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Total Results Found: 96

Biopharmaceutical Development Program (BDP)
Frederick, MD

Collaborative

The Biopharmaceutical Development Program (BDP) provides resources for the development of investigational biological agents. The BDP supports feasibility through development and Phase I/II cGMP manufacturing plus regulatory documentation.The BDP was established in 1993. We Read More...

Microbiome Analysis with QIIME2: Learning Objectives

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Bioinformatics

Understand the difference between alpha and beta diversity Introduce several alpha diversity metrics Understand what rarefaction is and why it is important Introduce the debate regarding rarefaction and other methods of normalization Often many questions Read More...

Microbiome Analysis with QIIME2: Lesson 5 Practice

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Bioinformatics

This practice lesson is associated with Lesson 5 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on choosing a sampling depth to rarefy, running core-metrics, and comparing alpha diveristy between our Read More...

Data Visualization with R: Combining two plots

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Bioinformatics

Let's combine our PCA and volcano plots. pca + volcano ## Warning: Using alpha for a discrete variable is not advised. The last plot included in patchwork statements is considered the active plot, to which we Read More...

Data Visualization with R: Combining two plots

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Bioinformatics

Let's combine our PCA and volcano plots. pca + volcano ## Warning: Using alpha for a discrete variable is not advised. The last plot included in patchwork statements is considered the active plot, to which we Read More...

R Introductory Series: Nice plot example

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Bioinformatics

These steps can be used to create a publish worthy figure. For example, let's create a volcano plot of our differential expression results. A volcano plot is a type of scatterplot that shows statistical Read More...

Data Visualization with R: Modifying legends

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Bioinformatics

We can modify many aspects of the figure legend using the function guide() . Let's see how that works and go ahead and customize some theme arguments. Notice that the legend position is specified in Read More...

R Introductory Series 2023: Nice plot example

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Bioinformatics

These steps can be used to create a publish worthy figure. For example, let's create a volcano plot of our differential expression results. A volcano plot is a type of scatterplot that shows statistical Read More...

BTEP Lessons: Changing axes scales

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Bioinformatics

To change the y axis scale, we will need a specific function. These functions generally start with scale_y.... In our case we want to reverse our axis so that increasingly negative is going in Read More...

BTEP Lessons: Modifying legends

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Bioinformatics

We can modify many aspects of the figure legend using the function guide(). Let's see how that works and go ahead and customize some theme arguments. Notice that the legend position is specified in Read More...

Microbiome Analysis with QIIME2: Phylogeny

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Bioinformatics

In addition to clasifying our organisms, we also want to reconstruct their phylogenetic relationships by generating a phylogenetic tree. We often assume that phylogenetic closeness can elucidate commonalities in phenotypic properties / functions, so it is Read More...

Microbiome Analysis with QIIME2: What is rarefaction?

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Bioinformatics

Rarefaction is the process of subsampling reads without replacement to a defined sequencing depth, thereby creating a standardized library size across samples. Any sample with a total read count less than the defined sequencing depth Read More...

Microbiome Analysis with QIIME2: What have we done?

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Bioinformatics

Using a small subset of data: Imported raw fastq files using qiime tools import . Data was paired-end CASAVA format. Checked for primers using qiime cutadapt trim-paired . Denoised with qiime dada2 denoise-paired and generated summaries of Read More...

Microbiome Analysis with QIIME2: Course Overview

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Bioinformatics

This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim sequences, denoise Read More...

Microbiome Analysis with QIIME2: Home

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Bioinformatics

Course Overview This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim Read More...

Data Visualization with R: Plot labels

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Bioinformatics

Let's change various aspects of the plot labels. plot_grid(pca,volcano,hmap,sc, labels=LETTERS[1:4],label_size = 14, label_fontface = "bold.italic", label_colour ="blue", label_fontfamily ="Times New Read More...

Data Visualization with R: The Data

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Bioinformatics

This is the sixth lesson in our Data Visualization with R Series. At this point, we have created quite a few plots. For this lesson, we will focus on the RNA-Seq plots that we created Read More...

Data Visualization with R: The Data

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Bioinformatics

This is the sixth lesson in our Data Visualization with R Series. At this point, we have created quite a few plots. For this lesson, we will focus on the RNA-Seq plots that we created Read More...

Microbiome Analysis with QIIME 2

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Bioinformatics

10/19/2022 - Welcome to the Microbiome Analysis with QIIME 2 course series!                   This course series was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME 2 platform. Attendees will learn how to Read More...

BTEP Lessons: Defaults

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Bioinformatics

There are many defaults when generating a plot with ggplot2, but almost everything you see can be customized. Here we can see: Assigned colors A legend axis titles a plot background tick marks The assignment Read More...

BTEP Lessons: Defaults

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Bioinformatics

There are many defaults when generating a plot with ggplot2, but almost everything you see can be customized. :::: {.columns} ::: {.column width="30%"} Here we can see: Assigned colors A legend axis titles a plot Read More...

BTEP Lessons: How can we modify colors?

