Search Results for: exome capture

03/18/2015 - This workshop will cover basics of exome-seq analysis including downstream interpretation of variants using a variety of open-source and commercial webtools (Golden Helix, IGV, Ingenuity Variant Analysis, GeneGrid (Genomatix), MuPit/Cravat). Day 1 - AM (9:30 Read More...

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...

05/09/2018 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of publicly available genomic data has grown exponentially in recent years.  While most of the analyses of these data Read More...

12/13/2016 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of publicly available genomic data has grown exponentially in recent years.  While most of the analyses of these data Read More...

Ranges can be used to for subsetting data (ie. extract data in rows 5 thru 10 of a data frame) or applied to iterate over a task in things like a for loop. For instance, a for Read More...

Lists and tuples are one dimensional collections of data. The tuple is an immutable list, in which the elements cannot be modified. To create a list, enclose the contents in square brackets. sequencing_list=[" 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...

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...

06/25/2025 - Dr. Cleary will pre ent their late t work developing Perturb-FI H, a method that capture the effect of genetic change within and between cell while pre erving the patial architecture of living y Read More...

12/07/2023 - This webinar will discuss and demonstrate experimental design considerations in variant analysis, including the origins of tissue samples (germline vs. somatic), whole exome (WES) or whole-genome sequencing (WGS), sample sizes and statistical power, quality Read More...

Make sure you have a clear plan for storing, managing and analysing your data. Also, ensure you have a method to capture all the pertinant metadata and document the data analysis steps that have been Read More...

03/18/2021 - Recording Link CD8 T cell dysfunction is observed in diverse settings of chronic antigen exposure, including in cancer and chronic viral infection. We carried out a unified analysis of over 300 ATAC-seq and RNA-seq experiments Read More...

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

06/11/2013 -   Common sample prep and library preparation pitfalls Understand what determines the quality of your NGS data Current publishing and data reporting standards for NGS studies Types of experimental designs used NGS studies Ensure efficient Read More...

05/28/2013 - Nexus Copy Number is a user-friendly desktop application for analysis and visualization of structural variation (copy number, allelic events, and small sequence variations) from CGH and SNP array- and NGS-generated data. The simple and Read More...

Lists and tuples are one dimensional collections of data. The tuple is an immutable list, in which the elements cannot be modified. However, lists are mutable. To create a list, enclose the contents in square Read More...

Loops and iterators are great for performing repeated tasks. In Python, users will see for and while loops. To learn about loops, first recreate sequencing_list. sequencing_list=["whole genome", "rna", & Read More...

Again, thanks to a wide array of packages, output data types are essentially limitless. There are some file types that are specific to R and noteworthy including .RData and .rds files. RData files are used Read More...

The green "Push" button in the Git pane can also be used to send to code to GitHub. Add the following code then save and commit the changes. # Correlation between displacement and quarter 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 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...

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...

Who says Unix programmers don't have a sense of humor? Let me introduce cat , head , and tail . The cat command (short for "concatenate") is an extremely useful command for creating new files Read More...

08/12/2022 - The NIH-funded International epidemiology Databases to Evaluate AIDS (IeDEA) consortium is a global HIV observational research network with seven geographic regions and over 350 participating HIV care and treatment clinics. The data scientists and data Read More...

04/28/2021 - Register/Join In this public workshop, participants will have the opportunity to discuss the challenges and opportunities involved in establishing effective data management and sharing practices. The organizers encourage anyone working with data to Read More...

03/24/2021 - WebEx: Register Accurate detection of somatic mutations is challenging but critical to understanding how cancer forms and progresses. Such detection is also critical for targeting more effective treatments. In this seminar, Dr. Mohammad Sahraeian, Read More...

03/15/2021 - Abstract: Cancer represents an evolutionary process through which growing malignant populations genetically diversify, leading to tumour progression, relapse and resistance to therapy. In addition to genetic diversity, the cell-to-cell variation that fuels evolutionary selection Read More...

09/28/2020 - Register/Join This webinar is intended for cancer researchers and bioinformaticians who are interested in learning more about the NCI Genomic Data Commons’ (GDC’s) bioinformatics pipelines for data harmonization. The GDC DNA-Seq analysis Read More...

06/08/2020 - Extensive investigations have revealed intra-genomic variation in somatic mutation rates influenced by the sequence composition, structure, and local chromatin features of the genome. I will review the literature on mechanisms underlying the intra-genome mutational Read More...

04/10/2019 - BTEP Wednesday, April 10, 2019 9:00 am  |  Eastern Daylight Time (New York, GMT-04:00)  |  2 hrs Meeting number (access code): 738 427 711 Meeting password: zPJpWP$6     10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked Read More...

