Frederick, MD
Repositories
Trans NIH Facility
DTP’s Natural Products Repository is the world’s largest storehouse of natural products. It houses close to >200,000 extracts from samples of more than 70,000 plants and >20,000 marine organisms collected from more than 29 countries, plus extracts Read More...
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Bioinformatics
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...
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Bioinformatics
To begin plotting, let's load our tidyverse library. #load libraries library(tidyverse) # Tidyverse automatically loads ggplot2 ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ## ✔ dplyr 1.1.3 ✔ readr 2.1.4 ## ✔ forcats 1.0.0 ✔ stringr 1.5.0 ## ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 ## ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 ## ✔ purrr 1.0.2 ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ## ✖ dplyr:: Read More...
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Bioinformatics
Used to perform specific tasks. R: product
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Bioinformatics
There are multiple ways to combine figures using R. In this lesson, we will learn how to combine figures primarily with patchwork . Though, we will also learn some components of cowplot . To get started, load Read More...
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Bioinformatics
There are multiple ways to combine figures using R. In this lesson, we will learn how to combine figures using two different R packages cowplot and patchwork , beginning with cowplot . To get started, load the Read More...
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Bioinformatics
To begin plotting, let's load our tidyverse library. #load libraries library(tidyverse) # Tidyverse automatically loads ggplot2 ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ## ✔ ggplot2 3.3.6 ✔ purrr 0.3.4 ## ✔ tibble 3.1.7 ✔ dplyr 1.0.9 ## ✔ tidyr 1.2.0 ✔ stringr 1.4.0 ## ✔ readr 2.1.2 ✔ forcats 0.5.1 ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ## ✖ dplyr::filter() masks stats:: 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
Used to perform specific tasks. R: ::: {.cell} product
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Bioinformatics
GO terms provide information about a gene product GO terms as a vocabulary are species agnostic, but there are species constraints ontology and annotations are updated regularly computer readable - suitable for bioinformatics GO integrates Read More...
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Bioinformatics
Each version of R loaded as a module includes a number of installed packages . However, you may want to install additional packages, which will by default be stored in " ~/R/%v/library where %v Read More...
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Bioinformatics
R Packages can be found at: CRAN METACRAN - to search for packages Bioconductor Github Python Python Package Index (PyPI)
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Bioinformatics
R Packages can be found at: CRAN METACRAN - to search for packages Bioconductor Github Python Python Package Index (PyPI)
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Bioinformatics
In this lesson, we will continue to use the ggplot2 package for plotting. To use ggplot2, we first need to load it into our R work environment using the library command. library ( ggplot2 )
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Bioinformatics
In this lesson, we will be using several external R packages. To utilize these, we need to first load them into our R working environment using the library command. library(ggplot2) #for plotting library(tidyr) # Read More...
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Bioinformatics
library(pheatmap) ## for heatmap generation library(tidyverse) ## for data wrangling library(ggplotify) ## to convert pheatmap to ggplot2 library(heatmaply) ## for constructing interactive heatmap
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Bioinformatics
library(ggplot2) library(pheatmap) library(tidyverse) library(ggplotify) library(heatmaply)
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Bioinformatics
library(pheatmap) ## for heatmap generation library(tidyverse) ## for data wrangling library(ggplotify) ## to convert pheatmap to ggplot2 library(heatmaply) ## for constructing interactive heatmap
Frederick, MD
Collaborative
The Molecular Targets Program (MTP) is an organizational entity within the Center for Cancer Research (CCR) at NCI. The MTP provides the focus and infrastructure to enable CCR tenured and tenure-track Principal Investigators to initiate Read More...
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Bioinformatics
libraries syntax variables functions data types loops and conditionals
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Bioinformatics
libraries syntax variables functions data types (dictionaries and tuples in python) loops and conditionals
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Bioinformatics
01/14/2025 - Join us for a webinar on EMERSE, a text processing system designed specifically for non-technical users, featuring David Hanauer, M.D., M.S. from the University of Michigan Medical School. EMERSE (Electronic Medical Record Read More...
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Bioinformatics
10/16/2024 - In this webinar, attendees will learn to call MATLAB from Python and to call Python libraries from MATLAB. In addition, they will learn how to use MATLAB’s Python integration to improve the compatibility Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
In Lesson 2, partipants will learn about ways to use R on Biowulf. The focus will be on interactively working with R on Biowulf. Two different ways of accessing RStudio will be demonstrated. In addition, there Read More...
