Search Results for: Reverse Phase Protein Array

09/13/2024 - Reverse-phase protein arrays (RPPAs) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and develop novel cancer therapies.   To facilitate community-based investigation of the large-scale protein expression data generated by Read More...

05/09/2023 - T he  C ancer  P roteome  A tlas (TCPA) : a major bioinformatics resource for cancer proteomics data using  reverse-phase protein arrays (RPPAs)   In contrast to the recent exploration of next-generation sequencing at both DNA Read More...

05/02/2023 - T he  C ancer  P roteome  A tlas (TCPA) : a major bioinformatics resource for cancer proteomics data using  reverse-phase protein arrays (RPPAs) In contrast to the recent exploration of next-generation sequencing at both DNA Read More...

11/05/2020 - Register Presenter: Dr. Han Liang Reverse-phase protein arrays (RPPAs) offer a powerful functional proteomic approach to evaluate biomarkers and mechanisms underlying sensitivity and resistance to cancer therapy. The MD Anderson Cancer Center platform currently 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...

The primary objective of the Protein Technology Core (PTC) is to establish an experimental screening pipeline for single-domain antibodies termed nanobodies. Nanobodies are antibody fragments consisting of a single monomeric variable antibody domain. The PTC, Read More...

03/10/2025 - AI Club is a weekly meeting that explores various topics relating to AI and deep learning in biomedical sciences, typically in a seminar, workshop, or journal club format. AI Club is intended to be Read More...

01/27/2025 - AI Club is a weekly meeting that explores various topics relating to AI and deep learning in biomedical sciences, typically in a seminar, workshop, or journal club format. AI Club is intended to be Read More...

-c -f 4 is counting alignments with the property/condition (-c) that the reads are unmapped (unaligned). Now we can reverse the flag (from -f to -F) and view the number of alignments. samtools view -c Read More...

-c -f 4 is counting alignments with the property/condition (-c) that the reads are unmapped (unaligned). Now we can reverse the flag (from -f to -F) and view the number of alignments. samtools view -c Read More...

We are a bioinformatics team within the Center for Biomedical Informatics and Information Technology’s (CBIIT’s) Cancer Informatics Branch (CIB)—soon to be referred to as the Informatics and Data Science (IDS) Program. Headed Read More...

05/15/2024 - In this one-hour webinar, you'll get a demonstration of DNASTAR Lasergene Software. DNASTAR offers software solutions for molecular biology, protein analysis, and genomics. This presentation will focus on an overview of the applications Read More...

Your job may be in a waiting phase ("Pending" or "PD") depending on available resources. You can specify a particular node partition using --partition . Use freen to see what's available. Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

Another way to run BLAST is to create your own custom database, and search against it with query sequences. Usually you will not have to create your own blast database, you can download prebuilt databases Read More...

CLC Genomics Workbench (Qiagen) is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and Next Generation Sequencing (NGS) analysis (see Listing of Analysis Functions below). {{Sdet}}{{Ssum}}Listing of Read More...

Geneious Prime is a graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and Next Generation Sequencing analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{Esum}} Classic Computational Molecular Read More...

05/16/2025 - This one-day in-person NIH AI Symposium will bring together researchers from a broad range of disciplines to share their AI-related research, with the goal of disseminating the newest AI research, providing an opportunity to Read More...

04/01/2025 - 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 Read More...

Now that we know what we mean by denoising, let's apply it to our data. We will use DADA2 , which seems to be the more popular method. To use DADA2, we need to make Read More...

We will use qiime cutadapt trim-paired because we are working with paired-end reads. We will also use more than one thread ( --p-cores ). The region sequenced was V4-V5 with the forward primer, AYTGGGYDTAAAGNG , and the Read More...

We will import a small subset of fastq files to demonstrate initial sequence processing steps. The main questions we need to answer to import our raw data are: Is the data demultiplexed or multiplexed? Often Read More...

{{Sdet}} Solution{{Esum}} qiime demux summarize \ --i-data 01_import/import.qza \ --o-visualization 01_import/import.qzv {{Edet}} Again, to view this file, you will need to move it to public . Note: It is easier to create the Read More...