12/05/2018 - THIS EVENT HAS BEEN CANCELLED 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked reads works SNVs, copy number variations, structural variants and phasing of the variants from linked read data Read More...

10/26/2018 - 10x Genomics: Whole Exome and Whole Genome Analysis How 10x Genomics linked reads works SNVs, copy number variations, structural variants and phasing of the variants from linked read data Walk through of 10x Genomics Read More...

06/20/2013 - This is repeat of the lecture given June 11th on the Bethesda Campus. Common sample prep and library preparation pitfalls Understand what determines the quality of your NGS data Current publishing and data reporting Read More...

05/07/2013 -   This 2 hour seminar will be an interactive discussion and demonstration of the types of applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies ( Read More...

02/26/2013 -   Comparison Study of NGS SNP Detection Tools Brief background and introduction for the current status of SNP detection field and each of the selected tools to be compared Description of our benchmark exome-seq data Read More...

11/29/2012 -   The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of Read More...

sequencing_list[1]="single cell RNA" sequencing_list ['whole genome', 'single cell RNA', 'whole exome'] sequencing_tuple[1]="single cell RNA" TypeError Traceback (most recent call last) Cell In[48], line 1 ----> 1 Read More...

sequencing_list[1]="single cell RNA" sequencing_list ['whole genome', 'single cell RNA', 'whole exome'] sequencing_tuple[1]="single cell RNA" TypeError Traceback (most recent call last) Cell In[48], line 1 ----> 1 Read More...

Who says Unix programmers don't have a sense of humor? Let me introduce cat, head, and tail. The cat command (short for "concatenate") is an extremely useful command for creating new files Read More...

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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 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 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 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...

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

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...

03/26/2025 - Developing artificial intelligence (AI) schemes to assist the clinician towards enabling precision medicine approaches requires development of objective markers that are predictive of disease response to treatment or prognostic of longer-term patient survival. The 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...

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...

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...

Plots condense complex and busy tabular data into a form that is easier to interpret. An expression heatmap is a common visualization used in RNA sequencing analysis. A heatmap shows numerical data on a color Read More...

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...

Unix, what is it, and why should biologists take the time to learn it? The Unix operating system forms the basis of many bioinformatics analyses resources, such as the NIH High Performance Cluster (HPC) Biowulf/ 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...

11/19/2021 - High-resolution, whole-brain microscopy provides unprecedented new insights into the brain’s structural organization, molecular diversity and connectivity. The Brain Image Library (BIL) provides infrastructure that facilitates the sharing of this valuable data, enabling investigators Read More...

09/22/2021 - Registration is required. During this upcoming webinar, Dr. Yanjun Qi will demonstrate AttentiveChrome, an attention-based deep learning approach that uses a unified architecture to model and interpret interactions and dependencies among the chromatin factors Read More...

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...

09/11/2020 - Speaker: James Zou, Ph.D., Assistant Professor, Biomedical Data Science, Computer Science, and Electrical Engineering, Stanford University Register Dr. Zou will present new computer vision algorithms to capture complex morphologies and phenotypes that are Read More...

08/10/2020 - Copy Number Variation (CNV) is a type of structural variation in which sections of the genome are duplicated or deleted. Associated with being causal mutations for disease phenotypes, it is important in clinical and Read More...

Plots condense complex and busy tabular data into a form that is easier to interpret. An expression heatmap is a common visualization used in RNA sequencing analysis. A heatmap shows numerical data on a color Read More...

Swarm is a way to submit multiple commands to the Biowulf batch system and each command will be run as an independent job, allowing for parallelization. Below is an example of swarm script (srp045416_download. Read More...

Data collected for a specific case in TCGA may have differed according to sample quality and quantity, cancer type, or technology available at the time of analysis. --- https://www.cancer.gov/ccg/research/genome-sequencing/ Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our 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 Neurorehabilitation and Biomechanics Research Section (also referred to as the NAB LAB) is a multidisciplinary group of highly qualified scientists, clinical and technical staff, and trainees with diverse backgrounds including medical, physical therapy, neuroscience 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 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...

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...

RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

Lesson 4: Useful Unix For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 3 Review Biowulf is the high performance computing cluster at NIH. When you apply for a Biowulf account 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...

05/22/2017 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of available genomic data has grown exponentially in recent years.  While most of the analyses of these data is Read More...

There are a number of core facilities available to NCI researchers. See more information from the Office of Science and Technology Resources. We most commonly see data from the following cores: CCR Sequencing Facility (CCR-SF) Read More...

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