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Search Results for: mRNA levels

Total Results Found: 116

Total Results Found: 116

Bioinformatics for Beginners 2022: Remember

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Bioinformatics

RNASEQ looks at steady state mRNA levels which is the sum of transcription and degradation Protein levels are assumed to be driven by mRNA levels RNASEQ can measure relative abundance not absolute abundance RNASEQ is Read More...

R Introductory Series: Important functions

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Bioinformatics

factor() - to create a factor and reorder levels as.factor() - to coerce to a factor levels() - view the levels of a factor nlevels() - return the number of levels For example: sex

Molecular Targets Database and Tools
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...

Past Seminars

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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...

Publications

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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...

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...

Data Visualization with R: Using factors

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Bioinformatics

class ( a1 $ dose ) ## [1] "numeric" As it turns out, dose is really an experimental factor, so if we specify factor(dose) it will be interpreted as categorical or discrete. Before fixing the x axis Read More...

Data Visualization with R: Using factors

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Bioinformatics

class(a1$dose) ## [1] "numeric" As it turns out, dose is really an experimental factor, so if we specify factor(dose) it will be interpreted as a categorical or discrete. Before fixing the x Read More...

cBioPortal for Cancer Genomics

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Bioinformatics

10/12/2021 - Speaker :  Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This Read More...

Data Visualization with R: Variable Types

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Bioinformatics

Before diving into the construction of bar plot, box & whisker plot, and histogram, we should do a quick review of the types of variables that we commonly work with in data analysis. Categorical variables Read More...

TCGA Data Analysis Workshop (2-day)

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Bioinformatics

01/07/2016 - REGISTRATION IS FULL FOR THIS WORKSHOP (25 ATTENDEES; 6 WAITLIST) The Cancer Genome Atlas (TCGA) is a large-scale study that has cataloged genomic data accumulated for many different types of cancers, and includes mutations, copy number Read More...

Homepage

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Bioinformatics

The Bioinformatics Training and Education Program (BTEP) was established by the Office of Science and Technology Resources (OSTR) for the purpose of providing training enabling scientists to understand and analyze their own experimental data, at Read More...

R Introductory Series: What are factors?

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Bioinformatics

Factors are an important data structure in statistical computing. They are specialized vectors (ordered or unordered) for the storage of categorical data. While they appear to be character vectors, data in factors are stored as Read More...

Data Wrangling with R: What are factors?

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Bioinformatics

Factors can be thought of as vectors which are specialized for categorical data. Given R’s specialization for statistics, this make sense since categorial and continuous variables are usually treated differently. Sometimes you may want Read More...

Data Wrangling with R: Subsetting and manipulating SummarizedExperiments

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Bioinformatics

First, notice that you can easily access columns from the sample metadata ( colData() ) using $ . Using brackets to subset: se$SampleName ## [1] GSM1275862 GSM1275863 GSM1275866 GSM1275867 GSM1275870 GSM1275871 GSM1275874 ## [8] GSM1275875 ## 8 Levels: GSM1275862 GSM1275863 GSM1275866 GSM1275867 ... GSM1275875 se$ Read More...

Data Visualization with R: Variable Types

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Bioinformatics

Before diving into the construction of bar plot, box & whisker plot, and histogram, we should do a quick review of the types of variables that we commonly work with in data analysis. Categorical variables Read More...

FAQ

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CRTP

No summary available.

NCI Genomics and Pharmacology Facility
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...

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...

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...

The Art and Science of Data Mining (1-day)

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Bioinformatics

06/19/2017 - Harvesting the Wealth of TCGA Data The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA Read More...

Next-Generation Clustered Heat Maps

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Bioinformatics

06/20/2024 - Clustered heat maps are widely used for visualizing patterns in molecular profiling data. But traditional, static heat maps have significant limitations when applied to large datasets (1000s of elements per axis). Presented in this Read More...

R Introductory Series: R base graphics

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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...

R Introductory Series: Filtering by row

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Bioinformatics

Now let's filter the rows based on a condition. Let's look at only the treated samples in scaled_counts using the function filter() . filter() requires the df as the first argument followed by Read More...

Data Wrangling with R: Practice problems

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Bioinformatics

Which of the following will throw an error and why? 4 _ chr :1:2: unexpected input ## 1: 4_ ## ^ . 4 chr :1:3: unexpected symbol ## 1: .4chr ## ^ {{Edet}} Create the following objects; give each object an appropriate name (your best guess at what name to Read More...

Data Wrangling with R: Lesson 2: Help Session

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Bioinformatics

This is our first coding help session. We have designed some practice problems to get you acquainted with using R before beginning to wrangle in our next lesson. Practice problems Which of the following will Read More...

Microbiome Analysis with QIIME2: Q2-longitudinal

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Bioinformatics

Luckily, there is a q2-longitudinal plugin to handle dependent longitudinal data. The q2-longitudinal plugin includes: interactive plotting (e.g., volatility plots) linear mixed effects models paired differences and distances non-metric microbial interdependence testing ( 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: Data Analysis

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Bioinformatics

Data Analysis Here are a pair of examples of RNASEQ complete workflows RNASEQ Pipeline from NCI CCBR https://github.com/CCBR/Pipeliner/blob/master/RNASeqDocumentation.pdf RNASEQ Nextflow Pipeline from nf-core https://nf-co.re/rnaseq Read More...

The Cancer Proteome Atlas

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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...

The Cancer Proteome Atlas

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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...

Data Visualization with R: Lesson 4

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Bioinformatics

/* Whole document: */ body{ font-family: Times; font-size: 16pt; } Stat Transformations: Bar plots, box plots, and histograms Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar Read More...

July 2021

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CREx News & Updates July 2021   Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Learn more about services from the NHLBI Read More...

NCI Patient-Derived Models Repository (PDMR)
Bethesda, MD

Collaborative

Repositories

The National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...

NCI High-Throughput Imaging Facility (HiTIF)
Bethesda, MD

Collaborative

The NCI High-Throughput Imaging Facility (HiTIF) works in a collaborative fashion with NCI/NIH Investigators by providing them with the necessary expertise, instrumentation, and software to develop and execute advanced High-Throughput Imaging (HTI) assays. These Read More...

STRIDES Initiative
Bethesda, MD

Trans NIH Facility

The Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative The STRIDES Initiative aims to help NIH and its institutes, centers, and offices (ICOs) accelerate biomedical research by reducing barriers in utilizing Read More...

July 2022 Newsletter

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CREx News & Updates July 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Click below to learn how easy it is to navigate the CREx platform. These short videos will Read More...

CCR Genomics Technology Laboratory (GTL)
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...

Protein Characterization Laboratory

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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...

CCR Protein Characterization Laboratory (PCL)
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...

Contacts

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Bioinformatics

General questions or comments about the BTEP program or classes should be addressed to: NCIBTEP@nih.gov Desiree Tillo, Ph.D . Staff Scientist desiree.tillo@nih.gov I have a broad research background in bioinformatics Read More...

BTEP Video Archive of Past Classes

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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...

Microbiome Analysis with QIIME2: Metadata and importing

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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...

Bioinformatics for Beginners 2022: 18. BLAST copy

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Bioinformatics

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment and create a directory for today's work. conda activate bioinfo mkdir blast cd blast What is Read More...