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Bioinformatics
02/12/2013 - This lecture will provide an overview of Illumina sequencing technology as implemented at the CCR Sequencing Facility (SF). It will outline the data and sample QC and analysis workflow performed by the facility and Read More...
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Bioinformatics
The first step in analyzing RNA sequencing is to perform quality assessment of the FASTQ files. This step ensures that the quality of the data is good and there no issues with contaminations such as Read More...
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Bioinformatics
QC all reads K-mer length, if specified will generate a report for each sample of the positions for the most commonly occurring k-mers (or sequence of nucleotides) of the specified length - can hint at Read More...
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Bioinformatics
The QC results table below indicates adapter trimming resulted in some samples losing reads. This is because not all reads passed the QC criteria. Also, the average read length has been reduced as the adapters Read More...
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Bioinformatics
After mapping, the next step is to perform post-alignment QC to determine things like overall alignment rate (ie. how many sequences aligned to the reference). To do this, select the "Aligned" reads data Read More...
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Bioinformatics
QA / QC reports are generated from programs such as fastqc and multiqc. FastQC runs several quality checks on raw NGS data to give you a general idea regarding the overall quality of your data. FastQC Read More...
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Bioinformatics
The quality of the cells should be assessed considering the above metrics jointly and not simply in isolation. QC can be applied manually by subjectively choosing and applying thresholds, which can be quite arbitrary. Alternatively, Read More...
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Bioinformatics
05/01/2024 - This lesson reviews many of the standard steps in a scRNA-Seq workflow: QC filtering, normalization, scaling, and clustering.
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Bioinformatics
03/06/2025 - This class introduces participants to the first steps to differential expression analysis in bulk RNA sequencing which involves filtering out noise from (ie. genes without expression across samples) and performing QC on the gene Read More...
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Bioinformatics
The quality metric information is stored in the metadata ( adp@meta.data ), so we really only need to work with the metadata file to get an idea of the thresholds we want to set for Read More...
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Bioinformatics
There are several metrics that can be used to assess overall quality. The base workflow from Seurat suggests the following: nCount_RNA - the absolute number of RNA molecules (UMIs) per cell (i.e., count Read More...
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Bioinformatics
Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we Read More...
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Bioinformatics
This tutorial assumes that all pre-processing steps (read demultiplexing, FASTQ QC, reference based alignment, error correction) have been completed. At this stage of the analysis, a gene-by-cell count matrix has been generated for each sample.
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Bioinformatics
Now that our HISAT2 indices have been built and the text file with the sample IDs has been generated, we can do the actual alignment. First, change into the ~/biostar_class/snidget/snidget_hisat2 folder Read More...
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Bioinformatics
04/29/2021 - BTEP_April29_2021 Slides Recording Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external Read More...
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Bioinformatics
11/14/2018 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...
Web Page
Bioinformatics
10/12/2018 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...
Web Page
Bioinformatics
Once we have read in the matrices, the next step is to create a Seurat object. The Seurat object will be used to store the raw count matrices, sample information, and processed data (normalized counts, Read More...
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Bioinformatics
Lesson 13 Practice Objectives In this lesson we learned how to align raw sequencing reads to reference and to process alignment results for downstream analysis. Here, we will test our knowledge by continuing with the Golden Read More...
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Bioinformatics
06/30/2022 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power QC, variant annotation, and analysis considerations Beyond GATK! A survey of variant calling tools The actual Best Read More...
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Bioinformatics
03/10/2022 - Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Read More...
Web Page
Bioinformatics
01/23/2020 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power WGS/WES Pipelines at NIH Pipeline performance Using Pipeliner for internal and external data Variant QC, Annotation Read More...
Web Page
Bioinformatics
04/25/2017 - This talk will be an introduction to Methyl-seq, where you will learn about leveraging the power of next-generation sequencing (NGS), both genome-wide and targeted approaches, that can provide insight into methylation patterns at a Read More...
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Bioinformatics
Adapter available from file Trim from both sides Run pre-alignment QC again after this step to make sure the trimming step did not affect the data - quality still great after trimming although the average Read More...
Bethesda, MD
Core Facility
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...
Bethesda, MD
Trans NIH Facility
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...
Web Page
Confocal
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...
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Bioinformatics
03/05/2024 - This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell Read More...
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Bioinformatics
11/16/2023 - This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Read More...
