to create a plot all you you need are data, geom_function(s), and mapping arguments. Here is the basic template Read More...
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Bioinformatics
Remember, to create a plot all you you need are the data , geom_function(s) , and mapping arguments. However, there are additional components that can be added to our core components to enable us to Read More...
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Bioinformatics
Last lesson we discussed the three basic components of creating a ggplot2 plot: the data , one or more geoms , and aesthetic mappings . ggplot(data = ) + (mapping = aes()) But, we also learned of other features that greatly Read More...
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Bioinformatics
This is where we left off at the end of lesson 3.
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Bioinformatics
one or more datasets, one or more geometric objects that serve as the visual representations of the data, – for instance, points, lines, rectangles, contours, descriptions of how the variables in the data are mapped to Read More...
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Bioinformatics
one or more datasets, one or more geometric objects that serve as the visual representations of the data, – for instance, points, lines, rectangles, contours, descriptions of how the variables in the data are mapped to Read More...
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Bioinformatics
Last lesson we discussed the three basic components of creating a ggplot2 plot: the data, one or more geoms, and aesthetic mappings. ggplot(data = ) + (mapping = aes()) But, we also learned of other features that greatly Read More...
Bethesda, MD
Trans NIH Facility
MAB provides visual communication solutions across all media to the entire NIH community. Our Medical Illustration section provides a complete range of biomedical visualization services, including manuscript/textbook figures, infographics, 3D modeling, animation, technical diagrams, Read More...
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Bioinformatics
06/11/2024 - ggplot2 is an R graphics package from the tidyverse collection. It is one of the most installed packages in R. It allows the user to create informative plots quickly by using a 'grammar of Read More...
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Bioinformatics
R for Data Science Hands-on Programming with R Statistical Inference via Data Science: A ModernDive into R and the Tidyverse The R Graphics Cookbook ggplot2: Elegant Graphics for Data Analysis Advanced R
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Bioinformatics
ggplot2 cheatsheet The R Graph Gallery The R Graphics Cookbook From Data to Viz ggplot2 extensions ggplot2: Elegant Graphics for Data Analysis
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Bioinformatics
For Further Reading Books and / or Book Chapters of Interest R for Data Science Hands-on Programming with R Statistical Inference via Data Science: A ModernDive into R and the Tidyverse The R Graphics Cookbook ggplot2: Read More...
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Bioinformatics
This is the grammar of graphics. Adding layers to create unique figures. ggplot(data = ) + ( mapping = aes(), ) + Note that there are a lot of invisible (default) layers that often go into each ggplot2, and there are Read More...
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Bioinformatics
R for Data Science Hands-on Programming with R Statistical Inference via Data Science: A ModernDive into R and the Tidyverse The R Graphics Cookbook ggplot2: Elegant Graphics for Data Analysis Advanced R
Web Page
Bioinformatics
ggplot2 cheatsheet The R Graph Gallery The R Graphics Cookbook From Data to Viz ggplot2 extensions ggplot2: Elegant Graphics for Data Analysis
Web Page
Bioinformatics
For Further Reading Books and / or Book Chapters of Interest R for Data Science Hands-on Programming with R Statistical Inference via Data Science: A ModernDive into R and the Tidyverse The R Graphics Cookbook ggplot2: Read More...
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Bioinformatics
Outside of base R plotting, one of the most popular packages used to generate graphics in R is ggplot2 , which is associated with a family of packages collectively known as the tidyverse. GGplot2 allows the Read More...
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Bioinformatics
ggplot2 cheatsheet The R Graph Gallery The R Graphics Cookbook
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Bioinformatics
Understand the difference between alpha and beta diversity Introduce several alpha diversity metrics Understand what rarefaction is and why it is important Introduce the debate regarding rarefaction and other methods of normalization Often many questions Read More...
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Bioinformatics
As mentioned above, instructions for using the Biostar module on Biowulf can be found in the course documents . The Biostars module loads the software used in this course series. A list of the software included Read More...
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Bioinformatics
Recall that the scripts used for differential expression analysis are in the folder /usr/local/code. We can also access this folder using the environmental variable CODE. How many scripts are in this folder (find Read More...
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Bioinformatics
An extremely useful feature of cowplot is ggdraw() combined with draw_plot() , draw_grob() , draw_image() and draw_label() . These can be used to add or combine text, images, and plots and create more complicated Read More...
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Bioinformatics
ggplot2 cheatsheet R Graph Gallery The R Graphics Cookbook R4DS
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Bioinformatics
Outside of base R plotting, one of the most popular packages used to generate graphics in R is ggplot2 , which is associated with a family of packages collectively known as the tidyverse. GGplot2 allows the Read More...
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Bioinformatics
ggplot2 cheatsheet The R Graph Gallery The R Graphics Cookbook Ggplot2 extensions
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Bioinformatics
Let's update our ggplot2 grammar of graphics template: ggplot(data = ) + ( mapping = aes(), stat = ) + + +
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Bioinformatics
Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar plots, box & whisker plots, and histograms.
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Bioinformatics
Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar plots, box & whisker plots, and histograms.
