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Bioinformatics
Tip File transfer using command line: Copy from data to Partek Flow uploads folder is OK Copy from data to Partek Flow project folder is not OK Copy from Partek Flow uploads folder to project Read More...
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Bioinformatics
Type cmd + spacebar and search for "terminal". Once open, right click on the app logo in the dock. Select Options and Keep in Dock . The default shell starting with Mac OSX version 10.14 is Read More...
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Bioinformatics
Type cmd + spacebar and search for "terminal". Once open, right click on the app logo in the dock. Select Options and Keep in Dock . The default shell starting with Mac OSX version 10.14 is Read More...
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Bioinformatics
10/23/2024 - CellMinerCDB is an interactive public web application ( https://discover.nci.nih.gov/cellminercdb/ ) that simplifies access and exploration of cancer cell line pharmacogenomic data across different sources such as the National Cancer Institute (NCI), Read More...
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Bioinformatics
If you are using a Windows operating system, Windows 10 or greater, you can use the Windows Subsystem for Linux (WSL) for your computational needs. The Windows Subsystem for Linux (WSL) is a feature of the Read More...
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Bioinformatics
If you are using a Windows operating system, Windows 10 or greater, you can use the Windows Subsystem for Linux (WSL) for your computational needs. The Windows Subsystem for Linux (WSL) is a feature of the Read More...
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Bioinformatics
Try QIIME 2 Galaxy implementation Nephele MicrobiomeAnalyst If you have any questions about your microbiome analysis, do not hesitate to email us at ncibtep@nih.gov.
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Confocal
Confocal Microscope Image of Fixed Mouse Embryonic Fibroblast (MEF) Cells Actin proteins (stained red) and Tubulin proteins (stained green) are involved in a number of cellular process such as cell motility, cell division and maintenance Read More...
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Bioinformatics
02/04/2025 - This lesson is part of a course, B4B: Unix and Biowulf. This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...
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Bioinformatics
01/30/2025 - This lesson is part of a course, B4B: Unix and Biowulf. This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...
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Bioinformatics
command line interactively.\ command line using a script .\ interactively through an environment. This course will demonstrate the utility of the RStudio integrated development environment (IDE). ::: notes I am also a fan of the R extension Read More...
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Bioinformatics
R can be used via command line interactively, command line using a script , or interactively through an environment. This course will demonstrate the utility of the RStudio integrated development environment (IDE).
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Bioinformatics
Q2studio Graphical user interface Q2cli Command line interface The classic way to use qiime2 Artifact API Python 3 application programming interface (API) for QIIME 2 Use with Jupyter notebook Recommended for advanced users Galaxy The Read More...
Rockville, MD
Repositories
Trans NIH Facility
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...
Frederick, Maryland
Core Facility
The Protein Expression Laboratory produces proteins to help CCR investigators achieve their research goals with the lowest possible cost in the shortest time. PEL is operated by Leidos Biomedical Research Inc. on behalf of NCI Read More...
Frederick, MD
Repositories
Trans NIH Facility
The Developmental Therapeutics Program (DTP) within NCI's Division of Cancer Treatment and Diagnostics (DCTD), has maintained a low temperature repository of transplantable in vivo-derived tumors and in vitro-established tumor cell lines from various species. This Read More...
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Confocal
General Microscopy Resources Confocal Listserv Email discussion list focused on confocal microscopy, but also including topics on fluorescence microscopy and digital imaging. MicroscopyU Online learning platform by Nikon. An online source for Microscopy education. Leica Read More...
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Bioinformatics
Recently, the NIH HPC Team has provided on demand access to HPC resources via web browser through integration of Open OnDemand , an open source project supporting "nearly 400 HPC centers around the world" . This Read More...
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Bioinformatics
02/11/2025 - This lesson is part of a course, B4B: Unix and Biowulf. This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...