We will create an alias for this command. sort | uniq -c | sort -rn The "sort" utility sorts text and binary files by lines. The "uniq" utility reads input, compares adjacent lines Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment when working on Biostar class material. conda activate bioinfo Let's start by creating a directory Read More...

The CPP is directly responsible for the pharmacokinetic (PK) analysis of numerous Phase I and II clinical trials conducted within the NCI. In addition, the CPP provides direct PK support for many studies performed elsewhere Read More...

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...

CCR VOLUME Electron Microscopy (CVEM) aims to develop new techniques in volume electron microscopy (vEM) and, in collaboration with CCR Investigators, apply these techniques to research cell biological questions well-suited for study by high-resolution 3D Read More...

The Biomedical Engineering and Physical Science (BEPS) shared resource supports NIH’s intramural basic and clinical scientists on applications of engineering, physics, imaging, measurement, and analysis. BEPS is centrally located on the main NIH campus Read More...

06/20/2025 - Emerging artificial intelligence—e pecially generative model and deep learning—i tran forming biomedical and biological cience. In thi talk, Profe or Juexin Wang of Indiana Univer ity will pre ent ca e tudie Read More...

04/10/2025 - The cost of handling rare and/or late-stage diseases far exceeds preventative strategies. Cell and gene therapies can be quite cost-effective when applied at large population scales (e.g. pandemic vaccines and transfusions).   AI 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...

10/08/2024 - Mass spectrometry is a powerful tool for analyzing protein regulation and function. This workshop, divided into two parts, will explain the fundamentals of mass spectrometry experiments and how proteins are identified. We will further Read More...

09/25/2024 - Please join us on Wednesday, September 25, 2024, where Gina Kuffel, B.S., and Steph Singleton, M.S., will demo the newly launched Clinical and Translational Data Commons (CTDC).    As the newest addition to NCI's Read More...

09/12/2024 - Dr. Nussinov will highlight some scientific questions bordering on physics and biology, where fundamental physics and chemistry can help biology. They span the behavior of a bird, protein activation, signaling in cancer, and neurodevelopmental 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...

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...

Another important data structure in R is the data matrix. Data frames and data matrices are similar in that both are tabular in nature and are defined by dimensions (i.e., rows (m) and columns ( Read More...

We will need to use a manifest file to import. See the Import tutorial . Note: The manifest file can be comma separated depending on the format that you use at import , despite what is written Read More...

The two methods used for denoising on QIIME 2 include: DADA2 - Uses a run specific error profile - Unclear how an incomplete run profile would impact results - There is a method available for Pacbio Read More...

12/06/2023 - This presentation will provide a one-hour overview demonstration on Geneious Prime, a software platform for molecular biology and sequence analysis. It is built to be highly visual, easy to use, and collaborative. & Read More...

Before diving into differential expression analysis, it is important to take a brief look at the concept of normalization. After obtaining expression counts, we will need to normalize the counts before performing differential expression analysis. Read More...

Download data from the SRA with fastq-dump split files into forward and reverse reads download part, not all, of the data Compare fastq-dump to fasterq-dump Introduce prefetch Look at XML-formatted data with sra-stat Grab SRA Read More...

Download data from the SRA with fastq-dump split files into forward and reverse reads download part, not all, of the data Compare fastq-dump to fasterq-dump Introduce prefetch Look at XML-formatted data with sra-stat Use e-utilities ( Read More...

RNASEQ looks at steady state mRNA levels which is the sum of transcription and degradation Protein levels are assumed to be driven by mRNA levels RNASEQ can measure relative abundance not absolute abundance RNASEQ is Read More...

Swarm is for running a group of commands (job array) on Biowulf. swarm reads a list of command lines and automatically submits them to the system as sub jobs. To create a swarm file, you Read More...

This page uses content directly from the Biostars Handbook by Istvan Albert (https://www.biostarhandbook.com). Always remember to load the bioinformatics environment. conda activate bioinfo SAM files SAM format is TAB-delimited, line-oriented, human-readable text Read More...

