Web Page
Bioinformatics
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...
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Bioinformatics
08/20/2020 - Single nucleotide polymorphism (SNP) & Variation Suite (SVS) is an analytic tool created to empower researchers to perform complex analyses and visualizations on genomic and phenotypic data. Genome-Wide Association Studies (GWAS) continues to be Read More...
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Bioinformatics
Given a list of numbers, it is difficult to perform mathematical operations. For instance list_of_numbers=[1,2,3,4,5] Multiplying list_of_numbers by 2 will duplicate this list. However, multiplying a list of numbers by two should Read More...
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Bioinformatics
Given a list of numbers, it is difficult to perform mathematical operations. For instance list_of_numbers=[1,2,3,4,5] Multiplying list_of_numbers by 2 will duplicate this list. However, multiplying a list of numbers by two should Read More...
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Bioinformatics
10/16/2012 - Fundamentals of DNA copy number analysis using Nexus Learn the basics of copy number analysis and its application to genomic research. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/ Read More...
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Software that offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP arrays as well as NGS WES/WGS and expression data. Nexus Copy Number – Accelerating Copy Read More...
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Bioinformatics
Work on this if you choose to, at your own leisure, or if time permits. How would you confirm that there is a potential single nucleotide variant at position 50,768,105 on chromosome 22 for the hcc1395_normal_ Read More...
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Bioinformatics
import numpy import matplotlib.pyplot as plt x=numpy.array([0,1,2,3,4]) y=numpy.array([0,2,4,6,8]) plt.scatter(x,y) plt.xlabel("x", size=15) plt.ylabel("y", size=15) plt.tick_params(labelsize=12) plt.title(& Read More...
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Bioinformatics
import numpy import matplotlib.pyplot as plt x=numpy.array([0,1,2,3,4]) y=numpy.array([0,2,4,6,8]) plt.scatter(x,y) plt.xlabel("x", size=15) plt.ylabel("y", size=15) plt.tick_params(labelsize=12) plt.title(& Read More...
Web Page
Bioinformatics
10/23/2012 - Learn the fundamentals in genomic data analysis of CGH and SNP arrays using BioDiscovery Nexus Copy Number software. In this hands-on training session, you will learn how to load, process, visualize, and analyze array Read More...
Rockville, MD
Collaborative
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...
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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...
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...
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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Bioinformatics
The CCR Collaborative Bioinformatics Resource (CCBR) is a 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 expertise in Read More...
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Bioinformatics
Everything assigned a value in R is technically an object. Mostly we think of R objects as something in which a method (or function) can act on; however, R functions, too, are R object. R Read More...
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Bioinformatics
Now that we have an R script, let's begin to work with R objects. Everything assigned a value in R is technically an object. Mostly we think of R objects as something in which Read More...
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Bioinformatics
Everything assigned a value in R is technically an object in which a method (or function) can act on. Therefore, objects are data structures with specific attributes and methods that can be applied to them. Read More...
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Bioinformatics
06/01/2020 - After nearly two decades of improvements, the current human reference genome is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of Read More...
Web Page
Bioinformatics
Partek Genomics Suite (Partek) is a graphical user interface (GUI) based bioinformatics package. It hosts a range of work flows that allow for gene expression, epigenetic, and association analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{ Read More...
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Bioinformatics
The example below will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
Web Page
Bioinformatics
The example below will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
Web Page
Bioinformatics
Objects (and functions) are key to understanding and using R programming. Everything assigned a value in R is technically an object. Mostly we think of R objects as something in which a method (or function) Read More...
Web Page
Bioinformatics
Nexus Copy Number can take data from various arrays as input including Affymetrix CEl. To see the full list, click on "Load" -> "Load Data" -> " Read More...
Web Page
Bioinformatics
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...
Bethesda, MD
Collaborative
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...
Web Page
Bioinformatics
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...
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Bioinformatics
10/23/2024 - Please send any questions and/or specific topic areas that you’re interested in hearing about for this presentation by Friday, 10/18 to Kayla Strauss . QIAGEN Ingenuity Pathway Analysis (IPA) is the leading Read More...
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Bioinformatics
10/23/2023 - QIAGEN Ingenuity Pathway Analysis (IPA) is the leading pathway analysis application among the life science research community and is cited in tens of thousands of articles for the analysis, integration and interpretation of data Read More...
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Bioinformatics
In this portion of the class, it is very important that you have IGV already opened on your computer. See Figure 1 and Figure 2 on how to load the relevant alignment outputs for HBR_1 and UHR_1 Read More...
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Bioinformatics
For visualizing the HBR and UHR alignment results, we will use the built in Human hg38 genome. To do this, we will just goto the genome selection box and select hg38 (Figure 2). In Figure 3, we Read More...
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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
Genomic variations are typically categorized into different classes and are often denoted with a shortened acronym: SNP, a single nucleotide polymorphism - A change of a single base. INDEL, an insertion or a deletion - Read More...
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Bioinformatics
R: Data types: integer, numeric, character, and logical Data structures: vectors, lists, data frames, matrices. x
Web Page
Bioinformatics
R: Data types: integer, numeric, character, and logical Data structures: vectors, lists, data frames, matrices. ::: {.cell} x ::: :::
Web Page
Bioinformatics
11/04/2021 - Abstract: Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and essential role in chromosome segregation. Now, the first complete, telomere-to-telomere Read More...
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Bioinformatics
11/04/2021 - Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=mf0f44a00dfd24b954e3b3574894b21c4 Abstract: Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near Read More...
