NATIONAL CANCER INSTITUTE - CANCER.GOV

Search Results for: Novel Transcripts

Total Results Found: 109

Total Results Found: 109

R Introductory Series: Using %in%

Web Page

Bioinformatics

%in% "returns a logical vector indicating if there is a match or not for its left operand". This logical vector can then be used to filter the datamframe to only matched values. For Read More...

R Introductory Series: Exercises: Lesson 2, Part 1

Web Page

Bioinformatics

Lesson 2 Exercise Questions: Part 1 (BaseR subsetting and Factors) 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 . We are going Read More...

Data Wrangling with R: The ggplot2 template

Web Page

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...

R Introductory Series: The ggplot2 template

Web Page

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...

R Introductory Series: Test your learning

Web Page

Bioinformatics

Using what you have learned about select() and filter() , use the pipe ( |> ) to create a subset data frame from scaled_counts that only includes the columns 'sample', 'cell', 'dex', 'transcript', and 'counts_scaled' and Read More...

R Introductory Series: Test your learning

Web Page

Bioinformatics

Using what you have learned about select() and filter() , use the pipe ( |> ) to create a subset data frame from scaled_counts that only includes the columns 'sample', 'cell', 'dex', 'transcript', and 'counts_scaled' and Read More...

Data Wrangling with R: Subsetting and manipulating SummarizedExperiments

Web Page

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 Wrangling with R: Introducing the SummarizedExperiment

Web Page

Bioinformatics

The SummarizedExperiment class and the inherited class RangedSummarizedExperiment are available in the R package SummarizedExperiment . SummarizedExperiment is a matrix-like container where rows represent features of interest (e.g. genes, transcripts, exons, etc.) and columns represent Read More...

Data Wrangling with R: Excel files (.xls, .xlsx)

Web Page

Bioinformatics

Excel files are the primary means by which many people save spreadsheet data. .xls or .xlsx files store workbooks composed of one or more spreadsheets. Importing excel files requires the R package readxl . While this Read More...

Bioinformatics for Beginners 2022: Replicates

Web Page

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 9 Practice

Web Page

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...

Genetics, Genomics, and Epigenetics

Web Page

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...

R Introductory Series: Exercises: Lesson 2 Tidyverse

Web Page

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...

R Introductory Series: Practicing the Tidyverse (Part 1)

Web Page

Bioinformatics

Lesson 4 Exercise Questions: 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 of Read More...

R Introductory Series: Practicing the Tidyverse

Web Page

Bioinformatics

Lesson 4 Exercise Questions: 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 of Read More...

R Introductory Series: Using arrange()

Web Page

Bioinformatics

Now, if we want the top five transcripts with the greatest median scaled counts by treatment, we need to organize our data frame and then return the top rows. We can use arrange() to arrange Read More...

R Introductory Series: Using arrange()

Web Page

Bioinformatics

Now, if we want the top five transcripts with the greatest median scaled counts by treatment, we need to organize our data frame and then return the top rows. We can use arrange() to arrange Read More...

R Introductory Series: Base R and data frames

Web Page

Bioinformatics

Lesson 3 Exercise Questions: BaseR dataframe manipulation and factors 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 . We are going Read More...

R Introductory Series: Practicing the Tidyverse (Part 2)

Web Page

Bioinformatics

Lesson 5 Exercise Questions: 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 of Read More...

Data Wrangling with R: Geom functions

Web Page

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...

Data Wrangling with R: mutate()

Web Page

Bioinformatics

mutate() adds new variables and preserves existing ones; transmute() adds new variables and drops existing ones. New variables overwrite existing variables of the same name. --- dplyr.tidyverse.org Let's create a column in Read More...

Data Wrangling with R: Colors

Web Page

Bioinformatics

ggplot2 will automatically assign colors to the categories in our data. Colors are assigned to the fill and color aesthetics in aes() . We can change the default colors by providing an additional layer to our Read More...

Bioinformatics for Beginners 2022: Lesson 16 Practice

Web Page

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: Things to consider:

Web Page

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: Alignment

Web Page

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: Where is my data?

Web Page

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...

Visium Spatial Gene Expression Technology

Web Page

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...

Xenium Spatial Profiling Technology

Web Page

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...

July 2021

Web Page

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 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...

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...

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...

Data Wrangling with R: Help Session Lesson 5

Web Page

Bioinformatics

All solutions should use the pipe. Import the file "./data/filtlowabund_scaledcounts_airways.txt" and save to an object named sc . Create a subset data frame from sc that only includes the columns Read More...

Data Wrangling with R: Accessors

Web Page

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

Web Page

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

Web Page

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...