Search Results for: Multiple patient specific peptide vaccines

09/21/2020 - Join Meeting The Surgery Branch (SB) of the National Cancer Institute (NCI) is a combined laboratory and clinical research unit devoted to the development of innovative cancer immunotherapies. Efforts run the gamut from basic Read More...

Unlike an atomic vector, a list can contain multiple elements of different types, (e.g., character vector, numeric vector, list, data frame, matrix). Lists are not the focus of this lesson, but you should be Read More...

We see a similar organization of information for other annotation categories. For instance, DAVID pulls information on biomolecular processes, functions, and pathways from several sources such as UniProt, GO, KEGG, Reactome, and Wikipathways. For Gene Read More...

BioProject (Prefix: PRJNA, example: PRJNA257197): provides a description of the research project associated with the sequencing study. It includes information such as the study’s abstract, links to publications (if available), and links to project Read More...

NCI established the Nanotechnology Characterization Laboratory (NCL) to support the extramural research community to accelerate the progress of nanomedicine by providing preclinical characterization and safety testing of nanoparticles. It is a collaborative effort between NCI, Read More...

The Department of Laboratory Medicine provides state-of-the-art laboratory testing in support of Clinical Center patient care and will serve as a center of excellence in research and training in laboratory medicine, particularly in areas which Read More...

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...

The NIH Clinical Center Pharmacy Department provides pharmaceutical care to inpatients and outpatients on NIH intramural research protocols at the NIH Clinical Center. The Clinical Center facility encompasses 200 inpatient beds, 93 day-hospital stations, and 15 clinics. Clinical Read More...

The Clinical Image Processing Service (CIPS) offers timely and accurate advanced image processing of diagnostic radiology images for clinical care, research, and training. CIPS’ functions include clinical services and scientific researches. Established Technologies: CIPS can Read More...

Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, 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...

select() - Filters data by column. Check out associated helper functions: Select specific columns: everything() last_col() Select columns by matching some aspect of the column name: starts_with() ends_with() contains() matches() num_range() Read More...

09/11/2023 - We invite you to attend the Biobanking for Precision Medicine seminar series. The seminar series is brought to you by NCI’s Biorepositories and Biospecimen Research Branch (BBRB) and addresses current topics 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...

NCBI BioProject : PRJN#### (example: PRJNA257197 ) contains the overall description of a single research initiative; a project will typically relate to multiple samples and datasets. NCBI BioSample : SAMN#### or SRS#### (example: SAMN03254300) describe biological source material; Read More...

NCBI BioProject : PRJN#### (example: PRJNA257197 ) contains the overall description of a single research initiative; a project will typically relate to multiple samples and datasets. NCBI BioSample : SAMN#### or SRS#### (example: SAMN03254300) describe biological source material; Read More...

08/03/2023 - Identification of evolutionarily related DNA or protein sequences (homologs) is a crucial step in many biology workflows. For example, homologous sequences are used to infer relationships between organisms, understand how sequence changes affect observable Read More...

:::: {.columns} ::: {.column width="50%"} R Programming Data Visualization (Base R and ggplot2) additional packages that enhance these, especially for -omics data More packages for data science / bioinformatics Bioconductor Report generation R Markdown Quarto more Read More...

Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types and the code Read More...

R Course FAQs Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types Read More...

11/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

09/01/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

06/15/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

02/11/2022 - The seminar is open to the public and registration is required each month. Dr. Hunter Mosely plans to discuss the richness of open data resources in biology and how they can support machine learning Read More...

02/07/2022 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

01/12/2022 - Recent technological advances in science provide novel opportunities to unravel the complex biology of diseases. Immunological changes in translational settings are often highly dynamic and involve multiple interconnected biological systems. We will discuss a Read More...

12/15/2021 - In this seminar, Mrs. Aya Abdelsalam Ismail will give an overview on interpreting neural networks, with a particular focus on the use of Deep Neural Networks (DNNs) to track and predict changes over time. Read More...