Web Page
Bioinformatics
To align FASTQ files for one sample, we construct the HISAT2 command with the following options. The "-x" flag prompts us to enter the base name (ie. without extension) of genome index. The Read More...
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Bioinformatics
We previously stored FASTQC results for the HBR and UHR raw sequencing data in the ~/biostar_class/hbr_uhr/QC directory (recall that ~ denotes home directory). So before getting started, change into this folder. cd ~/ Read More...
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Bioinformatics
Here, let's change back in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder. cd $hbr_uhr_hisat2 To align FASTQ files for one sample, we construct the HISAT2 command with the following options Read More...
Web Page
Bioinformatics
Lesson 14 Practice Objectives Here, we will practice using the Integrative Genome Viewer (IGV) to visualize the hcc1395 RNA sequencing alignment results. About the data and launching IGV We were introduced to the hcc1395 RNA sequencing Read More...
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Bioinformatics
03/08/2023 - Partek software provides a singular web based point and click environment for analyzing and visualizing high dimensional multi-omics sequencing data, making bioinformatics easily accessible to all researchers. Partek Flow software is available to NCI Read More...
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Bioinformatics
07/14/2021 - Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Read More...
Web Page
Bioinformatics
11/02/2020 - Attendees will learn how to use Partek Flow to identify cell subtypes using both gene and protein expression in a peripheral blood mononuclear cell (PBMC) sample using Cellular Indexing of Transcriptomes and Epitopes by Read More...
Web Page
Bioinformatics
08/28/2019 - Please bring your computer with Partek Genomics Suite to this hands-on workshop. You'll need to submit a request through “NCI at Your Service” to obtain the access to this software. Partek will demonstrate Read More...
Web Page
Bioinformatics
04/25/2018 - Join us for a seminar/webinar session where Partek Specialist will show you how to analyze your Single Cell RNA-Seq data in an intuitive, interactive and powerful way using Partek Flow. The solution simplifies Read More...
Web Page
Bioinformatics
03/20/2017 - BTEP Workshop on RNA-Seq Data Analysis (2-day) This 2-day workshop, which includes both lecture and hands-on components, will cover the fundamentals of and best practices for RNA-Seq Data Analysis. Learn everything from experimental design Read More...
Web Page
Bioinformatics
02/15/2017 - nSolver™ Analysis Software is a free analysis platform for storage, custom QC, and custom normalization of nCounter data. Generate highly-customized exports, basic statistical outputs, and publication-quality figures quickly and easily with the included tools. Read More...
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Bioinformatics
02/18/2014 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include Read More...
Web Page
Bioinformatics
Upon opening the MultiQC report, the user will be greeted with a navigation panel (similar to that found in the individual FASTQC reports) that allows users to quickly move to different sections of the report. Read More...
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Bioinformatics
After data has been transferred to the NIH Partek Flow server, the next step is to import them into a project. Sign onto Partek Flow and hit the "New project" button click to Read More...
Web Page
Bioinformatics
01/22/2025 - This three hour online training covers QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression. Read More...
Web Page
Bioinformatics
The goal of quality control is to keep only high quality cells (i.e., remove low quality cells (dead or dying cells), cell-free RNA, or doublets). Low quality cells will impact downstream analyses. Take care Read More...
Web Page
Bioinformatics
Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse Read More...
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Bioinformatics
05/14/2024 - This presentation will explain the difference between the mean and standard deviation of a set of values and the standard error of the mean. The parameters involved in comparing two normally distributed populations relative Read More...
Web Page
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...
Frederick, MD
Collaborative
Repositories
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...
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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...
Bethesda, MD
Collaborative
The NCI Clinical Research Correlatives Core provides non-CLIA-certified spectral flow cytometric assays to support clinical trials conducted in the CCR. The core specializes in immunophenotyping and immune monitoring assays. Established Technologies Spectral flow cytometry (Cytek), Read More...
Web Page
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...
Web Page
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...
Web Page
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...
Bethesda, MD
Core Facility
The Cancer and Inflammation Program – Microbiome and Genetics Core (CIP-MGC) grew out of the former CIP Genetics Core to meet the increasing need for sequencing and analysis of commensal microbiota within CIP and NCI. The Read More...
Frederick, MD
Core Facility
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...
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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...
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Back Services: Biophysics Facility offers ZetaView as an open-access instrument. First-time users must complete a short training session before using it for the first time. Training includes instrument calibration and size analysis of a standard Read More...
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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...
