Frederick, MD
Repositories
Trans NIH Facility
DTP’s Natural Products Repository is the world’s largest storehouse of natural products. It houses close to >200,000 extracts from samples of more than 70,000 plants and >20,000 marine organisms collected from more than 29 countries, plus extracts Read More...
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Bioinformatics
metadata
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Bioinformatics
Using data we downloaded previously: bwa mem refs/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq > SRR1972739.bwa.sam samtools view -S -b SRR1972739.bwa.sam > SRR1972739.bwa.bam samtools sort SRR1972739.bwa.bam -o Read More...
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Bioinformatics
Using data we downloaded previously: bwa mem refs/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq > SRR1972739.bwa.sam samtools view -S -b SRR1972739.bwa.sam > SRR1972739.bwa.bam samtools sort SRR1972739.bwa.bam -o Read More...
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Bioinformatics
We will download a new tool "csvkit" for working on the comma separated files. This tool is careful to cut only at the columns used as delimiters, and not commas that are part Read More...
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Bioinformatics
05/04/2022 - For our next CDSL webinar we will have a guest lecture by Dr. Julio Saez-Rodriguez from the Institute for Computational Biomedicine, Heidelberg. B io: Julio Saez-Rodriguez is Professor of Medical Bioinformatics and Data Analysis Read More...
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Bioinformatics
06/06/2023 - Dr. Maximilian Haeussler is the co-PI for the UCSC Genome Browser , an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with Read More...
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Bioinformatics
IPA and CLC Genomics Workbench are both Qiagen products, which allows us to more easily extract biological insight from analysis. For this reason, it is beneficial to use these two packages together.
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Bioinformatics
The hcc1395_fastq.tar is actually known as a tape archive (it has the .tar extension), which is a bundle of files and folders. The tar command is used to unpack its contents. The following Read More...
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Bioinformatics
The hcc1395_fastq.tar is actually known as a tape archive (it has the .tar extension), which is a bundle of files and folders. The tar command is used to unpack its contents. The following Read More...
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Bioinformatics
A vector is a collection of values that are all of the same type (numbers, characters, etc.) --- datacarpentry.org c() - used to combine elements of a vector When you combine elements of different Read More...
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Bioinformatics
The quality metric information is stored in the metadata ( adp@meta.data ), so we really only need to work with the metadata file to get an idea of the thresholds we want to set for Read More...
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Bioinformatics
04/11/2024 - Informaticians aim to bring the right information to the forefront at the right time to improve decision-making. Dr. Greene's lab develops computational methods that integrate distinct large-scale datasets to extract the rich and Read More...
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Bioinformatics
Filtering is done to keep or remove variants to satisfy certain constraints. Make a new directory and download the example data (VCF file and index). This file contains variants in chromosome 19:400kb-500kb mkdir hg19 Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Start by activating the bioinfo environment. conda activate bioinfo Create a new directory for the multiqc data. mkdir multi cd multi Retrieve the Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Start by activating the bioinfo environment. conda activate bioinfo Create a new directory for the multiqc data. mkdir multi cd multi Retrieve the Read More...
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Bioinformatics
To proceed with converting the bedGraph files to bigWig, we need to first create an index of our genome using SAMTOOLS and it's faidx feature. Where faidx will index/extract FASTA. samtools faidx refs/22. Read More...
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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...
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Bioinformatics
A vector is a collection of values that are all of the same type (numbers, characters, etc.) --- datacarpentry.org c() - used to combine elements of a vector When you combine elements of different Read More...
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Bioinformatics
To plot the first two axes of variation along with species information, we will need to make a data frame with this information. The axes are in pca$x . #Build a data frame pcaData
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Bioinformatics
03/06/2023 - Learn about a wide range of capabilities for image processing and computer vision including machine and deep learning using deep convolutional neural networks (CNNs). Transitioning image models from pixel-based to feature-based allows us to Read More...
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Bioinformatics
06/06/2022 - Join the June NCI Imaging and Informatics Community Webinar for a discussion on the recent contributions from Dr. Mirabela Rusu’s Personalized Integrative Medicine Laboratory (PIMed) at Stanford University. Recent laboratory contributions include: registering Read More...
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Bioinformatics
04/21/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e51f19be5660107b4b92118dc48be1781 Presenter: Kevin Kendal PhD CEO of MacVector Description: This workshop will focus on the analysis of Next Read More...
