Search Results for: huCC49-Delta-CH2 Anti Tag 72

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...

The core provides access to several different state-of-the-art 3D microscopes as well as computers to visualize and process image data. The facility houses equipment for 2D or 3D imaging of fixed and living specimens. High Read More...

The Protein Expression Laboratory produces proteins to help CCR investigators achieve their research goals with the lowest possible cost in the shortest time. PEL is operated by Leidos Biomedical Research Inc. on behalf of NCI Read More...

Try googling your problem or using some other search engine. rseek is an R specific search engine that searches several R related sites. If using google directly, make sure you use R to tag your Read More...

An OTU is an operational taxonomic unit. This is derived by binning sequences at a certain threshold of similarity. This threshold is generally set at 97%, which is associated with a species level assignment. Clustering can Read More...

09/28/2023 - The Trapnell Lab at the University of Washington's  Department of Genome Sciences  studies how genomes encode the program of vertebrate development and how that program goes awry in disease. Read More...

samtools flagstat SRR1972739.bwa.bam produces this 20740 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 740 + 0 supplementary 0 + 0 duplicates 15279 + 0 mapped (73.67% : N/A) 20000 + 0 paired in sequencing 10000 + 0 read1 10000 + 0 read2 14480 + 0 properly paired (72.40% : N/A) 14528 + 0 with itself and mate mapped 11 + 0 singletons (0.05% : N/ Read More...

samtools flagstat SRR1972739.bwa.bam produces this 20740 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 740 + 0 supplementary 0 + 0 duplicates 15279 + 0 mapped (73.67% : N/A) 20000 + 0 paired in sequencing 10000 + 0 read1 10000 + 0 read2 14480 + 0 properly paired (72.40% : N/A) 14528 + 0 with itself and mate mapped 11 + 0 singletons (0.05% : N/ Read More...

06/29/2023 - Please join us for a special presentation about the Fred Hutchinson’s data journal to the cloud, including an innovative cloud platform (Cirro:  https://cirro.bio/ ) to streamline data collection, Read More...

Try googling your problem or using some other search engine. rseek is an R specific search engine that searches several R related sites. If using google directly, make sure you use R to tag your Read More...

01/25/2021 - Presenter: Dr. Arjun Raj from the Perelman School of Medicine, UPenn. Abstract:Anti-cancer therapies can often kill the vast majority of tumor cells but a few rare cells remain and grow despite treatment. Non-genetic Read More...

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...

What is in the 22.gtf file? A gtf file is known as Genome Transfer File, which is essentially a tab delimited file (ie. columns in the file are separated by tab). It informs us of Read More...

Try googling your problem or using some other search engine. rseek is an R specific search engine that searches several R related sites. If using Google or other major search engine directly, make sure you Read More...

DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis Read More...

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...

The Bloomington Drosophila Stock Center (BDSC) collects, maintains, and distributes genetically defined strains of Drosophila melanogaster for research and education. The BDSC supports a large, worldwide community of scientists using Drosophila as a model organism Read More...

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) 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...

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 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...

Much like pseudobulk differential expression, the RNA expression can be collapsed into pre-defined components, such as the clusters, if it is believed that cell-to-cell variation is inducing too much confusion in the labeling. This collapsing Read More...

Some tools have been described in the previous session (see here ). Today, we will be focusing on the SingleR tool, which also requires the celldex package . In short, SingleR operates by comparing your current dataset Read More...

Let's grab some data. library ( tidyverse ) acount_smeta % dplyr :: rename ( "Feature" = "...1" ) acount #differential expression results dexp % filter ( ! Feature %in% dexp $ feature ) ## # A tibble: 48,176 × 9 ## Feature SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516 SRR1039517 ## ## 1 Read More...

Help Session Lesson 6 Let's grab some data. library ( tidyverse ) acount_smeta % dplyr :: rename ( "Feature" = "...1" ) acount #differential expression results dexp % filter ( ! Feature %in% dexp $ feature ) ## # A tibble: 48,176 × 9 ## Feature SRR1039508 SRR1039509 SRR1039512 Read More...

The grep utility is used to search files looking for a pattern match. It is used like this. grep pattern options filename As our first example we will look for restriction enzyme (EcoRI) sites in Read More...

This page contains content directly from The Biostar Handbook . Always remember to start the bioinformatics environment. conda activate bioinfo Pseudoalignment-based methods identify locations in the genome using patterns rather than via alignment type algorithms. It Read More...

This page contains content directly from The Biostar Handbook . Always remember to start the bioinformatics environment. conda activate bioinfo Pseudoalignment-based methods identify locations in the genome using patterns rather than via alignment type algorithms. It Read More...

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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

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...

“Gene set enrichment analysis” refers to the process of discovering the common characteristics potentially present in a list of genes. When these characteristics are GO terms, the process is called “functional enrichment.” Warning Overall GO Read More...

Objectives Combine multiple plots into a single figure Learn how to use aspects of cowplot and patchwork The primary purpose of this lesson is to learn how to combine multiple figures into a single multi-panel Read More...

02/12/2020 - This two-day instructor-led course gives participants a broad study of networking options on Google Cloud Platform. Through presentations, demonstrations, and hands-on labs, learners explore and deploy GCP networking technologies, such as Google Virtual Private Read More...

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...

Let's look at a more complicated example using the gene_expression data. We can use ggpubr to explore genes of interest. However, in cases where comparisons are more complicated and faceting is used, this Read More...

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...

You will need an annotation file in GTF format (for poorly annotated species you can use GTF file generated by cufflinks). ENSEMBL annotation is known to work well. Additionally, a STAR index (for appropriate STAR Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

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...

1. Introduction and Learning Objectives This tutorial has been 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 that 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...

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...

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...

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...

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...

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...

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...

How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR 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...

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. 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...

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...

Multi-figure panel Objectives Combine multiple plots into a single figure Learn how to use patchwork and cowplot The primary purpose of this lesson is to learn how to combine multiple figures into a single multi-panel 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...

ggpubr allows us to easily incorporate additional information into our plots (e.g., mean, individual case information, etc.). Where this package really shines is its ability to easily include the results of common statistical tests. Read More...

The program can be run in either interactive or batch mode Get interactive node: sinteractive -c 16 --mem 45g --gres=lscratch:20 Make sure you have requested enough resources, as the program can be quite memory- and Read More...

For this portion of the lesson, let's change back into our data directory. Again, username is the username you used to sign into Biowulf, this could be your NIH username if you have Biowulf Read More...

The resulting object eh is a gseaResult object. This object contains the results (eh@result) and other information that went into the analysis, for example, @organism type, @setType, the @geneSets used, the genes in our @ Read More...

For tabular data in the form of csv files, which could contain multiple columns, the columns do not print to the terminal nicely aligned. The column command can fix this. The options and arguments in Read More...