Bethesda, MD
Repositories
Trans NIH Facility
The CHTN is a unique NCI-supported resource that provides human tissues and fluids from routine procedures to investigators who utilize human biospecimens in their research. Unlike tissue banks, the CHTN works prospectively with each investigator Read More...
Bethesda, MD
Collaborative
Repositories
The National Clinical Trials Network Biospecimen Banks (NCTN) receive, store, and distribute human cancer biospecimens collected on NCTN clinical trials. NCTN Biobanks provide cancer researchers with quality, well-annotated biospecimens and associated clinical information. The NCTN Read More...
ROCKVILLE, MD
Repositories
Trans NIH Facility
The Specimen Resource Locator (SRL) is a biospecimen resource database designed to help researchers locate resources that may have the samples needed for their investigational use. This publicly searchable database includes information about biospecimen banks Read More...
Web Page
Biomarker Discovery with Morphological Context: Changing how tissue specimens are analyzed < https://youtu.be/mVhfZq8ppbc What is Digital Spatial Profiling? GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial Read More...
Web Page
Bioinformatics
We can add a spacer using plot_spacer() to add blank sections to our plot. These blank sections are the size of our figure panels and may be different depending on how the plot is Read More...
Web Page
Bioinformatics
We can add a spacer using plot_spacer() to add blank sections to our plot. These blank sections are the size of our figure panels and may be different depending on how the plot is Read More...
Web Page
Bioinformatics
You can annotate your code by starting annotations with # . Comments to the right of # will be ignored by R. Use # ---- to create navigable code sections. For report generation, use R Markdown or Quarto .
Web Page
Bioinformatics
VCF is a data representation format used to describe variations in the genome. VCF files can contain information on any number of samples (thousands). VCF is composed of two sections, a header section and record Read More...
Web Page
Bioinformatics
You can annotate your code by starting annotations with # . Comments to the right of # will be ignored by R. Use # ---- to create navigable code sections.
Web Page
Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.
Frederick, MD
Core Facility
The FNLCR Molecular Histopathology Laboratory (MHL) provides comprehensive veterinary pathology support for animal health monitoring, biomarker discovery and validation, drug development, genomics, and proteomics on a cost recovered basis. The MHL is organized into multiple Read More...
Web Page
Bioinformatics
04/11/2024 - Informaticians aim to bring the right information to the forefront at the right time to improve decision-making. Dr. Greene's lab develops computational methods that integrate distinct large-scale datasets to extract the rich and Read More...
Web Page
Bioinformatics
The NCI CCR Sequencing Facility will send researchers a link to the data, which is stored in their Data Management Environment (DME). Again, instructions for connecting DME to a Globus endpoint on Biowulf are in Read More...
Web Page
Bioinformatics
Those researchers who used the NCI CCR Sequencing Facility to get sequencing done will receive a link to their data. This data can be transferred to the "PartekFlow" folder on Biowulf using Globus. Read More...
Web Page
Bioinformatics
04/13/2023 - In this hands-on virtual lab, the participants will familiarize themselves with Deep Learning concepts and techniques, using MATLAB Online to train deep neural networks on GPUs in the cloud, create Read More...
Web Page
Bioinformatics
11/17/2022 - In this hands-on virtual lab, the participants will familiarize themselves with Deep Learning concepts and techniques, using MATLAB Online to train deep neural networks on GPUs in the cloud, create deep learning models from Read More...
Web Page
Bioinformatics
06/15/2021 - In this hands-on virtual lab, the participants will familiarize themselves with Deep Learning concepts and techniques, using MATLAB Online to train deep neural networks on GPUs in the cloud, create deep learning models from Read More...
Web Page
The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...
Frederick, MD
Core Facility
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...
Web Page
Bioinformatics
Accessing Partek Flow at NIH and tips for data transfer Learning objectives After consulting this guide, participants will Know how to access Partek Flow at NIH. Be able to transfer data from NCI CCR Sequencing Read More...
Web Page
Bioinformatics
Now we know a bit about using functions, but what if I had no idea what the function round() was used for or what arguments to provide? Getting help in R is fairly easy. In Read More...
Web Page
Bioinformatics
To create an R object, you need a name, a value, and an assignment operator (e.g.,
Web Page
Bioinformatics
10/20/2023 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with statistical Read More...
Web Page
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...
Web Page
Bioinformatics
Now we know a bit about using functions, but what if I had no idea what the function round() was used for or what arguments to provide? Getting help in R is fairly easy. In Read More...
Web Page
Bioinformatics
10/18/2022 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with statistical Read More...
Web Page
Bioinformatics
12/10/2021 - About the Seminar Dr. Greene plans to discuss the richness of open data resources in biology and how they can support machine learning approaches and be enriched by such methods. He’ll also discuss Read More...
Web Page
Bioinformatics
10/28/2020 - Register In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with Read More...
Web Page
Bioinformatics
Upon opening the MultiQC report, the user will be greeted with a navigation panel (similar to that found in the individual FASTQC reports) that allows users to quickly move to different sections of the report. Read More...
Web Page
Bioinformatics
Now we know a bit about using functions, but what if I had no idea what the function setwd() was used for or what arguments to provide? Getting help in R is fairly easy. In Read More...