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Bioinformatics
04/21/2021 - Register Description: MacVector is a sequence analysis application for macOS computers that provides users with a variety of tools and functions to simplify the analysis, manipulation, assembly, and documentation of DNA and protein sequences. Read More...
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Bioinformatics
01/14/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e968a58127acdb59b961e2ef13865c7ad Description: This workshop will focus on the analysis of Next Generation Sequencing (NGS) data using the Read More...
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Bioinformatics
11/14/2012 - This is a repeat class for those who couldn't make it into the class on October 9th Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Partek Pathway. As Read More...
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Bioinformatics
10/09/2012 - Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Partek Pathway. As we walk though hands-on analysis of a cancer dataset, you will learn the principles of experimental design, batch Read More...
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Bioinformatics
Earlier, we mentioned that the ".tar" extension stands for Tape Archive. Tape Archive allows us to package many files and folders into a single file for easy transfer and sharing. We use the Read More...
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Bioinformatics
Given that the elements in a data frame are referenced by its row and column positions, what would be the approach for extracting the element in row 60 and column 5? The solution is the command below, Read More...
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Bioinformatics
Ingenuity Pathway Analysis (IPA) (Qiagen) IPA works with differential expression data (derived from RNA sequencing, miRNA sequencing, microarray, proteomics, phosphoproteomics, or metabolomics) or genetic variant data to extract various biological insights. {{Sdet}}{{Ssum}}Listing of Read More...
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Bioinformatics
To plot the first two axes of variation along with species information, we will need to make a data frame with this information. The axes are in pca$x. #Build a data frame pcaData & Read More...
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Bioinformatics
Given that the elements in a data frame can be referenced by its row and column positions, what would be the approach for extracting the element in row 60 and column 5? The solution is the command Read More...
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Bioinformatics
There are several methods for subsetting a dictionary. See https://www.geeksforgeeks.org/get-a-subset-of-dict-in-python/. First, just enclosing one of the keys in square brackets will retrieve its associated value. my_dictionary['bananas'] yellow A for Read More...
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Bioinformatics
Ranges can be used to for subsetting data (ie. extract data in rows 5 thru 10 of a data frame) or applied to iterate over a task in things like a for loop. For instance, a for Read More...
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OSTR provides CCR investigators with access to a variety of software licenses for genomic, proteomic, pathway analysis and data visualization tools. These software are funded by OSTR and made available at no cost to CCR Read More...
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Bioinformatics
04/10/2025 - This one hour online training introduces participants to the tools and techniques for analyzing and quantifying microscopy images using MATLAB’s low-code algorithms. Participants will learn how to preprocess images, segment regions Read More...
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Bioinformatics
12/12/2024 - This class will introduce bulk RNA sequencing analysis using Qiagen software. Participants will learn how to process FASTQ files and obtain differential expression using CLC Genomics Workbench as well as extract biological insight using Read More...
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Bioinformatics
06/13/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...
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Bioinformatics
Let's learn how to further work with vectors, including creating, sub-setting, modifying, and saving. #Some possible RNASeq data cell_line
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Bioinformatics
Another important data structure in R is the data matrix. Data frames and data matrices are similar in that both are tabular in nature and are defined by dimensions (i.e., rows (m) and columns ( Read More...
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Bioinformatics
The recommended method involves applying a scikit-learn multinomial naive Bayes classifier. This uses machine learning to train a classifier on a referene database and then use the trained classifier to classify your ASVs. These classifiers Read More...
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Bioinformatics
First we will obtain the SRA data from the biostar handbook web site curl http://data.biostarhandbook.com/sra/sra-runinfo-2019-01.tar.gz --output sra-runinfo-2019-01.tar.gz Now we can unpack the data. tar Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * cd * mkdir * curl * tar * cat * grep * wc * outputting data * piping data from one command to another * cut Learn: * du * pip * csvkit * datamash Read More...
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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...
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Bioinformatics
Note that we now have differential expression by transcripts and our first column contains the transcript IDs. But what genes do these transcripts map to? We will need to do some data wrangling to find Read More...
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Bioinformatics
Here, let's download the HBR and UHR dataset to get acquainted with it. First, we will use pwd to make sure we are in the home directory. pwd If we are in the home Read More...