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Bioinformatics
Lesson 2 will focus on the basics of ggplot2, including the grammar of graphics philosophy and its application. This lesson will provide a hands on introduction to the ggplot2 syntax, geom functions, mapping and aesthetics, and Read More...
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Bioinformatics
10/20/2022 - An overview of the geospatial tools that are useful for characterizing areas of the country in terms of cancer incidence, mortality, screening frequency, risk factors, socio-demographic and environmental variables relevant to cancer. The presentation Read More...
Bethesda, MD
Trans NIH Facility
The Division of Veterinary Resources’ (DVR) mission is to contribute to the advancement of NIH biomedical research programs by providing excellence in animal care, customer service, and specialized research services to support intramural research efforts. Read More...
Bethesda, MD
Trans NIH Facility
The NIH Biowulf Cluster provides researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations, deep learning to model protein structures, and PET brain Read More...
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Bioinformatics
01/14/2025 - This one-hour online training will cover a basic overview of the functionality of R programming language and RStudio. R is a programming language and open-source environment for statistical computing and graphics. & Read More...
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Bioinformatics
09/12/2024 - This one-hour online training will cover a basic overview of the functionality of R programming language and RStudio. R is a programming language and open-source environment for statistical computing and graphics. & Read More...
Web Page
Bioinformatics
R is both a computational language and environment for statistical computing and graphics. It is open-source and widely used by scientists, not just bioinformaticians. Base packages of R are built into your initial installation, but Read More...
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Bioinformatics
05/28/2024 - This class provides a basic overview of creating plots using ggplot. ggplot is a part of the Tidyverse, a collection of R packages designed for data science. This class will Read More...
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Bioinformatics
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 general Read More...
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Bioinformatics
Both a computational language and environment for statistical computing and graphics. Open-source and widely used by scientists, not just bioinformaticians. Extensible. Maintained by a network of collaborators - The R Core Team A resource for Read More...
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Bioinformatics
R is both a computational language and environment for statistical computing and graphics. It is open-source and widely used by scientists, not just bioinformaticians. Base packages of R are built into your initial installation, but Read More...
Web Page
Bioinformatics
ggplot2 is an R graphics package from the tidyverse collection. It allows the user to create informative plots quickly by using a 'grammar of graphics' implementation, which is described as "a coherent system for Read More...
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Bioinformatics
02/06/2024 - This class provides a basic overview of creating plots using ggplot. ggplot is a part of the Tidyverse, a collection of R packages designed for data science. This class will focus on identifying the Read More...
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Bioinformatics
{{Sdet}} Answer{{Esum}} Tools that we will be using for RNA sequencing analysis in this course series include command line applications for raw data quality assessment, data cleanup, trimming, alignment, etc. We will also be Read More...
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Bioinformatics
Access the NIH network; this will require you to VPN if off campus. Connect to Biowulf ssh user_name@biowulf.nih.gov where user_name is your NIH username. Use sinteractive to work on an Read More...
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Bioinformatics
R is both a computational language and environment for statitical computing and graphics. It is open-source and widely used, not just by bioinformaticians. R is a particularly great resource for statistical analysis, plotting, and report Read More...
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Bioinformatics
released in 1993 a computational language and environment for statitical computing and graphics. complex statistical functions easily accessible easy to get started, but more difficult to learn Key features: open-source extensible (Packages on CRAN (> 19,000 packages), Read More...
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Bioinformatics
released in 1993 a computational language and environment for statitical computing and graphics. complex statistical functions easily accessible easy to get started, but more difficult to learn Key features: open-source extensible (Packages on CRAN (> 19,000 packages), Read More...
Web Page
Bioinformatics
06/14/2023 - Generative modeling is an artificial intelligence (AI) technique that creates unique content (such as text, graphics, audio, and video) by first analyzing training examples. Generative AI includes ChatGPT, which generates text in Read More...
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Bioinformatics
Lesson 3 will continue the discussion on the grammar of graphics, with a focus on ggplot2 plot customization including axes labels, coordinate systems, axes scales, and themes. This hands on lesson will showcase these features of Read More...
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Bioinformatics
For Further Reading Getting started with R Hands on Programming with R R for Data Science (R4DS) BTEP R Introductory Series Base R cheat sheet RStudio cheat sheet General help with ggplot2 ggplot2 cheatsheet Read More...
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Bioinformatics
04/18/2023 - Lesson 3 of the Data Visualization with R course series will continue the discussion on the grammar of graphics, with a focus on ggplot2 plot customization including axes labels, coordinate systems, axes scales, and themes. Read More...
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Bioinformatics
04/13/2023 - Lesson 2 of the Data Visualization with R course series will focus on the basics of ggplot2, including the grammar of graphics philosophy and its application. This lesson will provide a hands on introduction to Read More...
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Bioinformatics
ggplot2 is a R graphics package from the tidyverse collection. It allows the user to create informative plots quickly by using a 'grammar of graphics' implementation, which is described as "a coherent system for Read More...
Web Page
Bioinformatics
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 general Read More...