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Bioinformatics
A programming language is a formal language that specifies a set of instructions for a computer to perform specific tasks. It is used to write software programs and applications, and to control and manipulate computer Read More...
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Bioinformatics
07/13/2023 - In Lesson 2 of Toward Reproducibility with R on Biowulf , partipants will learn about ways to use R on Biowulf. The focus will be on interactively working with R on Biowulf. Two different ways of Read More...
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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
To begin plotting, we need to load our ggplot2 library. Package libraries must be loaded every time you open and use R. If you haven't yet installed the ggplot2 package on your local machine, Read More...
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Bioinformatics
The object ( scaled_counts ) that we imported is a data frame. Data frames hold tabular data, like much of the data stored in spreadsheets. They are collections of vectors of the same length, but can Read More...
Frederick, MD
Collaborative
The primary objective of the Protein Technology Core (PTC) is to establish an experimental screening pipeline for single-domain antibodies termed nanobodies. Nanobodies are antibody fragments consisting of a single monomeric variable antibody domain. The PTC, Read More...
Frederick, MD
Core Facility
NCI LASP Genome Modification Core (GMC) is a CCR-dedicated facility that provides advice, training, and reagents to NCI scientists seeking to utilize CRISPR and other nucleases to generate genome modifications in primary cells, cell lines, Read More...
Rockville, MD
Core Facility
Trans NIH Facility
The Functional Genomics Laboratory (formerly, the RNAi Screening Facility) of the National Center for Advancing Translational Sciences (NCATS) assist investigators with all stages of project planning and execution, beginning with assay development through genome-wide siRNA Read More...
Rockville, MD
Repositories
Trans NIH Facility
DTP maintains a repository of synthetic compounds and pure natural products that are available to investigators for non-clinical research purposes. The Repository collection is a uniquely diverse set of more than 200,000 compounds that have been Read More...
Bethesda, MD
Collaborative
The Antibody Engineering Program (AEP) is located at the Laboratory of Molecular Biology, which is part of the Center for Cancer Research (CCR), an intramural program at the National Cancer Institute (NCI). AEP focuses on 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
09/09/2025 - Join&nb p;the National Heart, Lung, and Blood In titute (NHLBI)&nb p;for a hybrid work hop to explore how medicine will be tran formed by the current artificial intelligence ( 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
09/30/2024 - In this webinar, you'll gain insights into the Electronic Medical Record Search Engine (EMERSE). EMERSE is a simple, powerful tool to help researchers like you identify key data within free text clinical notes Read More...
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Bioinformatics
The total number of detected transcripts expressed in a cell is dependent on the amount of mRNA in a cell. Cells naturally vary in the total amount of mRNA expressed. However, the chemistry of the Read More...
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Bioinformatics
In genomics, we work with a lot of tabular data - data organized in rows and columns. The data structure that stores this type of data is a data frame . Data frames are collections of Read More...
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Bioinformatics
To begin plotting, we need to load our ggplot2 library. Package libraries must be loaded every time you open and use R. If you haven't yet installed the ggplot2 package on your local machine, Read More...
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Bioinformatics
10/11/2023 - This session focuses on R data types and data structures. In R, more advanced libraries (code) may require data to be a particular data type or data structure to perform a function or analysis. Read More...
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Bioinformatics
Normalization - the process of scaling data to account for uncontrolled factors affecting variation. Effect size - "the quantitative measure of the magnitude of a phenomenon" (Biostar Handbook). P-value - "the probability Read More...
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Bioinformatics
ORA and FCS discard a large amount of information. These methods use gene sets, and even if the gene sets represent specific pathways, structural information such as gene product interactions, positions of genes, and types Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
Trim and/or filter sequence to remove sequencing primers/adaptor and poor quality reads. Example programs: FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/ FASTQ files preprocessing. SeqKit is an ultrafast comprehensive Read More...
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Bioinformatics
Thus far we have: Downloaded raw RNA-Seq data (.fastq files). Examined raw data quality using fastqc and multiqc . Performed adapter and quality trimming using Trimmomatic . Aligned the raw sequences to a reference genome (human chromosome 22 Read More...