Web Page
Bioinformatics
02/06/2025 - This lesson is part of a course, B4B: Unix and Biowulf. This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...
Web Page
Bioinformatics
01/28/2025 - This lesson is part of a course, B4B: Unix and Biowulf. This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...
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Bioinformatics
12/12/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...
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Bioinformatics
09/19/2024 - This one hour and half online training builds on the topics covered in the Data Visualization in ggplot training. It provides an overview of options for working with dates, times, and options for customizing Read More...
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Bioinformatics
09/06/2024 - This course provides an introduction to data visualization using R. Participants will learn data visualization with base R and using the R package ggplot2 to explore various types of data visualizations, including scatter plots, Read More...
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Bioinformatics
08/27/2024 - This hands-on workshop will help you advance your microbiome analysis and computing skills, and help you learn new ways to leverage computing resources for your research. What you’ll learn: ● The basics of interacting Read More...
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Bioinformatics
07/24/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...
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Bioinformatics
05/29/2024 - This class provides an overview of options for customizing a ggplot graph. This class will focus on methods for creating small multiples, options for customizing a graph, and how to apply ggplot themes.& Read More...
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Bioinformatics
Due to limits on computational resources, you may be interested in running your analysis on an HPC. Biowulf is the NIH high performance compute cluster. It has greater than 90k processors, and can easily perform Read More...
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Bioinformatics
03/19/2024 - This class is designed for those who want to extend the basics covered in the Introduction to Quarto for Scholarly Publishing to Formatting class. This class uses Quarto to render formatted citations and bibliographies Read More...
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Bioinformatics
A geom is the geometrical object that a plot uses to represent data. People often describe plots by the type of geom that the plot uses. --- R4DS There are multiple geom functions that Read More...
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Bioinformatics
Because we build plots using layers in ggplot2. We can add multiple geoms to a plot to represent the data in unique ways. #We can combine geoms; here we combine a scatter plot with a # Read More...
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Bioinformatics
You do not need to load a package to visually explore data. Rather, you can use base R graphics for plotting (from the graphics package). This plotting is fairly different from ggplot2 , which is based Read More...
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Bioinformatics
Quarto® is an open-source scientific and technical publishing system built on Pandoc --- https://quarto.org/ What does this mean? Quarto allows you to combine code, commentary, and other features to tell a story about Read More...
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Bioinformatics
As we learn more about R and start learning our first commands, we will keep a record of our commands using an R script. Remember, good annotation is key to reproducible data analysis. An R Read More...
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Bioinformatics
What geoms would you use to draw each of the following named plots? a. Scatterplot b. Line chart c. Histogram d. Bar chart e. Pie chart (Question taken from https://ggplot2-book.org/individual-geoms.html .) {{ Read More...
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Bioinformatics
Lesson 5 Exercise Questions: ggplot2 What geoms would you use to draw each of the following named plots? a. Scatterplot b. Line chart c. Histogram d. Bar chart e. Pie chart (Question taken from https://ggplot2 Read More...
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Bioinformatics
02/13/2024 - This class provides an overview of options for customizing a ggplot graph. This class will focus on methods for creating small multiples, options for customizing a graph, and how to apply ggplot themes.& Read More...
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Bioinformatics
01/22/2024 - This is the first lesson in the Introduction to Unix on Biowulf, January 2024 series. In this lesson, participants will learn to log onto Biowulf and receive an overview of Unix command line as well Read More...
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Bioinformatics
A geom is the geometrical object that a plot uses to represent data. People often describe plots by the type of geom that the plot uses. --- R4DS There are multiple geom functions that Read More...
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Bioinformatics
Once the job is running, wait about 4 minutes before clicking on the web address shown to the right of job status line. (It will look similar to this " https://job-GBb1xFQ0YKq8PqYJKx1bVv6 Read More...
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Bioinformatics
As you continue to work in R, at some point you will need to incorporate regular expressions into your code. We used a regular expression escape above \\. to denote that we wanted to match a Read More...