This page uses content directly from the Biostars Handbook by Istvan Albert (https://www.biostarhandbook.com). Always remember to load the bioinformatics environment. conda activate bioinfo SAM files SAM format is TAB-delimited, line-oriented, human-readable text Read More...

Variant annotation means predicting the effects of genetic variants (SNPs, insertions, deletions, copy number variations (CNV) or structural variations (SV)) on the function of genes, transcripts, and protein sequence, as well as regulatory regions. The Read More...

Let's use the tool Trimmomatic to clean up the adapters and the poor quality reads for SRR1553606. For help with Trimmomatic type trimmomatic --help at the command line. Before getting started with using trimmomatic, Read More...

The Center of Cellular Engineering (CCE) is a comprehensive facility that develops and manufactures a wide range of cell and gene therapies for early phase clinical trials. The CCE is currently manufacturing chimeric antigen receptor ( 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 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...

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 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 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...

OMAL focuses its research and development activities to quantitatively understand the molecular basis of three-dimensional (3D) cell organization, motility, invasion, and differentiation using fixed samples and live, 3D tissue culture models (i.e., translational models). Read More...

The CCR Building 41 Flow Cytometry Core is a full-service facility within the Center for Cancer Research that supports over 150 users representing 26 laboratories. The Core Facility provides instrument and software training, technical expertise, assay development, 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...

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...

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...

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...

The Blood Processing Core monitors viral load in patients with HIV and performs sequential studies using samples obtained from patients with cancer, AIDS, chronic granulomatous disease, or other diseases associated with immunologic dysfunction. The core 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 Mid-Atlantic CHTN is one of six participating divisions of the Cooperative Human Tissue Network (CHTN) and is based in the Pathology Department at the University of Virginia. While primarily a resource for cancer researchers, Read More...

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.

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...

Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status, and enzyme activity levels. You can choose to search for a 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 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...

The Staff Scientists/Clinicians (SSSC) Technical Enrichment Program (STEP) was established to provide SSSC’s an opportunity to compete for funding to gain comprehensive training in state-of-the-art techniques available through CCR Cores and Facilities. The 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 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...

The Metabolic Clinical Research Unit (MCRU) opened in 2007 as a key component of the Strategic Plan for NIH Obesity Research . The NIDDK worked closely with the Clinical Center to design the Unit, which houses state-of-the-art 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...

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...

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...

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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...

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...

Long read sequencing was recently named 2022’s method of the year by Nature Methods . Long read sequencing technologies, those that generate sequence reads with lengths of 10s of kilobases or longer have several advantages over Read More...

BTEP strives to maintain links to resources that should be of interest to CCR Bioinformatics Community.  Some of the resources to will be accessible through more than one of these lists, but since the lists Read More...

10/09/2024 - This session will give an overview of the NCI Cancer Research Data Commons and the variety of available cancer data such as RNA expression and protein abundance. These data are hosted in openly accessible Read More...

Congratulations, your experiments have been completed and you have a large amount of data. Now, it’s time to analyze these data. But where do you begin? How can you gain the most meaning from Read More...

06/20/2024 - Clustered heat maps are widely used for visualizing patterns in molecular profiling data. But traditional, static heat maps have significant limitations when applied to large datasets (1000s of elements per axis). Presented in this Read More...

The total number of detected transcripts expressed in a cell is dependent on the amount of mRNA in a cell. Cells naturally vary in the total amount of mRNA expressed. However, the chemistry of the Read More...

In this tutorial, we are using data from Nanduri et al. 2022, Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins , published in Nature Communications . The raw count matrices are Read More...

In this tutorial, we will continue to use data from Nanduri et al. 2022, Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins , published in Nature Communications . As a reminder, Read More...

In this tutorial, we will continue to use data from Nanduri et al. 2022, Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins , published in Nature Communications . As a reminder, Read More...

In Seurat (since version 4), differential analysis requires a preprocessing step to appropriately scale the normalized SCTransform assay across samples: adp = PrepSCTFindMarkers(adp) Found 8 SCT models. Recorrecting SCT counts using minimum median counts: 8146 As covered earlier, Read More...