10/13/2021 - Register for the  2021 Clinical Proteomics Tumor Analysis Consortium (CPTAC) Virtual Scientific Symposium  to hear CPTAC investigators share their latest discoveries in the field of cancer proteogenomics, cancer research, and  data analysis  tools. In addition Read More...

09/01/2021 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

05/03/2021 - Abstract: We will discuss technical advantages of a personalized and tumor-informed multiplex PCR next generation sequencing assay, called Signatera™, that enables a sensitive, specific, and dynamic detection of molecular disease burden in cell-free DNA ( Read More...

04/14/2021 - Register Session Description Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited Read More...

11/05/2020 - Register Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens Read More...

05/28/2020 - Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of Read More...

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...

Describe what method(s) you use for functional enrichment or pathway analysis clearly in any resulting publications. This should include parameters used and software versions. For ORA, select appropriate background genes. Use p-values corrected for Read More...

The Center for Advanced Tissue Imaging (CAT-I) is an NIAID and NCI supported effort involving collaborative studies between experts in the Laboratory of Immune System Biology, DIR, NIAID and investigators in the DIR, NIAID and Read More...

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...

The PET Department, CC, functions as a core facility that supports basic, translational, and clinical research using PET. It is a vertically integrated facility, with resources to produce positron-emitting radionuclides, manufacture PET radiopharmaceuticals in a 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...

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...

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...

CREx News & Updates March 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NIA Nonhuman Primate Core The NIA Nonhuman Primate Core supports multi-disciplinary translational aging projects for Read More...

The Center for Inherited Disease Research (CIDR)'s  mission is to support the genetics community by providing high-quality, cutting-edge genomics services and technologies in order to expand our understanding of disease and catalyze discoveries that Read More...

CREx is an easy-to-use platform that catalogues research resources available across the NIH. It also includes an expansive database of services offered by the biotechnology industry. All resources are organized by research areas and keywords Read More...

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...

The Antibody Characterization Laboratory (ACL) is the laboratory responsible for the development of well-characterized monoclonal antibody reagents. The NCI’s Office of Cancer Clinical Proteomics Research funds ACL as a resource to the entire cancer Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx Program Manager The CREx Team is happy to announce Deepika Velampati as the new CREx Program Read More...

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...

MAB provides visual communication solutions across all media to the entire NIH community. Our Medical Illustration section provides a complete range of biomedical visualization services, including manuscript/textbook figures, infographics, 3D modeling, animation, technical diagrams, Read More...

Total end-to-end system for single-cell research [embed]https://youtu.be/vMzhSzg1rUw[/embed] The BD Rhapsody Single-Cell Analysis system empowers and streamlines your research with a complete system of tools, including reagents and analysis software, Read More...

The Genomics and Pharmacology Facility is part of the NCI's Center for Cancer Research (CCR), within the Developmental Therapeutics Branch. Its mission is to manage and assess molecular interaction data obtained through multiple platforms, increase Read More...

NCI LASP Animal Research Technology Support (ARTS) provides customized technical support for basic and translational animal-based research to the scientific community. We offer a wide array of services ranging from expert colony management to the Read More...

The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management Read More...

Clinical Support Laboratory – Cellular Immunology offers a spectrum of bioassays to assess cellular responses to antigens and mitogens including ELISPOT, cytotoxicity assays, and proliferation assays. Established Technologies Elispot Assays, Dual or Triple Color Fluorospot Assays, Read More...

Protein Expression Laboratory The Protein Expression Laboratory develops, improves, and delivers protein-centric services. Our goal is to help client investigators achieve their research goals with the lowest possible cost in the shortest time. All PEL Read More...

Mass Spectrometry Section of the Collaborative Protein Technology Resource (Bldg. 37) Core Capabilities: Identification of proteins in complexes, organelles, subcellular fractions, or fluids. Global relative protein quantitation. Quantitation by isotopic labeling of cells in culture (SILAC) 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...