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Bioinformatics
developed as early as 1991 high-level, popular, general-purpose programming language that has a readable and easy to learn syntax Key features: easy to read easy to learn interpreted multi-platform wide community open source libraries (> 300,000) Two 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
developed as early as 1991 high-level, popular, general-purpose programming language that has a readable and easy to learn syntax Key features: easy to read easy to learn interpreted multi-platform wide community open source libraries (> 300,000) Two Read More...
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Bioinformatics
A programming language is a formal language that specifies a set of instructions for a computer to perform specific tasks. It's used to write software programs and applications, and to control and manipulate computer Read More...
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Bioinformatics
07/13/2023 - MATLAB provides two-way integration with many programming languages such as Python, which allows for greater collaboration between investigators. This webinar will cover how to call MATLAB from Python and how to call Python libraries Read More...
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Bioinformatics
05/23/2023 - NIH Text Mining and Natural Language Processing SIG is pleased to welcome you to a special event dedicated to Large Language Models. Abstract : The release of ChatGPT and the subsequent launch of GPT-4 by 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...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Intramural Core Resources NHGRI Flow Cytometry Core The Core performs high quality single cell analysis through the 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 Trans-NIH Metabolomics Core (TNMC) The TNMC is a shared research resource that provides targeted Read More...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Intramural CryoEM (NICE) Consortium NICE provides NCI, NIAID, NIEHS, NICHD, NIDCR, NEI, and NIA investigators with Read More...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Extramural Common Fund Resources Metabolomics Workbench Developed by the NIH Metabolomics Common Fund's National Metabolomics Data Repository ( Read More...
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The Antibody Engineering Program (AEP) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The program focuses on generating therapeutic antibodies by phage display technology, including human antibodies and Read More...
Rockville, MD
Trans NIH Facility
NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...
Frederick, MD
Collaborative
The Biopharmaceutical Development Program (BDP) provides resources for the development of investigational biological agents. The BDP supports feasibility through development and Phase I/II cGMP manufacturing plus regulatory documentation.The BDP was established in 1993. We Read More...
Bethesda, MD
Collaborative
The Behavioral Health Core (BHC) is comprised of the two separate but interrelated components: Psychosocial Support and Research Program, and, Health Psychology and Neurobehavioral Research Program., These teams provide specialized expertise, such as patient-reported and Read More...
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Bioinformatics
11/04/2024 - This one-hour interactive training will cover how to use the ScHARe cloud and Terra platform focusing on how to utilize over 260 social determinants of health (SDoH) data sets and analytic notebooks containing ready-to-use code. Read More...
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Bioinformatics
10/24/2024 - NIH Text Mining and Natural Language Processing SIG is pleased to welcome you to this special event featuring two extraordinary speakers focused on the applications of Deep Learning in Computational Biology. & Read More...
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Bioinformatics
04/21/2024 - Looking for an introduction to artificial intelligence (AI) or an opportunity to expand on what you already know? Attend this workshop hosted by the NIH-funded Bridge2AI CHoRUS network and the University of Florida Read More...
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Bioinformatics
The data type of an R object affects how that object can be used or will behave. Examples of base R data types include numeric, integer, complex, character, and logical. R objects can also have Read More...
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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
Factor in at least 3 replicates (absolute minimum), but 4 if possible (optimum minimum). Biological replicates are recommended rather than technical replicates. Always process your RNA extractions at the same time. Extractions done at different times lead Read More...
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Bioinformatics
Gene ontology and pathway analysis Objectives Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway Read More...
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Bioinformatics
Data Analysis Here are a pair of examples of RNASEQ complete workflows RNASEQ Pipeline from NCI CCBR https://github.com/CCBR/Pipeliner/blob/master/RNASeqDocumentation.pdf RNASEQ Nextflow Pipeline from nf-core https://nf-co.re/rnaseq Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...
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Bioinformatics
Another way to run BLAST is to create your own custom database, and search against it with query sequences. Usually you will not have to create your own blast database, you can download prebuilt databases Read More...
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Bioinformatics
Can you speed up your code with parallelization? Considerations: levels of parallelization: multiprocessing vs multithreads The most common form of parallelism in R is multiprocessing. This is usually explicitly done by you or package you Read More...