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Bioinformatics
Here, let's download the HBR and UHR dataset to get acquainted with it. First, we will use pwd to make sure we are in the home directory. pwd If we are in the home Read More...
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Bioinformatics
The code below generates a data frame, dfh, that contains information on the treatment group in which a sample was assigned. To create a data frame in R, we use the data.frame command. In Read More...
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Bioinformatics
The code below generates a data frame, dfh, that contains information on the treatment group in which a sample was assigned. To create a data frame in R, we use the data.frame command. In Read More...
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Bioinformatics
The code below generates a data frame, dfh, that contains information on the treatment group in which a sample was assigned. To create a data frame in R, we use the data.frame command. In Read More...
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Bioinformatics
Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types and the code Read More...
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Bioinformatics
R Course FAQs Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types Read More...
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Bioinformatics
Let's learn how to further work with vectors, including creating, sub-setting, modifying, and saving. #Some possible RNASeq data cell_line
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Bioinformatics
Another important data structure in R is the data matrix. Data frames and data matrices are similar in that both are tabular in nature and are defined by dimensions (ie. rows (m) and columns (n), Read More...
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Bioinformatics
02/11/2022 - The seminar is open to the public and registration is required each month. Dr. Hunter Mosely plans to discuss the richness of open data resources in biology and how they can support machine learning Read More...
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Bioinformatics
12/10/2021 - About the Seminar Dr. Greene plans to discuss the richness of open data resources in biology and how they can support machine learning approaches and be enriched by such methods. He’ll also discuss Read More...
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Bioinformatics
10/15/2021 - This course will introduce you to Google Cloud's big data and machine learning functions. You'll begin with a quick overview of Google Cloud and then dive deeper into its data processing capabilities. Read More...
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Bioinformatics
11/13/2017 - MetaCore™ is an integrated curated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, Read More...
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Bioinformatics
Mobaxterm is another open source and graphical based ssh client that Windows users can use to interact with Biowulf. To obtain Mobaxterm, goto https://mobaxterm.mobatek.net and click the Download tab at the top ( Read More...
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Bioinformatics
Mobaxterm is another open source and graphical based ssh client that Windows users can use to interact with Biowulf. To obtain Mobaxterm, goto https://mobaxterm.mobatek.net and click the Download tab at the top ( Read More...
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Bioinformatics
Lists and tuples are one dimensional collections of data. The tuple is an immutable list, in which the elements cannot be modified. However, lists are mutable. To create a list, enclose the contents in square Read More...
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Bioinformatics
Go back to /data/user/hcc1395_b4b. cd /data/user/hcc1395_b4b Create a directory called hcc1395_featurecounts. mkdir hcc1395_featurecounts Go back into /data/user/hcc1395_b4b/hcc1395_hisat2 for this Read More...
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Bioinformatics
All of the files in the alignment output folder have "hcc1395_" prepended. To make these files easier to work with, this exercise will remove the "hcc1395" from these files using the Read More...
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Bioinformatics
The wget command above downloaded the HCC1395 fastq files in the form of a tape archive or tar file. Tape archives are essentially packages or collections of files and folders and enable easy transfer and Read More...
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Bioinformatics
The module featureCounts from the subread package will be used to quantify gene expression. In the featureCounts command below: -p: specifies the presence of paired end data. --countReadPairs: specifies to count both reads in a Read More...
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Bioinformatics
For today's lesson, we will use data from the Bioconductor package airway. The airway data is from Himes et al. (2014). These data, which are contained within a RangedSummarizedExperiment, object are from a bulk RNAseq Read More...
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Bioinformatics
To subset a column of a pandas dataframe, the bracket notation followed by the column name can be used. For instance, to extract the Geneid column in hbr_uhr_chr22_counts do the following. hbr_ Read More...
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Bioinformatics
Geneious Prime is a graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and Next Generation Sequencing analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{Esum}} Classic Computational Molecular Read More...
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Bioinformatics
There may be moments where you want to retrieve a specific value or values from a vector. To do this, we use bracket notation sub-setting ([]).In bracket notation, you call the name of the vector Read More...
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Bioinformatics
CLC Genomics Workbench (Qiagen) is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and Next Generation Sequencing (NGS) analysis (see Listing of Analysis Functions below). {{Sdet}}{{Ssum}}Listing of Read More...