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...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

Lesson 6 . Learning Objectives Introduce several beta diversity metrics Discover different ordination methods Learn about statistical methods that are applicable Beta diversity Beta diversity is between sample diversity. This is useful for answering the question, how Read More...

Let's submit a batch job. We are going to download data from the Sequence Read Archive (SRA) , a public repository of high throughput, short read sequencing data. We will discuss the SRA a bit Read More...

The bulk RNA-Seq test data we've been working with is in FASTQ format. We'd like to do a BLAST search on a couple of these sequences. Data must be in FASTA format to Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to activate the bioinfo environment when working on Biostar class materials. conda activate bioinfo The bulk RNA-Seq test data we've Read More...

A search may take place in nucleotide space, protein space or translated spaces where nucleotides are translated into proteins. Searches may implement search “strategies”: optimizations to a specific task. Different search strategies will produce different Read More...

Lesson 17: RNA sequencing review 2 Learning objectives This lesson will serve as comprehensive review of Module 2. We will spend roughly the first hour reviewing the Module 2 material the second hour answering specific questions from the poll Read More...

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...

There are many ways to increase collaboration and document and share code and results using R. Some examples include: RMarkdown / Quarto (i.e., literate programming) R Markdown provides an unified authoring framework for data science, Read More...

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...

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...

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...

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...

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...

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...

The identification of cell types in single cell genomics data (cell type annotation) can provide new insights into cellular identities, heterogeneity, and functional roles. Cell type annotation is challenging Read More...

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...

Bioinformatics Training and Education Program 15 January – 15 February 2023 BTEP Bulletin Contact us at ncibtep@nih.gov FEATURED BIOINFORMATICS EVENTS Data Management Sharing: Part 1 and Part 2 DOE-NCI Collaboration: MOSSAIC for Advancing Computational Models for Cancer Research Variation Read More...

07/08/2022 - In this presentation, Drs. Hutson and Liu will provide a high-level overview of the data, software and model sharing capabilities and strategies developed as part of the Cancer Moonshot Immuno-Oncology Translational Network (IOTN) Data 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...

05/26/2021 - Register This month’s Cancer Genomics Cloud (CGC) webinar welcomes Dr. Wenming Xiao, a lead bioinformatics scientist at the U.S. Food and Drug Administration. Dr. Xiao specializes in researching how computational, technical, and Read More...

05/01/2020 - BioCyc.org [1] is an extensive web portal containing 17,000 microbial genomes and associated metabolic pathways. BioCyc databases are created through a process that combines computational inferences with imported and curated data from multiple sources. The Read More...

04/17/2017 - Probing DNA-Protein Interactions This 2-day workshop, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq data analysis. Topics to be covered include: experimental design; read alignment; 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...

The Division of Veterinary Resources Animal Surgery has supported large animal research and clinical care for more than 40 years. DVR surgeons provide outstanding and highly specialized large animal (rabbits, ungulates, etc.) research support in a Read More...

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...

[embed]https://youtu.be/yTl1Q0D7aZ0[/embed] 10x Genomics' supports multiple cancer research areas from single nucleotide and structural variant detection to single cell whole transcriptome gene expression analysis of thousands of individual Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Spotlight The NIH Lab Managers Working Group have developed a new NIH-wide database of cold 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...

The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...

The NCI Research Flow Facility provides cell sorting and benchtop flow cytometry services to NCI investigators. Services are program-specific and are not available to all NCI or NIH investigators. Please inquire as to availability. Established Read More...

The NHLBI Transgenic Core’s main mission is to keep up with the latest advancements in genome engineering technologies and to provide state-of-the-art services to assist NIH scientists in generating genetically engineered animal models. In Read More...

