Search Results for: Phage display

Let's look a bit into our RStudio layout. Source : This pane is where you will write/view R scripts. Some outputs (such as if you view a dataset using View() ) will appear as a Read More...

::: {.cell} readRDS ( "./data/diffexp_results_edger_airways.rds" ) |> #read data select ( transcript , logFC , FDR ) |> #select columns of interest filter ( transcript == "TSPAN6" | transcript == "DPM1" ) |> #filter ggplot ( aes ( Read More...

{{Sdet}} Solution{{Esum}} #multiple ways to find color blind friendly palettes. #using color brewer scales RColorBrewer :: display.brewer.all ( colorblindFriendly = TRUE ) ggplot ( iris ) + geom_point ( aes ( Petal.Length , Petal.Width , color = Species )) + coord_fixed ( ratio = 1 , Read More...

You will also need to know commands specific to the Biowulf job scheduling system: sbatch submit slurm job swarm submit a swarm of commands to cluster sinteractive allocate an interactive session sjobs show brief summary Read More...

A barplot is used to display the relationship between a numeric and a categorical variable. --- R Graph Gallery The tooth growth data can be visualized via a bar plot using geom_bar() , as dose Read More...

A barplot is used to display the relationship between a numeric and a categorical variable. --- R Graph Gallery The tooth growth data can also be visualized via bar plot using geom_bar . However, if Read More...

Change to color of the points by species to be color blind friendly, and change the legend title to "Iris Species". Label the x and y axis to eliminate the variable names and Read More...

Let's look a bit into our RStudio layout. (demonstrate minimize / maximize utility) Source : This pane is where you will write/view R scripts. Some outputs (such as if you view a dataset using View() ) Read More...

{{Sdet}} Solution{{Esum}} #multiple ways to find color blind friendly palettes. #using color brewer scales RColorBrewer :: display.brewer.all ( colorblindFriendly = TRUE ) ggplot ( iris ) + geom_point ( aes ( Petal.Length , Petal.Width , color = Species )) + coord_fixed ( ratio = 1 , Read More...

12/21/2020 - Register Meeting number: 172 414 1612 Meeting Password: AmWdZgu*775 Please see information below about the upcoming SS/SC Brown Bag Seminar on next Monday December 21, 2020. Slides are already available on our website https://ccrod.cancer.gov/confluence/ Read More...

salloc: Pending job allocation 3448569 salloc: job 3448569 queued and waiting for resources salloc: job 3448569 has been allocated resources salloc: Granted job allocation 3448569 salloc: Waiting for resource configuration salloc: Nodes cn4335 are ready for job srun: error: Read More...

There are a number of built-in data sets available for practicing with ggplot2. Check these out here! For example, mtcars is commonly used in ggplot2 documentation: ::: {.cell} ::: {.cell-output-display} ::: :::

Let's plot the same data using geom_boxplot().A boxplot can be used to summarize the distribution of a numeric variable across groups. ::: {.cell output-location='slide'} ggplot(data=exdata) + geom_boxplot(aes(x=Treatment, Read More...

We can see how easy it is to change the way the data is plotted. Let's plot the same data using geom_line(). ::: {.cell output-location='slide'} ggplot(data=exdata) + geom_line(aes(x=Number. Read More...

Let's look a bit into our RStudio layout. Source: This pane is where you will write/view R scripts. Some outputs (such as if you view a dataset using View()) will appear as a Read More...

You will also need to know commands specific to the Biowulf job scheduling system: sbatch submit slurm job swarm submit a swarm of commands to cluster sinteractive allocate an interactive session sjobs show brief summary Read More...

You will also need to know commands specific to the Biowulf job scheduling system: sbatch submit slurm job swarm submit a swarm of commands to cluster sinteractive allocate an interactive session sjobs show brief summary Read More...

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...

To load genomic data tracks, select "File" in the IGV menu bar. User can load from file, URL, or server. In this case, "Load from File" will be used to select Read More...