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Bioinformatics
Load in the comma separated file "./data/countB.csv" and save to an object named gcounts . {{Sdet}} Solution } gcounts `...1` colnames ( gcounts )[ 1 ] ## 1 Tspan6 703 567 867 71 970 242 ## 2 TNMD 490 482 18 342 935 469 ## 3 DPM1 921 797 622 661 8 500 ## 4 SCYL3 335 216 222 774 979 793 ## 5 FGR 574 574 515 584 941 344 ## 6 CFH 577 792 672 104 192 936 ## 7 FUCA2 798 766 995 27 756 546 ## 8 GCLC 822 874 923 705 667 522 ## 9 NFYA 622 793 918 868 334 64 {{Edet}} Plot the Read More...
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Bioinformatics
To create an R object, you need a name, a value, and an assignment operator (e.g.,
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Bioinformatics
11/15/2023 - This class provides an overview of options for customizing a ggplot graph. This class will focus on methods for creating small multiples, options for customizing a graph, and how to apply ggplot themes.& Read More...
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Bioinformatics
09/11/2023 - We invite you to attend the Biobanking for Precision Medicine seminar series. The seminar series is brought to you by NCI’s Biorepositories and Biospecimen Research Branch (BBRB) and addresses current topics Read More...
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The Center for Advanced Tissue Imaging (CAT-I) is an NIAID and NCI supported effort involving collaborative studies between experts in the Laboratory of Immune System Biology, DIR, NIAID and investigators in the DIR, NIAID and Read More...
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...
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...
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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...
Frederick, MD
Core Facility
Repositories
The Mouse Modeling Core assists NIH investigators by generating and preserving genetically-engineered mouse strains. Services include scientific consultation, gene-targeting in mouse embryonic stem cells, micro-injection of nucleic acids, proteins, or ES cells into mouse embryos, Read More...
Bethesda, MD
Collaborative
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...
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...
Frederick, MD
Core Facility
Molecular Cytogenetics Core Facility facilitates the assessment of structural and numerical genomic changes in pre-cancer and cancer research models. This core provides comprehensive support for the cytogenetic analysis of cells from human and research animal Read More...
Rockville, MD
Collaborative
Repositories
The NCI Cloud Resources are components of the NCI Cancer Research Data Commons (CRDC) that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers Read More...
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...
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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...
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...
Web Page
Confocal
FRET (Fluorescence Resonance Energy Transfer) FRET is a light microscopy method for detecting protein‐protein interactions within intact cells. FCS (Fluorescence Correlation Spectroscopy) Fluorescence correlation spectroscopy (FCS) is a correlation analysis of fluctuation of the Read More...
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Confocal
Our Mission The NCI Optical Microscopy Cores are instrumental in advancing cancer research through optical measurements and analysis. Serving the Center for Cancer Research community, which is home to approximately 250 Principal and Senior Investigators across 50 Read More...
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Confocal
2024 Senatorov IS, Bowman J, Jansson KJ, Alilin AN, Capaldo BJ, Lake R, Riba M, Abbey YC, Mcknight C, Zhang X, Raj S, Beshiri ML, Shinn P, Ngyuyen H, Thomas CJ, Corey E, Kelly K. Castrate Read More...
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Confocal
Techniques The Laboratory of Cancer Biology and Genetics Microscopy Core houses multiple systems that can be used to analyze cell structure, protein expression, and cell dynamics using immunofluorescence. These include inverted epifluorescence microscopes, a confocal Read More...
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Confocal
Our Team Tatiana S. Karpova Ph.D.Core Headkarpovat@nih.govBuilding 41, Room C615240-760-6637 David A. Ball Ph.D.Core Biologistballa@nih.govBuilding 41, Room B114D240-760-6577 Mohamadreza Fazel, Ph.D.Core Biologistmohamadreza. Read More...