Web Page
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...
Web Page
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...
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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...
Web Page
Back Services: Biophysics Facility offers fluorometers as open-access instruments. First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3226 Description: Some substances reemit light after Read More...
Web Page
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...
Bethesda, MD
Trans NIH Facility
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...
Bethesda, MD
Core Facility
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...
Bethesda, MD
Trans NIH Facility
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...
Web Page
Bioinformatics
12/05/2024 - This one and a half hour online training will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be Read More...
Web Page
Bioinformatics
Course Overview Partek Flow is a 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 Read More...
Web Page
Bioinformatics
09/13/2023 - 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...
Web Page
Bioinformatics
Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...
Web Page
Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...
Web Page
Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...
Web Page
Bioinformatics
Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...
Web Page
Bioinformatics
Below, you will find questions and answers brought up in the course polls for the BTEP Bioinformatics for Beginners course series that took place from September 13th, 2022 to December 13th, 2022. Question 1 : Normalization - when to Read More...
Web Page
Bioinformatics
BTEP Bioinformatics for Beginners (September 13th, 2022 - December 13th, 2022) Questions and Answers Below, you will find questions and answers brought up in the course polls for the BTEP Bioinformatics for Beginners course series that took Read More...
Web Page
Bioinformatics
11/14/2017 - The CCR Office of Science and Technology Resources (OSTR), along with the Bioinformatics Training and Education Program (BTEP), are pleased to organize this event for the CCR scientific community. The primary goal of single Read More...
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Bioinformatics
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...
Web Page
Bioinformatics
02/21/2017 - This BTEP Workshop will cover the fundamentals and best practices of Exome-Seq analysis, including downstream interpretation of variants using a variety of in-house and NCI-licensed software solutions. There will be hands-on training on CCBR Read More...
Web Page
Bioinformatics
10/03/2016 - The maximum number of registrations (25) allowed has been reached for this workshop. You will be put on the waitlist and informed if any cancellations do occur. You are welcome to come on the morning Read More...
Web Page
Bioinformatics
03/08/2016 - BTEP Workshop on Exome-Seq Data Analysis and Variant Annotation (2-day) This workshop will cover the basics and best practices of exome-seq analysis including downstream interpretation of variants using a variety of in-house, open-source and Read More...
Web Page
Bioinformatics
09/22/2015 - Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Open Source Tools. As we walk though hands-on analysis of a cancer dataset, you will learn the principles of experimental design, Read More...
Web Page
Bioinformatics
09/29/2014 - PLEASE NOTE: This 2 day workshop is a BYOC ( Bring your own LapTop Computer ) class. In order to provide more flexibility with room scheduling we are experimenting with a new format that involves students brining Read More...
Web Page
Bioinformatics
10/03/2013 - Due to the recent Government Furlough this talk had been POSTPONED and wil be rescheduled at a later date. This 2-day course, which includes both lecture and hands - on components, will teach the Read More...
Web Page
Bioinformatics
03/17/2025 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a several trainings that cover general concepts behind statistics and epidemiology. These trainings will help Read More...
Web Page
Bioinformatics
02/27/2025 - NGS produces millions of sequences per sample and the challenge is to identify where in the genome each sequence came from. Fortunately, there are aligners that help scientists with this task. After this class, Read More...
Web Page
Bioinformatics
12/03/2024 - This one and a half hour online training will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek Flow Read More...
Web Page
Bioinformatics
12/03/2024 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering classes geared to cover general concepts behind statistics and epidemiology. This four-part lecture series will Read More...
Web Page
Bioinformatics
11/08/2024 - Learn microbiome analysis basics in R with phyloseq. This workshop will cover different types of analysis frequently used in microbiome studies, including sample diversity, community composition, and differential taxa. The techniques we learn will Read More...
Web Page
Bioinformatics
09/27/2024 - This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over Read More...
Web Page
Bioinformatics
09/18/2024 - Learn how to use the FlowJo™ workspace, including how to load files, evaluate sample quality, draw gates, and generate tabular and graphical layouts. Designed for those new to the software Read More...
Web Page
Bioinformatics
08/14/2024 - In this introduction session, Dr. Yana Stackpole will discuss biologist-friendly ways to import and analyze RNAseq data in Qlucore, followed by integrated GSEA for biological interpretation. She will pick a public cancer-related Read More...