Recall The Biowulf login node is meant for job submission to the batch system and should not be used to perform any computation intensive tasks. For testing computation intensive tasks without submitting a job, request Read More...

These sets of exercises will create the following plots from the hbr_uhr_deg_chr22 and hbr_uhr_top_deg_normalized_counts data tables. Volcano plot for hbr_uhr_deg_chr22 using Python's Seaborn Read More...

These sets of exercises will create the following plots from the hbr_uhr_deg_chr22 and hbr_uhr_top_deg_normalized_counts data tables. Volcano plot for hbr_uhr_deg_chr22 using Python's Seaborn Read More...

To load genomic data tracks, select "File" in the IGV menu bar. User can load from file, URL, or server. In this case, "Load from File" will be used to select Read More...

The goal of quality control is to keep only high quality cells (i.e., remove low quality cells (dead or dying cells), cell-free RNA, or doublets). Low quality cells will impact downstream analyses. Take care Read More...

There are other reasons you may be interested in using pivot_wider or pivot_longer . In my experience, most uses revolve around plotting criteria. For example, you may want to plot two different but related Read More...

Many graphs, like scatterplots, plot the raw values of your dataset. Other graphs, like bar charts, calculate new values to plot: bar charts, histograms, and frequency polygons bin your data and then plot bin counts, Read More...

Lesson 6 Exercise Questions: ggplot2 Putting what we have learned to the test: The following questions synthesize several of the skills you have learned thus far. It may not be immediately apparent how you would go Read More...

We will use qiime cutadapt trim-paired because we are working with paired-end reads. We will also use more than one thread ( --p-cores ). The region sequenced was V4-V5 with the forward primer, AYTGGGYDTAAAGNG , and the Read More...

Interactive nodes are suitable for routine tasks. To start an interactive node, type "sinteractive" at the command line "$" and press Enter/Return on your keyboard. $ sinteractive You will see something like Read More...

Interactive nodes are suitable for routine tasks. To start an interactive node, type "sinteractive" at the command line "$" and press Enter/Return on your keyboard. $ sinteractive You will see something like Read More...

Interactive nodes are suitable for testing/debugging cpu-intensive code, pre/post-processing of data, graphical application, and to GUI interface to application. To start an interactive node, type "sinteractive" at the command line "$& Read More...

Compare the output from these commands: ls ls -S ls -lh ls -h (when used with -l option, prints file sizes in a human readable format with the unit suffixes: Byte, Kilobyte, Megabyte, Gigabyte, Terabyte. Read More...

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...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

07/13/2023 - The Comparative Genome Viewer (CGV) is a visualization tool that helps you quickly compare two genomes based on assembly-assembly alignments provided by NCBI. CGV includes eukaryotic (animal, plant and fungal) assemblies, and many cross-species Read More...

Until this point we have been plotting raw data with geom_point() , but now we will be introducing geoms that transform and plot new values from your data. Many graphs, like scatterplots, plot the raw Read More...

Until this point we have been plotting raw data with geom_point() , but now we will be introducing geoms that transform and plot new values from your data. Many graphs, like scatterplots, plot the raw Read More...

The following questions synthesize several of the skills you have learned thus far. It may not be immediately apparent how you would go about answering these questions. Remember, the R community is expansive, and there Read More...

Many graphs, like scatterplots, plot the raw values of your dataset. Other graphs, like bar charts, calculate new values to plot: bar charts, histograms, and frequency polygons bin your data and then plot bin counts, Read More...

Lesson 6 Exercise Questions: ggplot2 Putting what we have learned to the test: The following questions synthesize several of the skills you have learned thus far. It may not be immediately apparent how you would go Read More...

05/18/2022 - Powerful and Intuitive Gene Expression Visualization Tools to Interpret Biological Signals – Bulk and Single Cell Data The increasing use of genomic technologies, such as RNA-Seq and single cell RNA-Seq, to assess gene expression patterns Read More...