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Confocal
Software Image Acquisition Commercial imaging systems of LRBGE Optical Microscopy Core are controlled by acquisition software specifically designed for the appropriate microscope, such as ZEN (Zeiss confocal microscopes), Nikon Elements (Nikon), Imspector (Abberior). Custom-built HILO Read More...
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Confocal
General Usage Policies Principal investigators should read this document and sign it. PI’s/postdocs should attach a short-written summary of the project to the signed doc. If the project changes, Read More...
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Confocal
WIDE-FIELD MICROSCOPY Nikon Ti 2000 wide-field microscope Capabilities: This microscope is suited for live cell imaging (4D) and fixed cells (3D) imaging. This microscope produces high quality wide-field images that may be improved by Read More...
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Confocal
2024 L. Balagopalan, T. Moreno, H. Qin, B. C. Angeles, T. Kondo, J. Yi, K. M. McIntire, N. Alvinez, S. Pallikkuth, M. E. Lee, H. Yamane, A. D. Tran, P. Youkharibache, R. E. Cachau, N. Taylor, Read More...
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Confocal
Sign-Up for Microscopes and Computers Sign-up for EIB Microscopy Facility microscopes and image processing workstations is mandatory – please e-mail facility manager (“Contact” tab) and include your preferred date/time etc. Your request will be confirmed Read More...
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Confocal
Zeiss LSM 880 NLO Laser Scanning Microscope Laser scanning microscope: 355nm UV laser 405nm, 594nm, 561nm and 633nm diode lasers Argon laser (458nm, 488nm and 514nm lines) Coherent Chameleon Vision II tunable (680nm – 1080nm) IR multiphoton Read More...
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Confocal
2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...
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Confocal
Image Analysis Signals Imaging Artist Next generation image analysis and management platform for high-content screening and cell imaging data. Quickly process, analyze, share, and store the vast volumes of data. Cell Profiler CellProfiler is free, Read More...
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Confocal
A typical HTI screening project at HiTIF can be subdivided in 5 phases: Pre-Development The investigator contacts the Facility Head to inquire about the current availability of instrumentation time and manpower for the project to be Read More...
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Confocal
Yokogawa CV8000 High-throughput spinning disk confocal microscope The Yokogawa CV8000 is HiTIF second high-throughput imaging system. The CV8000 feature set is similar to the CV7000.When compared to the latter, the CV8000 has a newer Read More...
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Confocal
Stephen Lockett, Ph.D. Director, OMAL locketts@nih.gov 301-846-5515 Valentin Magidson, Ph.D. Scientist magidsonv@mail.nih.gov 301-846-6092 Will Heinz, Ph.D. Scientist heinzwf@nih.gov 301-846-1239 David Read More...
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Confocal
2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...
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Confocal
ZEISS Elyra 7 with Lattice SIM² Type: Wide-field structured illumination microscope Capabilities: Super resolution 2D and 3D imaging of live or fixed cells Apotome SIM: 170 nm lateral, 450 nm axial Apotome SIM2: 140 nm lateral, 300 nm axial Lattice Read More...
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Confocal
Research Mission The goal of OMAL’s research is to understand molecular mechanisms driving carcinogenesis and the reversal of this process through treatment, by utilization and advancement of optical microscopy techniques. These techniques include multiplex Read More...
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Confocal
2024 Mizunuma M, Redon CE, Saha LK, Tran AD, Dhall A, Sebastian R, Taniyama D, Kruhlak MJ, Reinhold WC, Takebe N, Pommier Y. Acetalax (Oxyphenisatin Acetate, NSC 59687) and Bisacodyl Cause Oncosis in Triple-Negative Breast Read More...
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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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Confocal
Optical Microscopy Core of the Experimental Immunology Branch (CCR/NCI) announces the introductory classes to Image J/FIJI: December 16th and 18th, 2020, 10 am to 4 pm with 1 hr break. Dr. Jan Wisniewski “Streamline Your Image Analysis: Read More...
