Search Results for: assays

The PPS encompasses all scientific analyses related to pharmacology, once the specimen has been collected and stored. There is a multi-step process to evaluate how the drug is being handled by the body after administration. Read More...

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...

October 6, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NIH Center For Human Immunology, Inflammation, And Autoimmunity (CHI) CHI is a Read More...

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...

The CCR-Frederick Flow Cytometry Core Facility provides research support to the Frederick-CCR community, including cytometry analysis and sorting services, instrument maintenance, new user training, and technical consultation. Typical Assays Performed by Core Instruments Immunophenotyping of Read More...

The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...

Protein and Metabolite Characterization Core (PMCC), formerly known as the Protein Characterization Lab (PCL),  offers various technologies to CCR investigators to characterize proteins and metabolites. The core develops and applies state-of-the-art analytical technologies, primarily mass Read More...

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

The NIH Metabolomics Consortium (NIH-MC) 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 NIH-MC is Read More...

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...

Home Biophysics Core Technologies Biophysics Core Services The Biophysics Core The Biophysics Core Facility (BCF) was established in 2008 in the NHLBI as an advanced service laboratory providing expertise, training, consultations, and instrument access for intramural Read More...

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...

The Molecular Pathology Unit is intended to spearhead opportunities for bridging basic and clinical research efforts by more precisely optimizing the development, characterization, and utilization of models of human disease. The initiative approach includes both Read More...

The Clinical Flow Cytometry Laboratory provides extensive support for NCI clinical protocols by providing diagnostic testing for leukemia and lymphoma in patients either on NCI clinical protocols or undergoing testing to determine eligibility for NCI 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 News & Updates June 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Visit here to learn about services from Read More...

The Biological Products Core provides the AIDS research community with high-quality purified preparations of various strains of Human Immunodeficiency Virus (HIV) and Simian Immunodeficiency Virus (SIV), economically prepared by leveraging the economy of scale. Materials 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...

As a multi-user facility, the different instruments provide a wide range of imaging modes for EIB scientists, from standard immunohistochemistry, through brightfield and wide-field epifluorescence imaging, to highly complex live cell confocal microscopy and super-resolution Read More...

Back Services: Biophysics Facility offers Tycho as an open-access instrument.  This instrument is very easy to use, and no formal training is required.  Core staff will help with their first experiment of new Read More...

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...

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...

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...

The Flow Cytometry Core (LGI) offers established technologies to support studies using flow cytometry and cell sorting. Established Technologies Applications that run on FACS Caliburs include: Immunophenotyping (up to 4-color), Intracellular markers, including cytokines and Read More...

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...

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

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...

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...

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...

Partek Flow is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data. Why Partek Flow? Partek Flow is compatible with all major genomic formats Read More...

Partek Flow is a graphical user interface (GUI) based bioinformatics software that is dedicated to the analysis of next generation sequencing (NGS) data. Why Partek Flow? Partek Flow is compatible with all major genomic formats Read More...

04/03/2025 - DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such Read More...

Transformed data will be available in the SCT assay, which is set as the default after running sctransform. During normalization, we can also remove confounding sources of variation, for example, mitochondrial mapping percentage The glmGamPoi Read More...

The Seurat v5 object doesn’t require all assays have the same cells. In this case, Cells() can be used to return the cell names of the default assay while colnames() can be used to Read More...

The Seurat Object is a data container for single cell RNA-Seq and related data. It is an S4 object, which is a type of data structure that stores complex information (e.g., scRNA-Seq count matrix, Read More...

First, notice that you can easily access columns from the sample metadata ( colData() ) using $ . Using brackets to subset: se$SampleName ## [1] GSM1275862 GSM1275863 GSM1275866 GSM1275867 GSM1275870 GSM1275871 GSM1275874 ## [8] GSM1275875 ## 8 Levels: GSM1275862 GSM1275863 GSM1275866 GSM1275867 ... GSM1275875 se$ Read More...

So far, this course series has addressed several areas that are important for anyone venturing into bioinformatics. These include: Available bioinformatics resources and tools at NIH Various assays to measure the different components of the Read More...

06/09/2020 - The presentation will cover cfDNA sequencing capabilities and what has been learned in quality control and ways to measure successful assays through the group's efforts to develop and validate processes for comprehensive (exome) Read More...

Included applications are fairly easy to navigate even for individuals with little to no bioinformatic experience. Tools facilitate the planning of molecular biology experiments and produce publishable visualizations. Lasergenes' molecular biology application is recommended for Read More...

No summary available.

Our Mission The NCI Optical Microscopy Cores are instrumental in advancing cancer research through optical measurements and analysis. Serving the Center for Cancer Research community, which is home to approximately 250 Principal and Senior Investigators across 50 Read More...

06/06/2024 - The CCR Genomics Core Facility is pleased to host a virtual technology workshop with EpiCypher on CUT&amp;RUN library prep/sequencing Presentation overview: The location of histone post-translational modifications and chromatin-associated proteins Read More...

Differential expression analysis is the process of identifying genes that have a significant difference in expression between two or more groups. For many sequencing experiments, regardless of methodology, differential analysis lays the foundation of the Read More...

Here, we will start with the data stored in a Seurat object. For instructions on data import and creating the object, see an Introduction to scRNA-Seq with R (Seurat) . adp

03/27/2024 - DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such Read More...

The SummarizedExperiment class and the inherited class RangedSummarizedExperiment are available in the R package SummarizedExperiment . SummarizedExperiment is a matrix-like container where rows represent features of interest (e.g. genes, transcripts, exons, etc.) and columns represent Read More...