You have to VPN using Cisco AnyConnect Secure Mobility Client . Click Connect button and follow usual instructions. Following NoMachine Installation for Biowulf , double click the connection shortcut. You should see something like below. Fill in Read More...

Running RStudio on Biowulf with NoMachine Using NoMachine to run Rstudio on Biowulf has the benefit of accessing data on the Biowulf/Helix drives. This comes at the cost of setup time and slower responsiveness. Read More...

03/17/2021 - Presenter: Himel Mallick, PhD Senior Scientist, Biostatistics Merck Research Laboratories Abstract Identifying clinically actionable features that display differential abundance and expression patterns across experimental conditions is an important first step toward characterizing the multi-omics Read More...

01/27/2021 - Please plan to attend the Earl Stadtman Investigator Program search seminar by: Qian Zhu, Ph.D. Dana Farber Cancer Institute/Boston Children's Hospital Dr. Zhu's research interests include: single-cell genomics; spatial transcriptomics; Read More...

01/12/2021 - Please plan to attend the Earl Stadtman Investigator Program search seminar by: Mikhail Kolmogorov, Ph.D. University of California, San Diego Dr. Kolmogorov's research focus is bioinformatics. Particularly, he is interested in algorithms Read More...

07/30/2020 - A panel of scientists with expertise in Single-Cell RNA-Seq will answer your questions on analysis of Single-Cell RNA-Seq data. Questions must be submitted in advance of the meeting by Weds, July 15. Please submit your Read More...

07/23/2020 - A panel of scientists with expertise in Single-Cell RNA-Seq will answer your questions about Single-Cell RNA-Seq experimental design. Please submit your question by July 15, to https://btep.ccr.cancer.gov/question/single_cell_rna_ Read More...

07/09/2020 - The recent breakthroughs in high-throughput technologies have resulted in a vast amount of big-data resources. However, it remains a significant challenge to transfer the knowledge from the public data to a new research project Read More...

01/13/2020 - Sushant Kumar, Ph.D. Yale University Moving beyond the canonical dichotomy of drivers and passengers in cancer hosted by the Cancer Data Science Laboratory (CDSL) on Monday, January 13th at 1:00 p.m. Dr. Kumar' Read More...

::: {.cell output-location='slide'} ggplot(exdata) + geom_point(aes(x=Number.of.Transcripts, y = Total.Counts, fill=Treatment), shape=21,size=3) + #can change labels of fill levels along with colors scale_fill_manual(values=c("purple& Read More...

There are a number of ways to specify the color argument including by name, number, and hex code. Here is a great resource from the R Graph Gallery for assigning colors in R. There are Read More...

Is there an application called salmon installed on Biowulf? {{Sdet}}{{Ssum}}Solution{{Esum}} module avail salmon salmon/1.7.0 salmon/1.10.0 salmon/1.10.1 (D) salmonte/0.4 Where: D: Default Module Module defaults are chosen based on Find First Rules due Read More...

Is there a relationship between treatment ("dex") and the number of transcripts or total counts? ::: {.cell output-location='slide'} #adding the color argument to our mapping aesthetic ggplot(exdata) + geom_point(aes(x=Number. Read More...

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...

What is the relationship between total transcript sums per sample and the number of recovered transcripts per sample? ::: {.cell output-location='slide'} #let's plot our data ggplot(data=exdata) + geom_point(aes(x=Number.of. Read More...

We use a command line interface and a Secure shell protocol (SSH) to establish a remote connection to the login node / head node. Most of us are likely used to a graphical user interface (GUI), Read More...

We use a command line interface and a Secure shell protocol (SSH) to establish a remote connection to the login node / head node. Most of us are likely used to a graphical user interface (GUI), Read More...

:root { --primary-action: rgb(0, 0, 0) !important; --primary-action: rgb(0, 0, 0) !important; } .container { width: 1440px; max-width: 100%; } #h2 { font-size: 2.2rem; margin-left: 20px; } /* Lazy Load Styles */ .card-image { display: block; min-height: 20rem; /* layout hack */ background: #fff center center no-repeat; background-size: cover; filter: blur(3 Read More...