The Stem Cell Unit (SCU) has established a database to which hESC lines, adult stem cells and induced pluripotent stem (iPS) cells may be directly compared. These data give scientists the information they need when Read More...

The AgingResearchBiobank was officially launched in January 2019 with a mission to provide a state-of-the-art inventory system for the storage, maintenance, and distribution of de-identified biospecimens and associated phenotypic, clinical, and imaging data from numerous NIA-funded Read More...

CREx News & Updates June 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Click below to learn how easy it is to navigate the CREx platform. These short videos will Read More...

The Bloomington Drosophila Stock Center (BDSC) collects, maintains, and distributes genetically defined strains of Drosophila melanogaster for research and education. The BDSC supports a large, worldwide community of scientists using Drosophila as a model organism Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH Read More...

The NMR Facility for Biological Research operates six NMR spectrometers with proton resonance frequencies from 850 to 500 MHz. Three of the highest field spectrometers (850, 700, 600) are equipped with higher sensitivity cryoprobes optimized for high-resolution multi-dimensional and relaxation Read More...

OSTR offers two distinct supplemental funding mechanisms for CCR PI’s to request additional funds for technologies and research services requiring exceptional costs. Eligible expenses include services from Cores and outside vendors.  A third program ( Read More...

Back Services: Biophysics Facility offers DSC as an open-access instrument. First-time users must complete training before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: The differential scanning calorimeter measures the constant pressure Read More...

NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, Read More...

The Pharmacogenetics Core is responsible for correlating outcome observations (toxicity, efficacy, survival, PK/PD) with genetic variants (germline or somatic) to identify key genetic determinants and biomarkers that predict response to specific treatments. We also Read More...

The Pan-Microbial Serology Facility (PMSF) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The PMSF focuses on determining individualized pan-microbial immune profiles associated with human diseases including immunological Read More...

The NCI Cloud Resources are components of the NCI Cancer Research Data Commons (CRDC) that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers Read More...

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...

Large STARS can be used to request supplemental funding exceeding $8,000 to offset experimental costs (e.g., core or vendor services or specialized reagents).  Applications require detailed scientific and budgetary justification and must be proposed in Read More...

The NIH Intramural Research Program Collaborative Research Exchange (CREx) The Collaborative Research Exchange (CREx) is an online CCR marketplace where investigators can search, browse, and request information for research services, technologies, or custom products (antibody Read More...

Back Services: This instrument is not user accessible.  We provide both data collection and data analysis services. Location: Building 50, room 3331 Description: An analytical ultracentrifuge is equipped with absorption and interference optical systems that monitor Read More...

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...

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...

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...

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...

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...

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...

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...

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...

Electron Microscopy Laboratory (EML) The EML offers investigators access to unique expertise and EM technologies that allow our partners to explore new avenues of research to enhance the knowledge of biological systems. To assist our Read More...

The EML offers investigators access to unique expertise and EM technologies that allow CCR Investigators to explore new avenues of research in order to enhance the knowledge of biological systems. To assist our customers, we 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...

[tabby title="Home"] About NICE-NIH Intramural CryoEM Consortium  NIH Intramural CryoEM Consortium (NICE) serves intramural investigators in all NIH IC’s. NICE provides access to state-of-the-art Titan Krios cryo-electron microscopes for atomic-resolution structure determination of Read More...

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...

The Central Repository provides the research community at the NCI with various cryogenic services, including low-temperature storage from +4° C to -196° C, controlled-rate freezing, computerized inventory and distribution of samples. The Central Repository is operated 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...

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...

The mission of Human Brain Collection Core (HBCC) within the National Institute of Mental Health, Division of Intramural Programs (NIMH IRP) is to conduct and support research on brain and behavior, with the goal of Read More...

.row { display: flex; justify-content: space-around; align-items: flex-start; margin: 20px; } .column { text-align: center; padding: 10px; width: 30%; } .column img { display: block; margin: 0 auto; width: 150px; height: 150px; } .column strong { display: block; margin-top: 10px; } Background: Intravital microscopy (IVM) 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...