We can use the airway package to see how this container works, including how to access and subset the data. What is the airway package? There are data sets available in R to practice with Read More...

10/25/2023 - Every week, thousands of biomedical research papers are published with a portion of them containing supporting tables with data about genes, transcripts, variants, and proteins. For example, supporting tables may contain differentially expressed genes Read More...

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...

03/23/2023 - This afternoon workshop will give attendees an understanding of how single cell technologies are used to study cancer. To start us off, Mike Kelly , head of the Single Cell Analysis Facility (SCAF), will give Read More...

05/25/2021 - Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m61e3ea39fde3a9a94a96efeaa519a656 TOPIC: AI in Drug Development, presented by the ATOM consortium In this class, we will Read More...

05/25/2021 - Registration:   https://btep.ccr.cancer.gov/classes/ai_one/ Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m61e3ea39fde3a9a94a96efeaa519a656 Description:  This talk will introduce basic Read More...

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...

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. &amp; Wink, D. A. NOS2 and Read More...

07/11/2024 - Please join us for this special event featuring three speakers on the topic of Single-Cell Spatial Transcriptomics. George Zaki, Ph.D., Director, Applied Scientific Computing, BACS, The Frederick National Lab for Cancer Research, NCI/ Read More...

One particular critique of differential expression in single cell RNASeq analysis is p-value "inflation," where the p-values get so small that there are far too many genes exist with p-values below 0.05, even after Read More...

It is next standard to scale and center the features in the data set prior to dimension reduction or visualization via heatmap. Scaling the data will keep highly expressed genes from dominating our analysis. This Read More...

Much like pseudobulk differential expression, the RNA expression can be collapsed into pre-defined components, such as the clusters, if it is believed that cell-to-cell variation is inducing too much confusion in the labeling. This collapsing Read More...

Some tools have been described in the previous session (see here ). Today, we will be focusing on the SingleR tool, which also requires the celldex package . In short, SingleR operates by comparing your current dataset Read More...

Here, we will start with the data stored in a Seurat object. For instructions on data import and creating the object, see an Introduction to scRNA-Seq with R (Seurat) and Getting Started with Seurat: QC Read More...

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

As you can see from the image, there are several accessor functions to access the data from the object: assays() - access matrix-like experimental data (e.g., count data). Rows are genomic features (e.g., Read More...

S4 objects store complex information that isn't necessarily simple to save. If you intend to work with the object further, try using saveRDS . saveRDS(se, "airways.rds") #save the object Note saveRDS() Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To better understand S4 objects as they relate to the Bioconductor core infrastructure. To learn more about a popular Bioconductor S4 Read More...

Why did we focus so heavily on the tidyverse if it can't be used to manipulate Bioconductor objects? Well, for one, regardless of whether you are a user of Bioconductor packages, you will often Read More...

The object class used by the DESeq2 package to store the read counts and the intermediate estimated quantities during statistical analysis is the DESeqDataSet. --- Analyzing RNA-seq data with DESeq2 Constructing this object from a Read More...

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

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

Bioconductor is an R package repository for free open-source software that "facilitates rigorous and reproducible analysis of data from current and emerging biological assays" . Bioconductor is released semi-annually, with two working Bioconductor releases Read More...

05/19/2023 - Patient-derived cancer models (PDCM) have become an essential tool in both cancer research and preclinical studies. Each model type offers unique advantages and is better suited for specific research areas: cell lines are low Read More...

04/22/2021 - Abstract: Single-cell RNA-sequencing has emerged as a popular technique for dissecting temporal processes such as tumor development and cell differentiation from snapshots of asynchronous ensembles of cells. Ongoing efforts in this area are now Read More...

04/20/2021 - Abstract: Single-cell genome-wide profiling offers an approach to map transitional cell states during cell differentiation, disease onset, and drug response. Lineage-tracing, in which cells are labeled with hereditary markers, offers an approach to establishing Read More...

No summary available.

WIDE-FIELD MICROSCOPY Nikon Ti 2000 wide-field microscope Capabilities:&nbsp;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 L. Balagopalan, T. Moreno, H. Qin, B. C. Angeles, T. Kondo, J. Yi, K. M. McIntire, N. Alvinez, S. Pallikkuth, M. E. Lee, H. Yamane, A. D. Tran, P. Youkharibache, R. E. Cachau, N. Taylor, Read More...

Software LAS Leica Application Suite X (LAS X) is the one software platform for all Leica microscopes: It integrates confocal, wide field, stereo, super-resolution, and light-sheet instruments from Leica Microsystems. MetaMorph The MetaMorph® Microscopy Automation Read More...

Gianluca Pegoraro, PhD gianluca.pegoraro@nih.gov Facility Head 240-760-6696 Bldg. 41, Room B909 Dr. Pegoraro received his Ph.D. in Molecular Genetics from the International School of Superior Studies in Trieste, Italy in 2004. After Read More...

Gianluca Pegoraro, PhD gianluca.pegoraro@nih.gov Facility Head 240-760-6696 Bldg. 41, Room B909 Dr. Pegoraro received his Ph.D. in Molecular Genetics from the International School of Superior Studies in Trieste, Italy in 2004. After Read More...

2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...

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...

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...

1. Introduction and Learning Objectives This tutorial has been 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 that Read More...

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...

Objectives Review important data wrangling functions Put our wrangling skills to use on a realistic RNA-Seq data set Data Wrangling Review Important functions by topic Importing / Exporting Data Importing and exporting data into the R 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...

Managing Bioinformatics Projects with Jupyter Lab Learning Objectives After this class, participants will have obtained the foundation needed to start using Jupyter Lab as an all-in-one place to maintain code, output, and other description of Read More...

No summary available.