Web Page
Bioinformatics
Read the documentation! Know what the functions you use actually do. Read package vignettes. Keep your code neat and clean. You can do this by following a style guide, for example, the tidyverse style guide. Read More...
Web Page
Bioinformatics
Read the documentation! Know what the functions you use actually do. Read package vignettes. Practice! The more you engage with R programming the more proficient you will become. With time, handling error messages will become Read More...
Web Page
Bioinformatics
The usethis package can also be used to set up version control for R Studio projects. Goto the console in R Studio and load the usethis package. If not installed, just do install.packages(usethis). Read More...
Frederick, Maryland
Core Facility
CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...
Web Page
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...
Web Page
Many established and emerging technologies are available to CCR scientists. This technology-rich environment makes the CCR a unique place to conduct scientific research. Through the OSTR, the CCR continues to find Read More...
Frederick, MD
Collaborative
The Medicinal Chemistry Accelerator (MCA) is a collaborative CCR resource that supports investigators in developing small molecule inhibitors for anticancer drug candidates. While CCR and NCATS have infrastructure to identify initial “hits” through high-throughput screening, Read More...
Web Page
Bioinformatics
Look at the distribution of nCount_RNA with a Violin plot: # set colors cnames% ggplot(aes(color=orig.ident, x=nCount_RNA, fill= orig.ident)) + geom_density(alpha = 0.2) + theme_classic() + scale_x_log10() + geom_vline( Read More...
Web Page
Bioinformatics
Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...
Web Page
Bioinformatics
Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...
Web Page
Bioinformatics
When analyzing high throughput sequencing data, we will need to trim away adapters. Adapters help anchor the unknown sequencing template to the Illumina flow cell and can interfere with alignment. We may also want to Read More...
Web Page
Bioinformatics
This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes Read More...
Web Page
Bioinformatics
10/25/2022 - Speaker: Jill S. Barnholtz-Sloan, Ph.D. Associate Director Informatics and Data Science at the Center for Biomedical Informatics and Information Technology Senior Investigator Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, NCI Dr. Read More...
Web Page
Bioinformatics
06/08/2021 - Do you want to know how to use Machine Learning (ML) for accelerating drug discovery? Join us on June 8, 1:00 pm – 2:00 pm ET, for the first in a series of workshops on how to use Read More...
Web Page
Bioinformatics
03/11/2021 - Abstract: Targeted quantitative proteomics using multiple/parallel reaction monitoring (MRM, PRM) is already being applied by many researchers in biology, biochemistry, and clinical research laboratories. These methods allow rapid and precise quantitation of proteins Read More...
Web Page
Bioinformatics
08/10/2020 - Copy Number Variation (CNV) is a type of structural variation in which sections of the genome are duplicated or deleted. Associated with being causal mutations for disease phenotypes, it is important in clinical and Read More...
Web Page
Bioinformatics
06/16/2000 - We present the AMARETTO-Hub as a Knowledge Graph-based software platform that leverages Neo4j and Shiny to embed and interactively interrogate results generated by the *AMARETTO software toolbox that offers modular and complementary solutions Read More...
Web Page
Bioinformatics
Upon opening the MultiQC report, the user will be greeted with a navigation panel (similar to that found in the individual FASTQC reports) that allows users to quickly move to different sections of the report. Read More...
Web Page
Bioinformatics
After data has been transferred to the NIH Partek Flow server, the next step is to import them into a project. Sign onto Partek Flow and hit the "New project" button click to Read More...
Web Page
Bioinformatics
Jupyter Notebook utilizes markdown for text editing. "Markdown is is a lightweight markup language for creating formatted text using a" -- https://en.wikipedia.org/wiki/Markdown We can use different size headings Read More...
Web Page
What is Xenium? Xenium is a high-resolution, imaging-based in situ spatial profiling technology from 10x Genomics that allows for simultaneous expression analysis of RNA targets (currently in range of 100’s) within the same tissue section. Read More...
Frederick, MD
Collaborative
The Center for Advanced Preclinical Research (CAPR) specializes in evaluating the efficacy of preclinical compounds, existing drugs, or biologics (therapeutics) in genetically engineered mouse models, GEM-derived allograft (GDA) models, or patient-derived mouse xenografts (PDX). We Read More...
Frederick, MD
Core Facility
The Clinical Support Laboratory offers processing, tracking, and testing of a broad range of clinical samples. Support can begin at the early stages of clinical trial development to aid in developing a comprehensive strategy for Read More...
Web Page
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...
Web Page
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...
Web Page
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
We previously stored FASTQC results for the HBR and UHR raw sequencing data in the ~/biostar_class/hbr_uhr/QC directory (recall that ~ denotes home directory). So before getting started, change into this folder. cd ~/ Read More...
Web Page
Bioinformatics
Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...
Web Page
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...
Web Page
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...
Web Page
Bioinformatics
Lesson 16: RNA sequencing review and classification based analysis Before getting started, remember to be signed on to the DNAnexus GOLD environment. Review In the previous classes, we learned about the steps involved in RNA sequencing Read More...
Web Page
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...
Web Page
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...
Web Page
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...
Web Page
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...