Radiation Oncology Branch is part of CCR. Bioinformatics core is a collaborative resource to support ROB branch and provide service to ROB investigators from NCI and other Institutes access to new technologies, bioinformatics, statistical analysis Read More...

The core provides access to several different state-of-the-art 3D microscopes as well as computers to visualize and process image data. The facility houses equipment for 2D or 3D imaging of fixed and living specimens. High Read More...

The facilities at AIM are available for use by the entire NIH intramural research community. While we welcome users with any size imaging project, AIM specializes in large, yearlong (or longer), collaborative research efforts with Read More...

The Trans-NIH Metabolomics Core (TNMC) is a shared research resource that performs metabolomics analysis (and related small molecule research) for investigators at all Institutes and Centers across the NIH Intramural Research Program. The TNMC is Read More...

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...

CREx News & Updates December 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the STRIDES Initiative. VIEW STRIDES INITIATIVE NIH Cores Read More...

Supplemental Technology Award Review System (STARS) Overview STARS Request Form STARS System The Supplemental Technology Award Review System (STARS) is a web-based interface for submission and review of S&S supplement requests by CCR Read More...

The OSTR offers cutting-edge technology platforms to the CCR scientific community through centralized facilities. The videos accessed through this page are designed to introduce the various scientific methodologies OSTR makes available through the cores on 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...

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...

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...

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...

Welcome! Welcome to the R Introductory Series! Who: Novices and beginners\ What: A course series introducing R and RStudio. This course will introduce the foundational skills necessary to begin to analyze and visualize data in Read More...

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...

This lesson will introduce data wrangling with R. Attendees will learn to filter data using base R and tidyverse (dplyr) functionality. Learning Objectives Understand the concept of tidy data. Become familiar with the tidyverse packages. 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 3: Creating a feature table Lesson Objectives Check for primers Generate an ASV count table and representative sequence file Understand the difference between OTU picking and denoising The two primary files that will be used 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...

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...

Introduction to dplyr and the %>% Objectives Today we will begin to wrangle data using the tidyverse package, dplyr . To this end, you will learn: how to filter data frames using dplyr how to employ Read More...

Lesson 5: Working on Biowulf Lesson 4 Review Flags and command options Wildcards ( * ) Tab complete Accessing user history with the "up" and "down" arrows cat , head , and tail Working with file content (input, Read More...

Lesson 6: sra-tools, e-utilities, and parallel This page uses some content directly from the Biostar Handbook by Istvan Albert. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch or swarm Read More...

Note that we now have differential expression by transcripts and our first column contains the transcript IDs. But what genes do these transcripts map to? We will need to do some data wrangling to find Read More...

Lesson 6: Downloading data from the SRA For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch Read More...

Before we can align the HBR and UHR raw sequencing data to human chromosome 22 transcriptome, we need to create an index of this transcriptome (like we did with the genome). This will make the alignment Read More...

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...

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...

Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...

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...

In lesson 9, we learned that reference genomes came in the form of FASTA files, which essentially store nucleotide sequences. In this lesson, we will learn about the FASTQ file, which is the file format that Read More...

Lesson 10: Introducing the FASTQ file and assessing sequencing data quality Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 9 Review In the previous lesson, we explored the reference genomes and Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

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...

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...

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...

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...

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...

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...

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...

/* 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...

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...

Introduction to Data Wrangling with the Tidyverse Objectives Wrangle data using tidyverse functionality (i.e., dplyr ). To this end, you should understand: 1. how to use common dplyr functions (e.g., select() , group_by() , arrange() , mutate() , Read More...

06/06/2016 - The 'NCBI Resources for CCR Scientists' workshop, on June 6 and June 8, 2016, will focus on teaching a wide range of resources developed within NCBI that are relevant for CCR scientists. It will include both hands-on Read More...