05/06/2024 - Have you been looking for ways to use artificial intelligence (AI) in clinical practice but not sure where to start? Attend this webinar for tips from Dr. Anant Madabhushi on applying AI in precision Read More...

04/22/2024 - Intended Audience This webinar targets researchers interested in exploring genomic mutation analysis capabilities within the recently introduced NCI Genomic Data Commons (GDC) 2.0 platform. It aims to accommodate individuals interested in analyzing genes and mutations Read More...

The following represents the basic ggplot2 template: ggplot(data = ) + (mapping = aes()) We need three basic components to create a plot: the data we want to plot , geom function(s) , and mapping aesthetics . Notice the + symbol Read More...

01/19/2024 - Trey Ideker, Ph.D., is a professor of medicine, bioengineering, and computer science, and former chief of genetics at the University of California San Diego (UCSD). Additionally, he is director or co-director of the Read More...

The following represents the basic ggplot2 template. ggplot(data = ) + (mapping = aes()) The only required components to begin plotting are the data we want to plot, geom function(s), and mapping aesthetics. Notice the + symbol following Read More...

Practice Lesson 2 For the help sessions, we will work on processing sequences generated in Zhang Z, Feng Q, Li M, Li Z, Xu Q, Pan X, Chen W. Age-Related Cancer-Associated Microbiota Potentially Promotes Oral Squamous Read More...

The QIIME2 platform can be used for different types of -omics data. For this course, we will be focusing on targeted amplicon sequencing of the 16S rRNA gene. The 16S rRNA gene (~1500 bp) codes for Read More...

The data type of an R object affects how that object can be used or will behave. Examples of base R data types include numeric, integer, complex, character, and logical. R objects can also have Read More...

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...

There are several functions that you will see repeatedly as you use R more and more. One of those is c() , which is used to combine its arguments to form a vector. Vectors are probably Read More...

This practice lesson is associated with Lesson 3 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on generating a feature table and representative sequences. We will continue working with the data Read More...

Practice Lesson 3 This practice lesson is associated with Lesson 3 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on generating a feature table and representative sequences. We will continue working with Read More...

NCI scientists have many choices available to them for bioinformatic analyses of Next Generation Sequencing (NGS) data. While some require expertise in programming, others provide a more user-friendly, point-and-click interface. These options include programs for Read More...

10/03/2023 - Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Significant advances in the field now allow high-parameter data collection (60+ targets); however, considerable expertise and capital are needed to validate Read More...

09/27/2023 - 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...

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...

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...

samtools flagstat SRR1972739.bwa.bam produces this 20740 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 740 + 0 supplementary 0 + 0 duplicates 15279 + 0 mapped (73.67% : N/A) 20000 + 0 paired in sequencing 10000 + 0 read1 10000 + 0 read2 14480 + 0 properly paired (72.40% : N/A) 14528 + 0 with itself and mate mapped 11 + 0 singletons (0.05% : N/ Read More...

samtools flagstat SRR1972739.bwa.bam produces this 20740 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 740 + 0 supplementary 0 + 0 duplicates 15279 + 0 mapped (73.67% : N/A) 20000 + 0 paired in sequencing 10000 + 0 read1 10000 + 0 read2 14480 + 0 properly paired (72.40% : N/A) 14528 + 0 with itself and mate mapped 11 + 0 singletons (0.05% : N/ Read More...

Using data we downloaded previously: bwa mem refs/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq > SRR1972739.bwa.sam samtools view -S -b SRR1972739.bwa.sam > SRR1972739.bwa.bam samtools sort SRR1972739.bwa.bam -o Read More...

Using data we downloaded previously: bwa mem refs/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq > SRR1972739.bwa.sam samtools view -S -b SRR1972739.bwa.sam > SRR1972739.bwa.bam samtools sort SRR1972739.bwa.bam -o Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment. conda activate bioinfo The jellyfish program is dependent on a program called "gcc" which is Read More...

