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Confocal
2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...
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Bioinformatics
03/06/2025 - This class introduces participants to the first steps to differential expression analysis in bulk RNA sequencing which involves filtering out noise from (ie. genes without expression across samples) and performing QC on the gene Read More...
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Bioinformatics
The first step in analyzing RNA sequencing is to perform quality assessment of the FASTQ files. This step ensures that the quality of the data is good and there no issues with contaminations such as Read More...
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Bioinformatics
The QC results table below indicates adapter trimming resulted in some samples losing reads. This is because not all reads passed the QC criteria. Also, the average read length has been reduced as the adapters Read More...
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Bioinformatics
After mapping, the next step is to perform post-alignment QC to determine things like overall alignment rate (ie. how many sequences aligned to the reference). To do this, select the "Aligned" reads data Read More...
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Bioinformatics
QC all reads K-mer length, if specified will generate a report for each sample of the positions for the most commonly occurring k-mers (or sequence of nucleotides) of the specified length - can hint at Read More...
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Bioinformatics
Ensure that alignment went without issues. Alignment rate Unique mappers Mapping quality (a mapping quality of 60 corresponds to 0.0001% error)
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Bioinformatics
There are several metrics that can be used to assess overall quality. The base workflow from Seurat suggests the following: nCount_RNA - the absolute number of RNA molecules (UMIs) per cell (i.e., count Read More...
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Bioinformatics
05/29/2024 - This talk will cover a scRNA-seq workflow available to NCI researchers on NIDAP. NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts user-friendly bioinformatics Read More...
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Bioinformatics
The CCBR Single-cell RNA-seq Workflow on NIDAP Josh Meyer, bioinformatics analyst (CCBR), will cover a scRNA-seq workflow available to NCI researchers on NIDAP . NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative Read More...
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Bioinformatics
11/16/2023 - This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Read More...
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Bioinformatics
12/05/2024 - This one and a half hour online training will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be Read More...
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Bioinformatics
12/03/2024 - This one and a half hour online training will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek Flow Read More...
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Bioinformatics
Josh Meyer, bioinformatics analyst (CCBR), will cover a scRNA-seq workflow available to NCI researchers on NIDAP . NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts 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
03/05/2024 - This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell Read More...
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Bioinformatics
03/30/2023 - Partek Flow provides a singular web based point and click environment for analyzing and visualizing high dimensional multi-omics sequencing data, making bioinformatics easily accessible to all researchers. Partek Flow software is available to NCI Read More...
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Bioinformatics
10/21/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
10/07/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
09/23/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
09/02/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
08/19/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
08/05/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
07/22/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
07/08/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
06/30/2021 - Registration is required to join this event. If you have not registered, please do so now. Register Speaker: Uchenna Emechebe, Ph.D., Field Application Scientist, Partek Incorporated. Partek® Flow® bioinformatics software which is available Read More...
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Bioinformatics
06/17/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
06/03/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
05/27/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
05/13/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
04/29/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
04/15/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
03/25/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
03/11/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
02/25/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
02/11/2021 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
01/28/2021 - THIS EVENT HAS BEEN CANCELLED RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow Read More...
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Bioinformatics
12/11/2020 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
11/20/2020 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
11/06/2020 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
Web Page
Bioinformatics
10/23/2020 - RNA sequencing (RNA-seq) is a widely used method in genomics, which enables the interrogation of whole cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a RNA-seq workflow on the NIDAP collaboration platform, Read More...
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Bioinformatics
10/25/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...
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Bioinformatics
09/13/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...
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Bioinformatics
Course setup Intro to DNAnexus and the GOLD learning system Learning Objectives Unix Bootcamp Brief Review of R (for R scripts in later analyses) Introduction to RNA Sequencing Central Dogma of Molecular Biology What is Read More...
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Bioinformatics
10/28/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
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Bioinformatics
10/14/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
09/30/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
09/16/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
08/26/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
08/12/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
07/29/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
07/15/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
06/24/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
06/10/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
05/20/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
05/06/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
04/22/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
04/08/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
03/18/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
03/04/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
02/18/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
02/04/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
01/21/2021 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
12/03/2020 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
11/13/2020 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
Web Page
Bioinformatics
10/30/2020 - Single-cell RNA sequencing (scRNA-seq) is a relatively new and powerful method in genomics, which enables the interrogation of whole single cellular transcriptomes. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a basic scRNA-seq workflow, Read More...
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Bioinformatics
01/22/2025 - This three hour online training covers QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression. Read More...
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Bioinformatics
Once we have read in the matrices, the next step is to create a Seurat object. The Seurat object will be used to store the raw count matrices, sample information, and processed data (normalized counts, Read More...