Web Page
Bioinformatics
08/08/2024 - What are common statistical analyses for binary data? What is the distribution of your binary dependent variable? What is the difference from normally distributed data? How do you model the binary outcome with multiple Read More...
Web Page
Bioinformatics
07/10/2024 - Qlucore Omics Explorer is a point-and-click software for analyzing various omics data including RNA sequencing (bulk and single cell), proteomics, and metabolomics. Participants will learn to perform QC, construct visualizations (ie. PCA, heatmap, volcano, Read More...
Web Page
Bioinformatics
06/20/2024 - What are common statistical analyses for continuous data? Can you check whether your continuous outcome is normally distributed? What are the methods when the data are not normal? How do you model the outcome Read More...
Web Page
Bioinformatics
05/29/2024 - This talk will cover a scRNA-seq workflow available to NCI researchers on NIDAP. NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts user-friendly bioinformatics Read More...
Web Page
Bioinformatics
Josh Meyer, bioinformatics analyst (CCBR), will cover a scRNA-seq workflow available to NCI researchers on NIDAP . NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts Read More...
Web Page
Bioinformatics
To look at how these metrics correlate, we can use FeatureScatter() , which can be used to visualize feature-feature relationships and also be applied to other data stored in our Seurat object (e.g., metadata columns, Read More...
Web Page
Bioinformatics
The CCBR Single-cell RNA-seq Workflow on NIDAP Josh Meyer, bioinformatics analyst (CCBR), will cover a scRNA-seq workflow available to NCI researchers on NIDAP . NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative Read More...
Web Page
Bioinformatics
Integration is the process of aligning the same cell types across samples, treatments, data sets, batches, etc. Clustering should represent biological differences and not technical artifacts. Integration is not always necessary. You should run through Read More...
Web Page
Bioinformatics
April 3, 2024 - The CCR Single Cell Analysis Facility (SCAF): An Overview (Mike Kelly, SCAF) ( Recording ) April 10, 2024 - Introduction to single cell RNA-Seq (Charlie Seibert, Saeed Yadranji Aghdam, SCAF) ( Recording ) April 17, 2024 - SCAF: Overview of Cell Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
Welcome to Getting Started with scRNA-Seq This is a mini seminar series designed to help attendees learn more about single cell RNA-Seq, from applicable technologies to data analysis. Seminar Schedule April 3, 2024 - The CCR Single Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
In addition to the Heatmap and the FeaturePlot shown previously, two other options easily accessible through Seurat are the Dot Plot and Violin Plot. The dot plot can visualize relative expression level and expression fraction. Read More...
Web Page
Bioinformatics
The metadata in the Seurat object is located in adp@metadata and contains the information associated with each cell. We can access the metadata using: head(adp@meta.data) #using head to return only the Read More...
Web Page
Bioinformatics
Because of the different layers, you will need to break down the object to apply different thresholds by group or sample. The easiest way to do this is to work with the metadata and use Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
03/26/2024 - Dear Colleagues, Developed by expert statisticians and programmers, SUDAAN is a software package designed for researchers who work with study data. SUDAAN procedures properly account for correlated observations, clustering, weighting, stratification, and Read More...
Web Page
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...
Web Page
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...
Web Page
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...
Research Training Park, NC
Core Facility
Trans NIH Facility
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...
Frederick, MD
Core Facility
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...
Frederick, MD
Core Facility
The Clinical Support Laboratory offers processing, tracking, and testing of a broad range of clinical samples. Support can begin at the early stages of clinical trial development to aid in developing a comprehensive strategy for Read More...
Web Page
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...
Web Page
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...
Web Page
Home About the Biophysics Core Biophysics Core Technologies We provide consultations and advice on the applications of biophysical methods. If you would like to discuss the requirements of a particular technique or consider selecting the Read More...
Web Page
What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and Read More...
Web Page
What is Xenium? Xenium is a high-resolution, imaging-based in situ spatial profiling technology from 10x Genomics that allows for simultaneous expression analysis of RNA targets (currently in range of 100’s) within the same tissue section. Read More...
Frederick, MD
Core Facility
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...
Web Page
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...
Frederick, Maryland
Collaborative
Bruker AVANCE 400 and 500 MHz NMR instruments. Helium Cryoprobe technology on the 500 MHz machine for added sensitivity, especially for Carbon-13 spectra. Access to a second 500 MHz instrument with Prodigy Liquid Nitrogen-cooled cryoprobe. User Accounts can be Read More...