Change in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder for this portion of the class. cd ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 Now that we have our SAM files generated for the Read More...

fastq-dump and fasterq-dump can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. fastq-dump SRR1553607 creates the file: SRR1553607.fastq Check the file to make Read More...

fastq-dump and fasterq-dump can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. fastq-dump SRR1553607 creates the file: SRR1553607.fastq Check the file to make Read More...

There should not be spaces in Unix file names or directories. Here is a good method to use: Use the underscore (_) where a space would go, like this, to name a directory containing RNA-Seq data. Read More...

Provides a gene-centric view which lists the genes and their associated annotation terms... -- DAVID help documents See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717906/ for difference between pathway and network analysis DAVID 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 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...

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...

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 research conducted within the Synthetic Biologics Core (SBC) Facility has a dual role: Generate chemical biology tools and drug candidates for molecular targets identified by NCI research groups, Develop novel effective methods and tools Read More...

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...

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

The Advanced Biomedical Computational Sciences (ABCS) group provides technology development, scientific consultation, collaboration and training, research, software development, and high-performance computing support. ABCS encompasses specialized groups focusing on machine learning applied to the interpretation of 2 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 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...

Back Services: Biophysics Facility offers DLS as an open-access instrument. First-time users must complete a short training session before gaining access to the instrument reservation calendar. Training includes DLS analysis of small- and large-molecular size 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...

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 Antibody Engineering Program (AEP) is located at the Laboratory of Molecular Biology, which is part of the Center for Cancer Research (CCR), an intramural program at the National Cancer Institute (NCI). AEP focuses on Read More...

Back Services: Biophysics Facility offers MDS 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 standard molecular 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...

CREx News & Updates July 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...

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...

Back Services: Biophysics Facility offers ITC calorimeters as open-access instruments.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes performing a test experiment and 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More. New Resources on CREx NIMH Human Brain Collection Core (HBCC) The HBCC obtains human brain tissue, hair, and blood 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...

OSTR provides CCR investigators with access to a variety of software licenses for genomic, proteomic, pathway analysis and data visualization tools. These software are funded by OSTR and made available at no cost to CCR 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...

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...

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...

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 Biophysics Core’s mission is to provide support in the study of macromolecular interactions, dynamics, and stability by offering consultations, training, professional collaborations, and instrument access. General Services: Multi-technique molecular interaction studies, Kinetic 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Technology Event Biophysical Methods for Protein Interactions Monday, May 15 – Friday, May 19, 2023 This workshop will review the strategies of Read More...

The rapid advancement of single-cell technology has provided new powerful tools to answer many biological questions, such as identifying new or rare cell populations and characterizing the complexities of tumor heterogeneity. Realizing the great potential 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...

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...

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 protein, macromolecular complexes, membrane receptors, cellular organelles, and 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...

The centrally funded Statistics team within the Advanced Biomedical Computational Science group at the Frederick National Lab provides statistical consultation and data analysis support for NCI laboratories. We have broad-range expertise in biomedically relevant areas 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...

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...

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...

[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 National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...

The NIH Biowulf Cluster provides researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations, deep learning to model protein structures, and PET brain Read More...

The Antibody Engineering Program (AEP) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The program focuses on generating therapeutic antibodies by phage display technology, including human antibodies and Read More...

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...

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...

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...

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...

Lesson 15: Finding differentially expressed genes Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 14 review In the previous lesson, we learned to visualize RNA sequencing alignment results in the Integrative Read More...

Anaconda ( https://www.anaconda.com/ ) is a package manager and distributor for a wide array of data science software. Package managers are ideal for scientists who conduct analysis on a personal computer as they eliminate Read More...

General questions or comments about the BTEP program or classes should be addressed to: NCIBTEP@nih.gov Desiree Tillo, Ph.D . Staff Scientist desiree.tillo@nih.gov I have a broad research background in bioinformatics 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...

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...

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 Learn about data structures including factors, lists, data frames, and matrices. Load, explore, and access data in a tabular format (data frames) Learn to write out (export) data from the R environment Data Read More...

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...

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...