Web Page
Bioinformatics
04/21/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e51f19be5660107b4b92118dc48be1781 Presenter: Kevin Kendal PhD CEO of MacVector Description: This workshop will focus on the analysis of Next Read More...
Web Page
Bioinformatics
01/14/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e968a58127acdb59b961e2ef13865c7ad Description: This workshop will focus on the analysis of Next Generation Sequencing (NGS) data using the Read More...
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Bioinformatics
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...
Web Page
Bioinformatics
05/01/2013 - Intended Audience: This day-long training course is intended for Users who want to apply Next Generation Sequencing methodologies for DNA-Seq, Methyl-Seq, small RNA-Seq, RNA-Seq and ChIP-Seq studies. All analyses are done on the Genomatix Read More...
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Bioinformatics
04/30/2013 - Intended Audience: This day-long training course is intended for users who wish to get an introduction to the central concepts, strategies, and analysis software offered by Genomatix for transcription factor binding site and promoter Read More...
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Bioinformatics
An important step to learning any new programming language and data analysis is to understand its data types and structures. Common data types and structures that will be encountered include the following. Text (str) Numeric Read More...
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Bioinformatics
An important step to learning any new programming language and data analysis is to understand its data types and data structures. Common data types and structures that will be encountered include the following. Text (str) Read More...
Web Page
Bioinformatics
The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
Web Page
Bioinformatics
The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
Web Page
Bioinformatics
Participants can work on these practice questions on their own time as a Biowulf account or local installation of IGV is needed. Open the bigWig files for HBR_Rep1 (HBR_Rep1_hisat2.bw) and UHR_ Read More...
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Bioinformatics
To plot using Seaborn, start the command with seaborn followed by the plot type, separated by a period. seaborn.plot_type This section will use Seaborn's scatterplot to explore how to work with and Read More...
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A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. One favorite use is inspection of alignments to rule out alignment artifacts resulting in false-postive variant calls.The Integrative Genomics Viewer (IGV) is Read More...
Web Page
QIAGEN CLC Workbench is a user-friendly solution for DNA, RNA and protein data sequence analysis. It houses tools for molecular biology and next generation sequencing (NGS) data analysis. QIAGEN CLC Genomics Workbench The CLC Genomics Read More...
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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...
Bethesda, MD
Repositories
Trans NIH Facility
The CHTN is a unique NCI-supported resource that provides human tissues and fluids from routine procedures to investigators who utilize human biospecimens in their research. Unlike tissue banks, the CHTN works prospectively with each investigator Read More...
Bethesda, MD
Collaborative
Repositories
The National Clinical Trials Network Biospecimen Banks (NCTN) receive, store, and distribute human cancer biospecimens collected on NCTN clinical trials . NCTN Biobanks provide cancer researchers with quality, well-annotated biospecimens and associated clinical information. The NCTN Read More...
ROCKVILLE, MD
Repositories
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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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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Bioinformatics
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...
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Bioinformatics
First we will retrieve the Ebola reference genome and put it in the "refs" directory. Next we need to create the index for the aligner (bwa index) and for IGV (samtools faidx). Let' Read More...
Web Page
Bioinformatics
VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create a "bwa index" Read More...
Web Page
Bioinformatics
Lesson 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain Read More...
Web Page
Bioinformatics
Lesson 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain Read More...
Web Page
Bioinformatics
This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
06/29/2022 - The CCR Genomics, Sequencing and Single Cell Analysis Core Facilities are pleased to host a virtual technology seminar with Illumina. Presentation overview : For decades cancer methylation studies have provided insights into tumorigenic pathways and Read More...
Web Page
Bioinformatics
05/24/2021 - Dr. Adam Phillippy, a Senior Investigator at NHGRI will give an extremely interesting talk on Monday, 5/24 at 11 am via WebEx at https://nih.webex.com/nih/j.php?MTID=m237a8e77868c23cc4 Read More...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
11/13/2017 - MetaCore™ is an integrated curated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, 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...
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Bioinformatics
02/09/2016 - BTEP Workshop on Pathway Analysis with MetaCore NOTE: This is a Bring Your Own Computer (BYOC) class, and will be simultaneously shared via GoToMeeting with attendees at the Advanced Technology Research Facility (ATRF) in Read More...
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Bioinformatics
11/09/2015 - A Short Course in R for Biologists "A Short Course in R for Biologists" is a two-day course given in four three-hour sessions entitled: Introduction to R, Introduction to Bioconductor, Introduction to Read More...
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Bioinformatics
10/22/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...
Web Page
Bioinformatics
01/29/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...
Web Page
Bioinformatics
12/17/2014 - Day 1 - AM (9:30 AM – 12:30 PM) Ingenuity IPA - Basic Training ( Kate Wendelsdorf, Ph.D. - Ingenuity Pathway Analysis) Ingenuity IPA® is the industry leading software solution to model, analyze, and understand complex biological and Read More...
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Bioinformatics
To plot using Seaborn, start the command with seaborn followed by the plot type (where plot type can be any plot, for instance if the user wants a scatter plot then the command would be Read More...
Web Page
Bioinformatics
Arguments and options for Python commands are enclosed in parentheses. In general, the anatomy is command(argument, option). For example, the command below is print and it will display the argument, "Hello BTEP" Read More...
Frederick, MD
Core Facility
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...
Bethesda, MD
Core Facility
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...
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...
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Bioinformatics
Objectives To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By the end Read More...
Web Page
Bioinformatics
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...
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Bioinformatics
Generating VCF Files (Simulated data) VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create Read More...
Web Page
Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
Web Page
Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
Web Page
Bioinformatics
R basics Objectives : To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By Read More...
Web Page
Bioinformatics
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...