Web Page
Bioinformatics
R is both a computational language and environment for statitical computing and graphics. It is open-source and widely used by scientists, not just bioinformaticians. Base packages of R are built into your initial installation, but Read More...
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Bioinformatics
11/16/2022 - Attend this webinar to hear a moderated, five-person panel expand on the presentation, “Perspectives on CMS Linkage for Cancer Research in Cohort Studies.” This presentation is from the recent 2022 Annual Meeting of the NCI Read More...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx NCI CLIA Molecular Diagnostics Laboratory (CMDL) The NCI CMDL is available to assist all Read More...
Research Training Park, NC
Core Facility
Trans NIH Facility
The Trans-NIH Metabolomics Core (TNMC) is a shared research resource that performs metabolomics analysis (and related small molecule research) for investigators at all Institutes and Centers across the NIH Intramural Research Program. The TNMC is Read More...
Bethesda, MD
Trans NIH Facility
The Division of Veterinary Resources Animal Surgery has supported large animal research and clinical care for more than 40 years. DVR surgeons provide outstanding and highly specialized large animal (rabbits, ungulates, etc.) research support in a 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
11/12/2024 - Join us at the upcoming hybrid NIH BRAIN NeuroAI Workshop on November 12 and 13, with virtual access to in-person panels and discussions at the NIH Campus in Bethesda, MD. Artificial intelligence (AI) is reshaping technology Read More...
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Bioinformatics
07/25/2024 - This hour and half in-person training will explore the topics of perception and cognition, and how these apply to data visualization. There will also be a discussion on “pre-attentive” properties Read More...
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Bioinformatics
07/24/2024 - This hour and half in-person training will explore the topics of perception and cognition, and how these apply to data visualization. There will also be a discussion on “pre-attentive” properties Read More...
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Bioinformatics
06/20/2024 - Clustered heat maps are widely used for visualizing patterns in molecular profiling data. But traditional, static heat maps have significant limitations when applied to large datasets (1000s of elements per axis). Presented in this Read More...
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Bioinformatics
05/09/2024 - This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is Read More...
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Bioinformatics
03/29/2024 - This first of five webinars will introduce NIH’s All of Us Research Program, including the program’s mission and core values. Learn about the current size and diversity of Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
01/09/2024 - This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is a programming language and Read More...
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Bioinformatics
10/04/2023 - This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is a programming language and Read More...
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Bioinformatics
Throughout this module, we will be running various tools, including helper R scripts on the Unix command line to analyze the HBR and UHR RNA sequencing dataset. The helper R scripts were developed by the Read More...
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Bioinformatics
Throughout this module, we will be running various tools, including helper R scripts on the Unix command line to analyze the HBR and UHR RNA sequencing dataset. The helper R scripts were developed by the Read More...
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Bioinformatics
Biostars on Biowulf To complement this course, there is a module available on Biowulf with installed programs associated with the Biostar Handbook. During class, we will work on the command line on the GOLD system Read More...
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Bioinformatics
Here, let's change back in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder. cd $hbr_uhr_hisat2 To align FASTQ files for one sample, we construct the HISAT2 command with the following options Read More...
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Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, 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
Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...
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Bioinformatics
07/13/2023 - The Comparative Genome Viewer (CGV) is a visualization tool that helps you quickly compare two genomes based on assembly-assembly alignments provided by NCBI. CGV includes eukaryotic (animal, plant and fungal) assemblies, and many cross-species Read More...
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Bioinformatics
06/06/2023 - This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is Read More...
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Bioinformatics
Course Overview Welcome to the Data Visualization with R Series A series of lessons designed to introduce learners to the R package ggplot2 This course will include a series of lessons for scientists with beginner Read More...
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Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
01/18/2023 - This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is a programming language and 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
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
Lesson 5: Microbial diversity, alpha rarefaction, alpha diversity Learning Objectives Understand the difference between alpha and beta diversity Introduce several alpha diversity metrics Understand what rarefaction is and why it is important Introduce the debate regarding Read More...
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Bioinformatics
Lesson 17: RNA sequencing review 2 Learning objectives This lesson will serve as comprehensive review of Module 2. We will spend roughly the first hour reviewing the Module 2 material the second hour answering specific questions from the poll Read More...
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Bioinformatics
Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...
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Bioinformatics
Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...
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Bioinformatics
Lesson 1: Introduction to Biowulf, Unix, and R Learning Objectives Learn about why you may want to use R on Biowulf. Refresh Unix and R skills. This lesson will not be hands on. Why use R Read More...
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Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
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Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
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Bioinformatics
Objectives Combine multiple plots into a single figure Learn how to use aspects of cowplot and patchwork The primary purpose of this lesson is to learn how to combine multiple figures into a single multi-panel 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
Stat Transformations: Bar plots, box plots, and histograms Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar plots, box & whisker plots, and histograms. 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
/* Whole document: */ body{ font-family: Times; font-size: 16pt; } Stat Transformations: Bar plots, box plots, and histograms Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar Read More...
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Bioinformatics
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...
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Bioinformatics
Introduction to R and RStudio IDE 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 3. Read More...