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Search Results for: Whole transcriptome

Total Results Found: 98

Total Results Found: 98

Bioinformatics for Beginners 2022: Objectives

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Bioinformatics

In this lesson, we learned about the classification based approach for RNA sequencing analysis. In this approach, we are aligning our raw sequencing reads to a reference transcriptome rather than a genome. Here, we will Read More...

Bioinformatics for Beginners 2022: Mapping Challenges

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Bioinformatics

Reads not perfect Duplicate molecules (PCR artifacts skew quantitation) Multimapped reads - Some regions of the genome are thus classified as unmappable Aligners try very hard to align all reads, therefore fewest artifacts occur when Read More...

Spatial Biology

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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.

Bioinformatics for Beginners 2022: Replicates

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Bioinformatics

Technical Replicates It’s generally accepted that they are not necessary because of the low technical variation in RNASeq experiments Biological Replicates (Always useful) Not strictly needed for the identification of novel transcripts and transcriptome Read More...

Bioinformatics for Beginners 2022: Lesson 16 Practice

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Bioinformatics

Lesson 16 Practice Objectives In this lesson, we learned about the classification based approach for RNA sequencing analysis. In this approach, we are aligning our raw sequencing reads to a reference transcriptome rather than a genome. Read More...

Bioinformatics for Beginners 2022: Where is my data?

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Bioinformatics

The Golden Snidget reference genome is located at http://data.biostarhandbook.com/books/rnaseq/data/golden.genome.tar.gz. Can you download and extract? {{Sdet}} Solution{{Esum}} Download wget http://data.biostarhandbook.com/books/rnaseq/ Read More...

Next generation transcriptomics-based precision oncology

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Bioinformatics

08/24/2022 - Precision oncology has made significant advances, mainly by targeting actionable mutations and fusion events involving cancer driver genes. Aiming to expand treatment opportunities, recent studies have begun to explore the utility of tumor transcriptome Read More...

Deep Learning by Example on Biowulf - Class #3

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Bioinformatics

08/25/2021 - This introductory course teaches the basics of deep learning and of different types of deep learning networks through a set of hands-on biological examples implemented in Keras, one example per class. Class #3 will focus Read More...

Visium Spatial Gene Expression Technology

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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...

10X Genomics

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[embed]https://youtu.be/yTl1Q0D7aZ0[/embed] 10x Genomics' supports multiple cancer research areas from single nucleotide and structural variant detection to single cell whole transcriptome gene expression analysis of thousands of individual Read More...

BD Genomics Rhapsody System

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Total end-to-end system for single-cell research [embed]https://youtu.be/vMzhSzg1rUw[/embed] The BD Rhapsody Single-Cell Analysis system empowers and streamlines your research with a complete system of tools, including reagents and analysis software, Read More...

Bioinformatics for Beginners 2022: Lesson 9 Practice

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Bioinformatics

Lesson 9 Practice Objectives In this practice session, we will apply our knowledge to learn about the reference genome and annotation file for the Golden Snidget dataset visualize the Golden Snidget genome using the Integrative Genome Read More...

Bioinformatics for Beginners 2022: Outline

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Bioinformatics

Course setup Intro to DNAnexus and the GOLD learning system Learning Objectives Unix Bootcamp Brief Review of R (for R scripts in later analyses) Introduction to RNA Sequencing Central Dogma of Molecular Biology What is Read More...

Bioinformatics for Beginners 2022: Alignment

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Bioinformatics

Alignment RNASeq Mapping Challenges The majority of mRNA derived from eukaryotes is the result of splicing together discontinuous exons, and this creates specific challenges for the alignment of RNASEQ data. Mapping Challenges Reads not perfect Read More...

Bioinformatics for Beginners 2022: Things to consider:

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Bioinformatics

STAR 2-pass mode --sjdbGTFfile is the path to the file with annotated transcripts in standard GTF format, STAR extracts splice junctions from this file, improves accuracy of mapping. Using annotations is highly recommended whenever they Read More...