Bethesda, MD
Core Facility
The Blood Processing Core monitors viral load in patients with HIV and performs sequential studies using samples obtained from patients with cancer, AIDS, chronic granulomatous disease, or other diseases associated with immunologic dysfunction. The core Read More...
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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...
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...
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Back Services: Biophysics Facility offers MST as an open-access instrument. First-time users must complete a short training session before gaining access to the instrument reservation calendar. Training includes the KD determination of a Read More...
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Home About the Biophysics Core Biophysics Core Services [tabby title="Instrumentation"] NHLBI Biophysics Core The Biophysics Core Facility: Overview Core Facilities provide scientific resources, cutting-edge technologies and novel approaches to support DIR scientists. Availability of Read More...
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Bioinformatics
Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we 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
Objectives To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By the end 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
Lesson 4: Feature table filtering, taxonomic classification, and phylogeny Learning objectives learn how to apply different types of filtering to your ASV table and representative sequence data. classify your ASVs. Generate a phylogenetic tree. Now that Read More...
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Bioinformatics
We are going to download some bulk RNA-Seq test data and learn how to decompress it. First we will create a place to store the data. Go to the directory you've created for working Read More...
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Bioinformatics
Let's download the data and learn how to decompress it. First, we will create a place to store the data. Go to the directory you created for working with class material. If you haven' Read More...
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Bioinformatics
This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes Read More...
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Bioinformatics
This page uses content directly from the Biostars Handbook by Istvan Albert (https://www.biostarhandbook.com). Always remember to load the bioinformatics environment. conda activate bioinfo SAM files SAM format is TAB-delimited, line-oriented, human-readable text Read More...
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Bioinformatics
This page uses content directly from the Biostars Handbook by Istvan Albert (https://www.biostarhandbook.com). Always remember to load the bioinformatics environment. conda activate bioinfo SAM files SAM format is TAB-delimited, line-oriented, human-readable text Read More...
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Bioinformatics
The bulk RNA-Seq test data we've been working with is in FASTQ format. We'd like to do a BLAST search on a couple of these sequences. Data must be in FASTA format to Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to activate the bioinfo environment when working on Biostar class materials. conda activate bioinfo The bulk RNA-Seq test data we've Read More...
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Bioinformatics
We will build a database out of all features of the 2014 Ebola genome under accession number KM233118. This data will go into a new directory named "db_2014". mkdir -p db_2014 # Get the 2014 Ebola Read More...
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Bioinformatics
Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...
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Bioinformatics
Lesson 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain Read More...
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Bioinformatics
Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...
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Bioinformatics
Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...
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Bioinformatics
Lesson 16: RNA sequencing review and classification based analysis Before getting started, remember to be signed on to the DNAnexus GOLD environment. Review In the previous classes, we learned about the steps involved in RNA sequencing Read More...
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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...
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Bioinformatics
Lesson 1: Introduction to Biowulf, Unix, and R Learning Objectives Learn about why you may want to use R on Biowulf. Refresh Unix and R skills. This lesson will not be hands on. Why use R Read More...
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Bioinformatics
Scatter plots and plot customization Objectives Learn to customize your ggplot with labels, axes, text annotations, and themes. Learn how to make and modify scatter plots to make fairly different overall plot representations. Load a Read More...
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Bioinformatics
Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn to construct cluster heatmap using the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify Read More...
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Bioinformatics
Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn to construct cluster heatmap using the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify Read More...
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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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Bioinformatics
R basics Objectives : To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By Read More...
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Bioinformatics
Data frames Objectives To be able to load, explore, and access data in a tabular format. To this end, students should understand the following: 1. how to import and export data 2. how to create, summarize, and Read More...
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Bioinformatics
04/17/2017 - Probing DNA-Protein Interactions This 2-day workshop, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq data analysis. Topics to be covered include: experimental design; read alignment; Read More...
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Bioinformatics
10/03/2016 - The maximum number of registrations (25) allowed has been reached for this workshop. You will be put on the waitlist and informed if any cancellations do occur. You are welcome to come on the morning Read More...
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Bioinformatics
09/22/2015 - Learn the basics of microarray gene expression analysis using Partek Genomics Suite and Open Source Tools. As we walk though hands-on analysis of a cancer dataset, you will learn the principles of experimental design, Read More...