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Bioinformatics
Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class Read More...
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Bioinformatics
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...
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Bioinformatics
nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the Read More...
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Bioinformatics
04/15/2025 - What to bring: Laptop capable of connecting to internet via NIH wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...
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Bioinformatics
04/15/2025 - What to bring: Laptop capable of connecting to internet via NIH wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...
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Bioinformatics
03/21/2025 - Partek Flow is a point-and-click software for analyzing multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. Input options include FASTQ, BAM, or expression tables, thus enabling scientists Read More...
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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...
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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
What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...
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Bioinformatics
Cancer research is a complex and data-intensive field. Cloud computing offers a powerful solution for researchers to store, analyze, and share large datasets efficiently. In this month’s topic spotlight, we will explore cloud resources Read More...
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Bioinformatics
Please see https://bioinformatics.ccr.cancer.gov/btep/self-learning/ to sign up for a license. Contact ncibtep@nih.gov with any questions about obtaining a license. Did you know that CCR researchers have access to Read More...
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Bioinformatics
07/24/2024 - Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is hosted on Biowulf, the NIH high performance computing Read More...
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Bioinformatics
Partek Flow enables scientists to build comprehensive workflows for analyzing multi-omics high throughput sequencing data including DNA and variant calling, bulk and single cell modalities for RNA, ChIP, and ATAC, spatial transcriptomics, CITE, and immune Read More...
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Bioinformatics
ALWAYS, ALWAYS, ALWAYS read the documentation. Use the help pane in the lower right of RStudio or the functions, help() and help.search() or ? and ?? . Check out package vignettes ( vignette() ). Check the Github site if 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
03/06/2024 - The National Institutes of Health (NIH) promotes the use of Common Data Elements (CDEs) to standardize data collection, sharing, and interoperability in health and disease research. In line with Congressional Appropriations language, the Office Read More...
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Bioinformatics
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 analyzing sequencing Read More...
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Bioinformatics
Accessing Partek Flow at NIH and tips for data transfer Learning objectives Instructions for accessing Partek Flow NCI researchers can find instructions for accessing Partek Flow at https://bioinformatics.ccr.cancer.gov/btep/partek-flow-bulk-and-single-cell-rna-seq-data-analysis/ . But Read More...
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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...
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Bioinformatics
02/21/2024 - https://cap-lab.bio (link is external) https:// (link is external) qiime2.org (link is external) The QIIME platform, including QIIME 1 and QIIME 2 ( https://qiime2.org (link is external) ), has been extensively applied in microbiome Read More...
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Bioinformatics
Quarto helps you tell others exactly what you did and how you derived your conclusions - code, results, and conclusions wrapped up in a single document. Advantages of Quarto compared with other publishing systems: Can Read More...
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Bioinformatics
#Setting a theme my_theme
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Bioinformatics
Now we are ready to work with some of our first R commands. We are going to run commands directly from our R script rather than typing into the R console. Our first command will Read More...
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Bioinformatics
Let's explore how piping streamlines this. Piping (using |> ) allows you to employ multiple functions consecutively, while improving readability. The output of one function is passed directly to another without storing the intermediate steps Read More...
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Bioinformatics
Let's explore how piping streamlines this. Piping (using |> ) allows you to employ multiple functions consecutively, while improving readability. The output of one function is passed directly to another without storing the intermediate steps Read More...
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Bioinformatics
There are data sets available in R to practice with or showcase different packages. For today's lesson and the remainder of this course, we will use data from the Bioconductor package airway to showcase Read More...
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Bioinformatics
Let's look a bit into our RStudio layout. Source : This pane is where you will write/view R scripts. Some outputs (such as if you view a dataset using View() ) will appear as a Read More...
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Bioinformatics
Welcome! Welcome to the R Introductory Series! Who: Novices and beginners\ What: A course series introducing R and RStudio. This course will introduce the foundational skills necessary to begin to analyze and visualize data in Read More...