Bioinformatics for Beginners 2022: Module2 outline

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Bioinformatics

Bioinformatics for beginners Module 2: Introduction to RNA sequencing In this module, we will use the Human Brain Reference and Universal Human Reference RNA sequencing datasets to learn about RNA sequencing. Each lesson will be followed Read More...

Bioinformatics for Beginners 2022: Lesson 14 Practice

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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...

Data Visualization with R: Import data

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Bioinformatics

The data that we will be working with comes from the airway study that profiled the transcriptome of several airway smooth muscle cell lines under either control or dexamethasone treatment Himes et al 2014 . The dataset Read More...

Data Visualization with R: Import data

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Bioinformatics

The data that we will be working with comes from the airway study that profiled the transcriptome of several airway smooth muscle cell lines under either control or dexamethasone treatment Himes et al 2014 . The dataset Read More...

Data Visualization with R: Import data

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Bioinformatics

The data that we will be working with comes from the airway study that profiled the transcriptome of several airway smooth muscle cell lines under either control or dexamethasone treatment Himes et al 2014 and the Read More...

Next Generation Transcriptomics-based Precision Oncology

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Bioinformatics

06/29/2022 - During this webinar, Computational Biologist Dr. Eytan Ruppin will present on “SELECT,” a computational approach that aims to identify clinically relevant synthetic lethal interactions, thereby harnessing them to predict patient response to cancer therapy Read More...

Multimodal analysis of single cell trajectories

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Bioinformatics

04/22/2021 - Abstract: Single-cell RNA-sequencing has emerged as a popular technique for dissecting temporal processes such as tumor development and cell differentiation from snapshots of asynchronous ensembles of cells. Ongoing efforts in this area are now Read More...

Bioinformatics Workshop: Single Cell RNA-Seq Analysis

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Bioinformatics

05/20/2020 - Advances in technology have reduced the cost of single cell sequencing, opening the doors to many new areas of study including transcriptome, DNA genomics, epigenomics and microbial systems. This workshop, provided by experts from Read More...

Comprehending the Message: RNA-Seq Data Analysis

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Bioinformatics

03/20/2017 - BTEP Workshop on RNA-Seq Data Analysis (2-day) This 2-day workshop, which includes both lecture and hands-on components, will cover the fundamentals of and best practices for RNA-Seq Data Analysis. Learn everything from experimental design Read More...

RNA-Seq Data Analysis Workshop (2-day)

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Bioinformatics

02/19/2015 - 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...

BTEP Coding Club: Data types

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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...

NCI Genetics Branch: OMICS Technology Facility
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...

CCR Sequencing Facility
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...

CCR Spatial Imaging Technology Resource (SpITR)
Bethesda, MD

Collaborative

The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...

CCR Genomics Core
Bethesda, MD

Core Facility

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

NIH Intramural Sequencing Center (NISC)
Rockville, MD

Trans NIH Facility

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...

NCI Center for Advanced Preclinical Research (CAPR)
Frederick, MD

Collaborative

The Center for Advanced Preclinical Research (CAPR) specializes in evaluating the efficacy of preclinical compounds, existing drugs, or biologics (therapeutics) in genetically engineered mouse models, GEM-derived allograft (GDA) models, or patient-derived mouse xenografts (PDX). We Read More...

Technology Video Library

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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...

Data Wrangling with R: Accessors

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Bioinformatics

As you can see from the image, there are several accessor functions to access the data from the object: assays() - access matrix-like experimental data (e.g., count data). Rows are genomic features (e.g., Read More...

Bioinformatics for Beginners 2022: RNA-SEQ Overview

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Bioinformatics

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...

Bioinformatics for Beginners 2022: B4b 2022 rnaseq jw

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Bioinformatics

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

Data Visualization with R: Lesson5

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Bioinformatics

Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn how to work with the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify to Read More...

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