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Bioinformatics
Course Overview Welcome to Toward Reproducibility with R on Biowulf This course includes a series of four lessons designed for beginner to intermediate R users interested in working with R on Biowulf. The purpose of Read More...
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Bioinformatics
Once we have done this, we can activate renv within our project. But, first, let's verify the location of our renv cache. R renv::paths$cache() # Check the cache location renv::init(bioconductor = "3.16& Read More...
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Bioinformatics
Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...
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Bioinformatics
A common question posed to the Bioinformatics Training and Education Program (BTEP) is “How can I learn R and Python to analyze my data?”. First, it’s important to state that learning any programming language Read More...
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Bioinformatics
High resolution single cell profiling assays have provided an unprecedented view of many biological systems and processes, but the spatial context in which this biology is occurring is often crucial. Spatial profiling, including spatial transcriptomic Read More...
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Bioinformatics
In this lesson we will use two different sets of data. First, we will use data available with your base R installation, the iris data set, which is stored in object iris . These data include Read More...
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Bioinformatics
R objects have certain attributes, and these attributes will be important for how they can interact with certain methods / functions. Understanding the mode (storage type) or the class of an object will be important for Read More...
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CREx News & Updates November 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the NINDS Quantitative Magnetic Resonance Imaging Core. NINDS Read More...
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What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and Read More...
Frederick, MD
Core Facility
The research conducted within the Synthetic Biologics Core (SBC) Facility has a dual role: Generate chemical biology tools and drug candidates for molecular targets identified by NCI research groups, Develop novel effective methods and tools Read More...
Bethesda, MD
Collaborative
The NCI High-Throughput Imaging Facility (HiTIF) works in a collaborative fashion with NCI/NIH Investigators by providing them with the necessary expertise, instrumentation, and software to develop and execute advanced High-Throughput Imaging (HTI) assays. These Read More...
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CREx News & Updates August 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Learn more about services from the NHLBI Read More...
Frederick, MD
Core Facility
Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...
Bethesda, MD
Trans NIH Facility
The Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative The STRIDES Initiative aims to help NIH and its institutes, centers, and offices (ICOs) accelerate biomedical research by reducing barriers in utilizing Read More...
Bethesda, MD
Core Facility
The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...
Frederick, MD
Core Facility
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...
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Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols. This service is intended for the occasional users of this system. Researchers who expect to use this instrument Read More...
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Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols. This service is intended for the occasional users of this system. Researchers who expect to use this instrument Read More...
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Bioinformatics
The computational chemistry and protein modeling team in the Advanced Biomedical Computational Science (ABCS) group provides novel solutions in structural modeling and computational chemistry. Computational scientists in the group collaborate with NCI researchers by using Read More...
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Bioinformatics
Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we 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
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...
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Bioinformatics
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...
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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
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
RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...
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Bioinformatics
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...
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Bioinformatics
Lesson 1: Introduction to Unix and the Shell Lesson Objectives Course overview. Introduce Unix and describe how it differs from other operating systems. Introduce and get set up on DNAnexus and the GOLD system. Discuss ways 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
This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment and create a directory for today's work. conda activate bioinfo mkdir blast cd blast What is Read More...
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Bioinformatics
Lesson 2: Getting Started with R on Biowulf Learning objectives Understand how R can be deployed on Biowulf Understand how to access and use R modules Learn to create a custom R library on Biowulf Deploying Read More...
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Bioinformatics
Lesson 4: Submitting R Scripts via command line Learning Objectives Learn how to use R with less interaction Learn how to deploy sbatch R jobs, and learn about alternatives such as swarm . Learn about R job Read More...
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Bioinformatics
Lesson 3: R Project Management and renv Learning objectives Discuss the importance of reproducibility Learn ways to make R analyses more reproducible Learn how to set up and organize an R project Learn how to use Read More...
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Bioinformatics
Multi-figure panel Objectives Combine multiple plots into a single figure Learn how to use patchwork and cowplot 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
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
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
/* 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
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
Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn to construct cluster heatmap using the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify 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
Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn to construct cluster heatmap using the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify Read More...
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Bioinformatics
Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn how to work with the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify to 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
R basics 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 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
Data frames Objectives To be able to load, explore, and access data in a tabular format. To this end, students should understand the following: 1. how to import and export data 2. how to create, summarize, and Read More...