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Bioinformatics
The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of class here . The diffexp_ Read More...
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Bioinformatics
Lesson 2 Exercise Questions: Part 2 (Tidyverse) The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
Learning Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help how R can enhance data Read More...
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Bioinformatics
Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...
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Bioinformatics
Objectives Review the grammar of graphics template. Learn about the statistical transformations inherent to geoms. Learn more about fine tuning figures with labels, legends, scales, and themes. Learn how to save plots with ggsave() . Review Read More...
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Bioinformatics
In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...
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Bioinformatics
In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...
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Bioinformatics
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...
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Bioinformatics
R is both a computational language and open-source environment for statistical computing and graphics. While R programming was ranked 20 th in popularity when compared with other programming languages in December 2023, it remains a favorite among Read More...
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Bioinformatics
The QIIME platform, including QIIME 1 and QIIME 2, has been extensively applied in microbiome research, repeatedly making analyses that were challenging or impossible into routine tasks. While QIIME began as a marker gene (e.g., 16S, Read More...
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Bioinformatics
Step 1 : Login to DNAnexus Step 2 : Once you login, you should see the Projects page. If you have used DNAnexus previously, you may see more than one project listed. If this is your first time using Read More...
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Bioinformatics
In lesson 3, we learned how to read and save excel spreadsheet data to a R object using the tidyverse package readxl . Today we will use some example data from an excel spreadsheet to learn the Read More...
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Bioinformatics
Lesson 1: Toward fully reproducible microbiome multi-omics bioinformatics with QIIME 2 Lesson 1 does not include a hands on component, but rather includes an introduction to QIIME2 by guest speaker, Dr. Greg Caporaso, a leading developer of the Read More...
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Bioinformatics
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...
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Bioinformatics
DNAnexus Basics Setting up the R-Studio environment outside of Class hours These instructions should be followed if you are setting up the R-Studio Web environment outside the normal class hours. Log into DNAnexus Each student Read More...
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Bioinformatics
Often we will apply multiple functions to wrangle a data frame into the state that we need it. For example, maybe you want to select and filter. What are our options? We could run one Read More...
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Bioinformatics
Help Session Lesson 4 Plotting with ggplot2 For the following plots, let's use the diamonds data ( ?diamonds ). The diamonds dataset comes in ggplot2 and contains information about ~54,000 diamonds, including the price, carat, color, clarity, and Read More...
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Bioinformatics
In tab delimited files, data columns are separated by tabs. To import tab-delimited files there are several options. There are base R functions such as read.delim() and read.table() as well as the readr Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
Lesson 7: Course Wrap-Up Learning Objectives Introduce the QIIME2 microbiome workflow for Biowulf Review key concepts Showcase additional plugins QIIME 2 on Biowulf As mentioned previously, QIIME 2 is installed on Biowulf. To see available versions use module Read More...
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Bioinformatics
Data import and reshape Objectives 1. Learn to import multiple data types 2. Data reshape with tidyr : pivot_longer() , pivot_wider() , separate() , and unite() Installing and loading packages So far we have only worked with objects that Read More...
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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
Introduction to dplyr and the %>% Objectives Today we will begin to wrangle data using the tidyverse package, dplyr . To this end, you will learn: how to filter data frames using dplyr how to employ Read More...
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Bioinformatics
11/06/2023 - UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. The database is regularly augmented with additional data and is globally accessible Read More...
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Bioinformatics
10/25/2023 - 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...
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Bioinformatics
10/11/2023 - 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...
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Bioinformatics
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...
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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...
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Bioinformatics
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...
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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...
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CRTP
empanada v1.2 now released empanada-napari now comes with: MitoNet v1, NucleoNet v0.1 and DropNet v0.1(and other new useful modules) Empanada (EM PANoptic Any Dimension Annotation) is a tool Read More...