Search Results for: ffpe slides

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...

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...

11/06/2024 - Neuro-Oncology Branch Visiting Scholar Program Lecture

09/24/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/1985cbcbb8ad4c07ac58ea7e3a4d7927/playback

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https://bioinformatics.ccr.cancer.gov/docs/analyzing-data-without-coding-event/NIDAP/NIDAP_Overview/

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...

Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.

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...

q2book Some useful slides from UCSD

Lesson 8: Introduction to RNA sequencing Slides

12/17/2020 - Recording In this final seminar of "BTEP RNA-Seq Weeks", the major steps of bulk RNA-seq analysis will be presented, utilizing tools (NIDAP) available to CCR researchers.The discussion will focus on a Read More...

05/07/2025 - Join Dr. Eytan Ruppin, NCI investigator in the Center for Cancer Research, as he discusses Path2Space, a new and unpublished deep learning approach that predicts spatial gene expression directly from histopathology slides. Spatial Read More...

10/24/2024 - Recent advances in artificial intelligence (AI) have revolutionized the use of hematoxylin and eosin (H&E)-stained tumor slides for precision oncology, enabling data-driven approaches to predict molecular characteristics and therapeutic outcomes. In Read More...

Use the jupyter nbconvert command at the command prompt to convert Jupyter Notebook to various available formats, including html, pdf, and slides. The format is specified after the --to option. jupyter nbconvert --to format

11/01/2022 - Join us to learn how Visium Spatial and Xenium In Situ platforms from 10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune Read More...

12/21/2020 - Register Meeting number: 172 414 1612 Meeting Password: AmWdZgu*775 Please see information below about the upcoming SS/SC Brown Bag Seminar on next Monday December 21, 2020. Slides are already available on our website https://ccrod.cancer.gov/confluence/ Read More...

11/06/2012 - Introduction of Next-Generation Sequencing   This seminar will provide an overview of Next Generation DNA Sequencing. Highlighting Illumina sequencing technology, and its application in the areas of DNAse-seq, ChIP-seq, and RNA-seq, as well as Genomic Read More...

## Unix for Bioinformatics Beginners by Joe Wu, PhD (BTEP)

The package reprex is used to Prepare reprexes for posting to GitHub issues, StackOverflow, in Slack messages or snippets, or even to paste into PowerPoint or Keynote slides. ---https://reprex.tidyverse.org/index.html

The package reprex is used to Prepare reprexes for posting to GitHub issues, StackOverflow, in Slack messages or snippets, or even to paste into PowerPoint or Keynote slides. ---https://reprex.tidyverse.org/index.html

No summary available.

CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...

Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.

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...

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...

Additional Resources The QIIME 2 docs and forum For general support throughout your microbiome data analysis, see the QIIME 2 documentation and the QIIME 2 forum . Related readings q2book Some useful slides from UCSD Linux help Introduction Read More...

11/12/2021 - The Cancer Genomics Cloud (CGC) is a cloud-based bioinformatics ecosystem supported by the National Cancer Institute (NCI). The CGC allows users to run computational workflows defined in the Common Workflow Language (CWL) on a Read More...

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...

01/28/2021 - Meeting Link The session recording and slides will be available after the webinar. Single-cell RNA-Seq (scRNA-seq) is the most widely used high-throughput technology to measure genome-wide gene expression at the single-cell level. However, single-cell Read More...

12/16/2020 - Recording Slides are here. Hands-on portion is here. Bioconductor is a large, NIH-funded project that provides tools and data resources for the analysis and comprehension of high-throughput biological data. Bioconductor uses the R statistical Read More...

05/28/2020 - This workshop will teach the basic concepts and practical aspects of ChIP-Seq data analysis. Topics covered will include: experimental approach, quality control, peak calling, and basic biological interpretation. No computer is required for this Read More...

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...

10/02/2012 - Microarray Technology and Preprocessing Quality Control Normalization Using MAS5 and RMA Filtering Batch Effect Correction Basic Statistical Tests for Differentially Expressed Genes T-test ANOVA SAM Calculating False Discovery Rate Principal Components Analysis and Clustering Read More...

Use the jupyter nbconvert command at the command prompt to convert Jupyter Notebook to various available format, including html, pdf, and slides. The format is specified after the --to option. jupyter nbconvert --to format

Use the jupyter nbconvert command at the command prompt to convert Jupyter Notebook to various available format, including html, pdf, and slides. The format is specified after the --to option. jupyter nbconvert --to format

With this plugin you can add a chalkboard to reveal.js. The plugin provides two possibilities to include handwritten notes to your presentation: you can make notes directly on the slides, e.g. to comment Read More...

The yaml header or file allows us to control document level or project level options. Here, we can specify formats, themes, executable options, and others. --- title: "Volcano" author: "Alex Emmons, Ph. Read More...

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...

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...

The LCBG Microscopy Core offers imaging technologies and training. The Core has established instrumentation for for 2D and 3D imaging of both fixed and living specimens.

Biomarker Discovery with Morphological Context:  Changing how tissue specimens are analyzed < https://youtu.be/mVhfZq8ppbc What is Digital Spatial Profiling? GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial Read More...

The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...

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...

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...

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

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...

03/22/2024 - This 3-hour seminar is tailored for biologists, data analysts, and researchers who are eager to dive into the essentials of computational flow cytometry analysis using R. Flow cytometry is a crucial technique in cell Read More...

05/13/2021 - Meeting Link The slides and recording of the webinar will be available within a day of the event. Heterogeneity poses a major challenge in translational research. For example, inter-tumor heterogeneity limits the biomarker discovery Read More...

03/29/2021 - For coming Monday's CDSl webinar, we'll be hosting Dr. Yun Liu from Google Health. Abstract: This talk will briefly cover two categories of our work: deep learning to identify dermatology conditions from Read More...

11/13/2020 - https://ncihub.org/resources/2404 Abstract: In many applications in genomics, large data sets are created and lightly used before being shared with other researchers (ideally) or simply tossed away on hard drives. The Cancer Read More...

06/27/2017 - NGS Series Open Forum: Meet the Bioinformatics Experts You are invited to a Q &amp; A session with a panel of bioinformatics analysts, most of whom were presenters at the BTEP NGS Workshop Read More...

12/07/2015 - 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...

12/01/2015 - REGISTRATION FULL - Please signup for Session 2 December 7/8 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 Read More...

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...

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...

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...

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...

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...

Managing Bioinformatics Projects with Jupyter Lab Learning Objectives After this class, participants will have obtained the foundation needed to start using Jupyter Lab as an all-in-one place to maintain code, output, and other description of Read More...

04/04/2016 - 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...