/*color variables main= #1E1E1E secondery= #333333 highlight= #073254 */ * { box-sizing: border-box; } body, html { font-family: "Open Sans", sans-serif; } .clearfix:before, .clearfix:after { content: " "; display: table; } .clearfix:after { clear: both; } h1, h2, h3, h4, h5, h6 { font-weight: 300; } body Read More...

.row { display: flex; justify-content: space-around; align-items: flex-start; margin: 20px; } .column { text-align: center; padding: 10px; width: 30%; } .column img { display: block; margin: 0 auto; width: 150px; height: 150px; } .column strong { display: block; margin-top: 10px; } Background: Intravital microscopy (IVM) Read More...

The Office of Collaborative Biostatistics, Office of the Clinical Director, is the statistical and data management component of CCR. The Section provides statistical leadership and data management consultation for CCR’s major clinical activities and Read More...

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...

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...

Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols.  This service is intended for the occasional users of this system.  Researchers who expect to use this instrument Read More...

Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols.  This service is intended for the occasional users of this system.  Researchers who expect to use this instrument Read More...

[tabby title="Home"] About NICE-NIH Intramural CryoEM Consortium  NIH Intramural CryoEM Consortium (NICE) serves intramural investigators in all NIH IC’s. NICE provides access to state-of-the-art Titan Krios cryo-electron microscopes for atomic-resolution structure determination of Read More...

2024 Senatorov IS, Bowman J, Jansson KJ, Alilin AN, Capaldo BJ, Lake R, Riba M, Abbey YC, Mcknight C, Zhang X, Raj S, Beshiri ML, Shinn P, Ngyuyen H, Thomas CJ, Corey E, Kelly K. Castrate Read More...

Partek Flow enables scientists to build comprehensive workflows for analyzing multi-omics high throughput sequencing data including DNA and variant calling, bulk and single cell modalities for RNA, ChIP, and ATAC, spatial transcriptomics, CITE, and immune Read More...

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...

Learning Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help how R can enhance data Read More...

In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...

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...

Lesson 3: Creating a feature table Lesson Objectives Check for primers Generate an ASV count table and representative sequence file Understand the difference between OTU picking and denoising The two primary files that will be used Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learning objectives: 1. Understand what a sequence alignment is and how different algorithms can effect alignments. 2. Learn how scoring matrices and gap penalties (gap Read More...

Let's use the tool Trimmomatic to clean up the adapters and the poor quality reads for SRR1553606. For help with Trimmomatic type trimmomatic --help at the command line. Before getting started with using trimmomatic, Read More...

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...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

We previously stored FASTQC results for the HBR and UHR raw sequencing data in the ~/biostar_class/hbr_uhr/QC directory (recall that ~ denotes home directory). So before getting started, change into this folder. cd ~/ Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...

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...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Lesson 5: Working on Biowulf Lesson 4 Review Flags and command options Wildcards ( * ) Tab complete Accessing user history with the "up" and "down" arrows cat , head , and tail Working with file content (input, Read More...

Lesson 4: Useful Unix For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 3 Review Biowulf is the high performance computing cluster at NIH. When you apply for a Biowulf account Read More...

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...

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...

Learning Objectives Understand the components of an HPC system. How does this compare to your local desktop? Learn about Biowulf, the NIH HPC cluster. Learn about the command line interface and resources for learning. What Read More...

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 plots, box & whisker plots, and histograms. Read More...

/* 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...

Introduction to R and RStudio IDE Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help 3. Read More...

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...

02/21/2017 - This BTEP Workshop will cover the fundamentals and best practices of Exome-Seq analysis, including downstream interpretation of variants using a variety of in-house and NCI-licensed software solutions. There will be hands-on training on CCBR Read More...

10/22/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...

01/29/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...