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Bioinformatics

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

BTEP Coding Club: Return to R

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Bioinformatics

Let's reshape the data. I will rely heavily on dplyr functions to perform these tasks. First, I want to isolate the alpha chain and beta chain data. #isolate alpha and beta dfTRA< Read More...

Bio-Layer Interferometry (BLI) - Octet RED96

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Back Services: Biophysics Facility offers Octet as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes a full analysis of a Read More...

NCI Medicinal Chemistry Accelerator (MCA)
Frederick, MD

Collaborative

The Medicinal Chemistry Accelerator (MCA) is a collaborative CCR resource that supports investigators in developing small molecule inhibitors for anticancer drug candidates. While CCR and NCATS have infrastructure to identify initial “hits” through high-throughput screening, Read More...

NCI LASP Animal Research Technology Support (ARTS)
Frederick, MD

Core Facility

NCI LASP Animal Research Technology Support (ARTS) provides customized technical support for basic and translational animal-based research to the scientific community. We offer a wide array of services ranging from expert colony management to the Read More...

NCI LASP Gnotobiotics Facility (GF)
Frederick, MD

Core Facility

The Laboratory Animal Sciences Program (LASP) of the Frederick National Laboratory operates a Gnotobiotics Facility (GF) to support research focused on the role of microbiota in cancer inflammation, pathogenesis, and treatment response. The GF can Read More...

Microbiome Analysis with QIIME2: Course Outline

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Bioinformatics

Work through DNAnexus? Find a nice cancer data set for 16S and shotgun Divide into two workshops or courses? Course structure or workshop structure? Amplicon processing and analysis (5 week course) (4 weeks) 1. Talk by Greg Caparaso? 1. Read More...

Microbiome Analysis with QIIME2: Microbiome Course

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Bioinformatics

Microbiome Course Course Outline Work through DNAnexus? Find a nice cancer data set for 16S and shotgun Divide into two workshops or courses? Course structure or workshop structure? Amplicon processing and analysis (5 week course) (4 weeks) 1. Read More...

Data Visualization with R: Themes

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Bioinformatics

The plot above is looking pretty good, but there are many more features that can be customized to make this publishable or fit a desired style. Changing non-data elements (related to axes, titles subtitles, gridlines, Read More...

Single Cell RNA-Seq Trajectory Analysis in Partek Flow

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Bioinformatics

06/24/2020 - Join us for a webinar:  How to Analyze Single Cell RNA-Seq Data: Point, Click, Done Register:  https://www.partek.com/webinar/how-to-analyze-single-cell-rna-seq-data-point-click-done/ Single cell mRNA sequencing allows for the identification of different cell subtypes Read More...

BTEP Lessons: Changing the color of all points

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Bioinformatics

Aesthetics that are not mapped to our variables are placed outside of the aes() function. These aesthetics are manually assigned and do not undergo the same scaling process as those within aes(). For example, we Read More...

BTEP Lessons: Changing the color of all points

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Bioinformatics

Aesthetics that are not mapped to our variables are placed outside of the aes() function. These aesthetics are manually assigned and do not undergo the same scaling process as those within aes(). ::: {.cell output-location='slide'} # Read More...

BTEP Lessons: Plot Customization: Using themes

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Bioinformatics

To create a publication quality plot, you will need to make several modifications to your basic PCA biplot code. We have already seen how to modify the default coordinate system, how to add additional statistics ( Read More...

BTEP Coding Club: Using Excel

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Bioinformatics

These questions can be answered in excel. However, the data would need to be reshaped. To see what I mean, let's take a brief look at the data in Excel. Notice that there are Read More...

Pan-Microbial Serology Facility (PMSF)
Bethesda, MD

Collaborative

The Pan-Microbial Serology Facility (PMSF) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The PMSF focuses on determining individualized pan-microbial immune profiles associated with human diseases including immunological Read More...

NCI SAXS Facility
Frederick, MD

Collaborative

In order to meet increasing demands from both NIH intramural and extramural communities for access to a small angle X-ray scattering (SAXS) resource, the Center for Cancer Research (CCR) under the leadership of Drs. Jeffrey Read More...

Class Documents

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Bioinformatics

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...

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: Course Wrap-Up

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Bioinformatics

Lesson 7: Course Wrap-Up Learning Objectives Introduce the QIIME2 microbiome workflow for Biowulf Review key concepts Showcase additional plugins QIIME 2 on Biowulf As mentioned previously, QIIME 2 is installed on Biowulf. To see available versions use module 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...

R Introductory Series 2023: ggplot2 Continued

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Bioinformatics

Objectives Review the grammar of graphics template. Learn about the statistical transformations inherent to geoms. Learn more about fine tuning figures with labels, legends, scales, and themes. Learn how to save plots with ggsave() . Review Read More...

BTEP Coding Club: Committing changes

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Bioinformatics

Changes to a coding project (including scripts, data, and other content) should be saved periodically, similar to clicking on the "save" button to periodically save changes when constructing a word document. This is Read More...