Search Results for: Lattice Light Sheet

The Biophysics Resource (BR) was established in January 2001. Our mission is to provide CCR investigators with access to both the latest instrumentation and expertise in characterizing the biophysical aspects of systems under structural investigation. The Read More...

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...

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...

The NIH Library is a biomedical research library, whose collection and services are available at no cost to NIH staff: Electronic Resources: Over 20,000 electronic journals, 190,000 eBooks, and 50 databases. , Training classes covering topics such as data Read More...

Home About the Biophysics Core Biophysics Core Services [tabby title="Instrumentation"] NHLBI Biophysics Core The Biophysics Core Facility: Overview Core Facilities provide scientific resources, cutting-edge technologies and novel approaches to support DIR scientists. Availability of Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. We would greatly appreciate Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

The LCBG Microscopy Core offers imaging technologies and training. The Core has established instrumentation for for 2D and 3D imaging of both fixed and living specimens.

Back Services: Biophysics Facility offers Octet as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes a full analysis of a Read More...

Back Services: Biophysics Facility offers MST as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes the KD determination of a Read More...

Services: Biophysics Facility offers CD as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: CD spectroscopy measures the difference Read More...

Back Services: Biophysics Facility offers CD as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: CD spectroscopy measures the Read More...

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...

The Chemistry and Synthesis Center (CSC) of the National Heart, Lung, and Blood Institute (NHLBI) provides IRP scientists with targeted imaging probes and chemical tools that help accelerate cell-based assays, in vivo imaging studies, and Read More...

In order to meet increasing demands from both NIH intramural and extramural communities for access to a small angle X-ray scattering (SAXS) resource, the Center for Cancer Research (CCR) under the leadership of Drs. Jeffrey Read More...

The lattice package is another prominent graphic system in R. Like ggplot2 this is also based on the grid package. For more information comparing the three plotting systems, see this chapter from Exploratory Data Analysis Read More...

The lattice package is another prominent graphic system in R. Like ggplot2 this is also based on the grid package. For more information comparing the three plotting systems, see this chapter from Exploratory Data Analysis Read More...

09/12/2024 - Telomere to telomere (T2T) genome assemblies represent a paradigm shift in comparative genomics, offering insights into chromosome structure, evolution, and function at the highest resolution. Dr. O'Neill's lab has made recent Read More...

Hands on Programming with R R for Data Science (R4DS) BTEP R Introductory Series Base R cheat sheet RStudio cheat sheet

The best way to sign onto Biowulf from a Mac is to use the built-in terminal (Figure 4). Use the Spot Light search at the Mac menu bar to search for the Terminal application. Click on Read More...

The best way to sign onto Biowulf from a Mac is to use the built-in terminal (Figure 4). Use the Spot Light search at the Mac menu bar to search for the Terminal application. Click on Read More...

There are 3 primary plotting systems with R: base R, ggplot2 , and lattice . Check out the R Graph Gallery for data visualization examples and code.

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...

05/29/2025 - Prostate cancer exhibits significant intratumoral heterogeneity, driving a spectrum of phenotypes ranging from indolent disease to aggressive metastasis, challenging risk stratification and treatment. A key feature of this heterogeneity is clonal diversity, encompassing both Read More...

There are 3 primary plotting systems with R: base R, ggplot2 , and lattice . Data visualization functions from Seurat primarily use ggplot2 and can easily be customized by adding additional ggplot2 layers. Check out the R Graph Read More...

Base R cheat sheet Other cheat sheets can be found here . There is also a nice review here . There are a ton of free tutorials. There are at least 230 Git repositories that focus on R Read More...

BashScripting_LinuxCommands from the NIH HPC team Fosswire linux reference sheet

Base R cheat sheet Other cheat sheets can be here . There is also a nice review here .

BashScripting_LinuxCommands from the NIH HPC team Fosswire linux reference sheet

R is a computational language and environment for statistical computing and graphics. Advantages of R programming: open-source extensible (Packages on CRAN (> 19,000 packages), Github, Bioconductor) Wide community allows reproducibility (R scripts, Rmarkdown, Quarto). includes Read More...

Include a cheat sheet and flow diagram of how the versioning process works with Git. Git detached HEAD

ZEISS Elyra 7 with Lattice SIM² Type: Wide-field structured illumination microscope Capabilities: Super resolution 2D and 3D imaging of live or fixed cells Apotome SIM: 170 nm lateral, 450 nm axial Apotome SIM2: 140 nm lateral, 300 nm axial Lattice Read More...

07/08/2025 - Thi pre entation de cribe the ba ic mechanic of con tructing a deci ion tree and interpreting the re ult . Deci ion tree will be u ed to determine factor a ociated with 2 Read More...

[et_pb_section bb_built="1" _builder_version="3.0.84" custom_margin="0px|||" custom_padding="0px|||"][et_pb_row _builder_version="3.0.47" background_size="initial" background_position=& Read More...

:::: {.columns} ::: {.column width="10%"} ::: :::{.column width="80%"} R is a computational language and environment for statistical computing and graphics. ::: :::: Advantages of R programming: open-source extensible (Packages on CRAN (> 19,000 packages), Github, Bioconductor) Read More...

Each participant will be assigned a student account. See here for student account assignment. Please use this account throughout this course. Enter NIH credentials to see the student account assignment sheet after clicking the link.