Bethesda, MD
Trans NIH Facility
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...
Frederick, MD
Collaborative
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...
Bethesda, MD
Collaborative
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...
Web Page
[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...
Web Page
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...
Bethesda, MD
Repositories
Trans NIH Facility
The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...
Web Page
CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx Interested in imaging large scale biological samples? Volume electron microscopy allows for Read More...
Rockville, MD
Repositories
Trans NIH Facility
DTP maintains a repository of synthetic compounds and pure natural products that are available to investigators for non-clinical research purposes. The Repository collection is a uniquely diverse set of more than 200,000 compounds that have been Read More...
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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...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Cores on CREx NIBIB BEPS Micro Analytical Immunochemistry Unit The Micro Analytical Immunochemistry Unit employs a variety Read More...
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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...
ROCKVILLE, MD
Repositories
Trans NIH Facility
The Specimen Resource Locator (SRL) is a biospecimen resource database designed to help researchers locate resources that may have the samples needed for their investigational use. This publicly searchable database includes information about biospecimen banks Read More...
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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...
Frederick, MD
Core Facility
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...
Rockville, MD
Collaborative
Repositories
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...
Frederick, MD
Core Facility
The Laboratory Animal Sciences Program (LASP) of the Frederick National Laboratory operates a Gnotobiotics Facility (GF) to support research focused on the role of microbiota in cancer inflammation, pathogenesis, and treatment response. The GF can Read More...
Bethesda, MD
Core Facility
Trans NIH Facility
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...
Bethesda, MD
Core Facility
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...
Bethesda, MD
Collaborative
The NCI High-Throughput Imaging Facility (HiTIF) works in a collaborative fashion with NCI/NIH Investigators by providing them with the necessary expertise, instrumentation, and software to develop and execute advanced High-Throughput Imaging (HTI) assays. These Read More...
Bethesda, MD
Core Facility
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...
Frederick, MD
Collaborative
The Center for Advanced Preclinical Research (CAPR) specializes in evaluating the efficacy of preclinical compounds, existing drugs, or biologics (therapeutics) in genetically engineered mouse models, GEM-derived allograft (GDA) models, or patient-derived mouse xenografts (PDX). We Read More...
Bethesda, Maryland
Core Facility
Repositories
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...
Bethesda, MD
Collaborative
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...
Rockville, MD
Trans NIH Facility
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...
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Bioinformatics
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...
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Bioinformatics
This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
11/06/2024 - Join Our Training on Spatial Omics Data Analysis with MAWA (Multiplex Analysis Web Apps). Want to learn how to process and analyze your spatial proteomics/transcriptomics data? Join us for four virtual hour-long sessions Read More...
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Bioinformatics
10/29/2024 - Join Our Training on Spatial Omics Data Analysis with MAWA (Multiplex Analysis Web Apps). Want to learn how to process and analyze your spatial proteomics/transcriptomics data? Join us for four virtual hour-long sessions Read More...
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Bioinformatics
10/22/2024 - Join Our Training on Spatial Omics Data Analysis with MAWA (Multiplex Analysis Web Apps). Want to learn how to process and analyze your spatial proteomics/transcriptomics data? Join us for four virtual hour-long sessions Read More...
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Bioinformatics
10/15/2024 - Join Our Training on Spatial Omics Data Analysis with MAWA (Multiplex Analysis Web Apps). Want to learn how to process and analyze your spatial proteomics/transcriptomics data? Join us for four virtual hour-long sessions Read More...
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Bioinformatics
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...
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Bioinformatics
Following Cell Ranger and/or other pre-processing tools, you will have a gene-by-cell counts table for each sample. The three most popular frameworks for analyzing these count matrices include: R ( Seurat ). Seurat, brought to you Read More...
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Bioinformatics
When using SingleR, the 3 primary parameters are the experimental dataset, the reference dataset, and the labels being used. Continuing with the main labels of the MouseRNASeq dataset on the full dataset looks like this: annot = Read More...
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Bioinformatics
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...
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Bioinformatics
Clustering is used to group cells by similar transcriptomic profiles. Seurat uses a graph based clustering method. You can read more about it here . The first step is to compute the nearest neighbors of each Read More...
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Bioinformatics
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...
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CRTP
How do I determine which EM technique should be used for my research? Schedule a free consultation with the Head of EML, Dr. Ru-ching Hsia, to discuss the aim of your research project. Dr.& Read More...