Each participant will be assigned a student account. See here for student account assignment. Please use this account throughout this course. Enter NIH credentials to see the student account assignment sheet after clicking the link.

BashScripting_LinuxCommands from the NIH HPC team Fosswire linux reference sheet

BashScripting_LinuxCommands from the NIH HPC team Fosswire linux reference sheet

Click on the "Add project" tab to create a new analysis project. Import data: Partek Flow handles many data types but for this class, we will select bulk and then RNA. Partek Flow Read More...

03/20/2024 - Our series of talks continues with two 20-minute presentations.  There will be light refreshments (coffee and donuts) provided, so please consider attending in person! We encourage attendees to stay and chat with Read More...

01/10/2024 - Our series of talks continues next month with two 20-minute presentations focused on single cell genomics studies in the model organism zebrafish.  There will be light refreshments and we encourage attendees to Read More...

Import data from the sheet "iris_data_long" from the excel workbook (file_path = "./data/iris_data.xlsx"). Make sure the column names are unique and do not contain spaces. Save Read More...

Excel files are the primary means by which many people save spreadsheet data. .xls or .xlsx files store workbooks composed of one or more spreadsheets. Importing excel files requires the R package readxl . While this Read More...

10/04/2023 - Our series of talks continues this month with two 20-minute presentations.  There will be light refreshments and we encourage attendees to stay and chat with colleagues after the presentations.   & Read More...

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...

01/07/2022 - Environmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases including lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to Read More...

02/17/2021 - Speaker is Dr. Michal Linial from the Hebrew University of Jerusalem, Israel. Abstract: Incredible progress has also been made in the field of cancer genetics with the sequencing and molecular profiling of tens of Read More...

Sign onto Biowulf using the assigned student account. Remember, Windows users will need to open the Command Prompt and Mac users will need to open the Terminal. Also remember to connect to the NIH network Read More...

Sign onto Biowulf using the assigned student account. Remember, Windows users will need to open the Command Prompt and Mac users will need to open the Terminal. Also remember to connect to the NIH network Read More...

The data used in this practice exercise can be found here. Q1. Import data from the sheet "iris_data_long" from the excel workbook (file_path = "./data/iris_data.xlsx"). Make Read More...

Sign onto Biowulf using the assigned student account. Remember, Windows users will need to open the Command Prompt and Mac users will need to open the Terminal. Also remember to connect to the NIH network Read More...

Sign onto Biowulf using the assigned student account. Remember, Windows users will need to open the Command Prompt and Mac users will need to open the Terminal. Also remember to connect to the NIH network Read More...

Sign onto Biowulf using the assigned student account. Remember, Windows users will need to open the Command Prompt and Mac users will need to open the Terminal. Also remember to connect to the NIH network Read More...

Sign onto Biowulf using the assigned student account. Remember, Windows users will need to open the Command Prompt and Mac users will need to open the Terminal. Also remember to connect to the NIH network Read More...

WIDE-FIELD MICROSCOPY Nikon Ti 2000 wide-field microscope Capabilities: This microscope is suited for live cell imaging (4D) and fixed cells (3D) imaging. This microscope produces high quality wide-field images that may be improved by Read More...

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...

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...

Help Session Lesson 3 Loading data Import data from the sheet "iris_data_long" from the excel workbook (file_path = "./data/iris_data.xlsx"). Make sure the column names are unique and 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...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Activate the bioinformatics environment. conda activate bioinfo First let's make a place to store today's work. In your biostar_class Read More...

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...

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...

06/22/2022 - Cancer origination and progression is a complex process that can be viewed as a somatic evolutionary progression with clonal cellular expansion(s) driven by accumulation of survival-/evasion-beneficial genomic mutations, alongside constantly changing selective Read More...

02/16/2022 - For our next CDSL webinar we will have a guest lecture by Dr. Leng Han from the Center for Epigenetics and Disease Prevention at Texas A&M University. Abstract: Despite advancements in Read More...

Q1. Import data from the sheet "iris_data_long" from the excel workbook (file_path = "./data/iris_data.xlsx"). Make sure the column names are unique and do not contain spaces. Read More...

Excel files are the primary means by which many people save spreadsheet data. .xls or .xlsx files store workbooks composed of one or more spreadsheets. Importing excel files requires the R package readxl. While this Read More...

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...

Navigate to the GDC Data Portal at https://portal.gdc.cancer.gov/ To select your cases of interest, you can navigate to "Projects" or "Cohort Builder" Let's use breast cancer Read More...

Load the data: library(readxl) TCR_fp<-file.path("..","data","S1_VLOOKUP","TCR_example", "4261-R1_filtered_contig_annotations.xlsx") df<-read_ Read More...

Software Image Acquisition Commercial imaging systems of LRBGE Optical Microscopy Core are controlled by acquisition software specifically designed for the appropriate microscope, such as ZEN (Zeiss confocal microscopes), Nikon Elements (Nikon), Imspector (Abberior). Custom-built HILO Read More...

General Usage Policies Principal investigators should read this document and sign it. PI’s/postdocs should attach a short-written summary of the project to the signed doc. If the project changes, 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...

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...

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...

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...

Learning Objectives Understand the components of an HPC system. How does this compare to your local desktop? Learn about Biowulf, the NIH HPC cluster. Learn about the command line interface and resources for learning. What Read More...

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...

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...