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Bioinformatics
Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse Read More...
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Bioinformatics
April 3, 2024 - The CCR Single Cell Analysis Facility (SCAF): An Overview (Mike Kelly, SCAF) ( Recording ) April 10, 2024 - Introduction to single cell RNA-Seq (Charlie Seibert, Saeed Yadranji Aghdam, SCAF) ( Recording ) April 17, 2024 - SCAF: Overview of Cell Read More...
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Bioinformatics
Welcome to Getting Started with scRNA-Seq This is a mini seminar series designed to help attendees learn more about single cell RNA-Seq, from applicable technologies to data analysis. Seminar Schedule April 3, 2024 - The CCR Single Read More...
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Bioinformatics
After this class, participants will Become familiar analyzing single cell RNA sequencing data using Partek Flow including Importing of data into a Partek Flow project QA/QC, filtering, and normalizing of single cell RNA data Read More...
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Bioinformatics
Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find out which genes Read More...
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Bioinformatics
Bioinformatics for beginners Module 2: Introduction to RNA sequencing In this module, we will use the Human Brain Reference and Universal Human Reference RNA sequencing datasets to learn about RNA sequencing. Each lesson will be followed Read More...
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Bioinformatics
Un-ordered lists: use * or - - DNA - RNA - protein - metabolite Ordered list: use numbers 1. Obtain sequencing data 2. Perform pre-alignment QC 3. Adapter and/or quality trim 3. Align sequencing data to reference genome 4. Obtain Read More...
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Bioinformatics
01/28/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=eb967c2ec79b87a5972c6b2ee2fc13281 Partek Flow software aids in the analysis of next generation sequencing data: RNA, small RNA, Read More...
Bethesda, MD
Core Facility
The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...
Bethesda, MD
Trans NIH Facility
The Center for Inherited Disease Research (CIDR)'s mission is to support the genetics community by providing high-quality, cutting-edge genomics services and technologies in order to expand our understanding of disease and catalyze discoveries that Read More...
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Bioinformatics
07/10/2024 - Qlucore Omics Explorer is a point-and-click software for analyzing various omics data including RNA sequencing (bulk and single cell), proteomics, and metabolomics. Participants will learn to perform QC, construct visualizations (ie. PCA, heatmap, volcano, Read More...
Web Page
Bioinformatics
Course Overview Partek Flow is a start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with Read More...
Web Page
Bioinformatics
Data Analysis Here are a pair of examples of RNASEQ complete workflows RNASEQ Pipeline from NCI CCBR https://github.com/CCBR/Pipeliner/blob/master/RNASeqDocumentation.pdf RNASEQ Nextflow Pipeline from nf-core https://nf-co.re/rnaseq Read More...
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Bioinformatics
We were introduced to the hcc1395 RNA sequencing data in Lesson 12 practice session . This study compared the transcriptome of hcc1395 normal and cancer cell lines so it's a normal versus tumor comparison. This dataset Read More...
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Bioinformatics
Lesson 12 Practice Objectives In this practice session, we will work with something new, which is a dataset from the Griffith lab RNA sequencing tutorial. Here, we will have a chance to practice what we have Read More...
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Bioinformatics
Lesson 13 Practice Objectives In this lesson we learned how to align raw sequencing reads to reference and to process alignment results for downstream analysis. Here, we will test our knowledge by continuing with the Golden Read More...
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Bioinformatics
03/08/2023 - Partek software provides a singular web based point and click environment for analyzing and visualizing high dimensional multi-omics sequencing data, making bioinformatics easily accessible to all researchers. Partek Flow software is available to NCI Read More...
Web Page
Bioinformatics
04/21/2021 - Registration Session Description QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression and for variant calling. In Read More...
Frederick, MD
Core Facility
The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...
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Biomarker Discovery with Morphological Context: Changing how tissue specimens are analyzed < https://youtu.be/mVhfZq8ppbc What is Digital Spatial Profiling? GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial Read More...
Bethesda, MD
Repositories
Trans NIH Facility
The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...
Bethesda, MD
Trans NIH Facility
The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...
Frederick, MD
Core Facility
Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...
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Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...
Web Page
Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.
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Biophysics Core Facility assists NIH investigators in measuring molecular interactions and in characterizing macromolecular properties. This includes binding studies of proteins, DNA, RNA, and their ligands in buffers, cell lysate, plasma, and other media. We Read More...
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...
Web Page
CREx News & Updates November 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the NINDS Quantitative Magnetic Resonance Imaging Core. NINDS Read More...
Bethesda, MD
Core Facility
Repositories
The mission of Human Brain Collection Core (HBCC) within the National Institute of Mental Health, Division of Intramural Programs (NIMH IRP) is to conduct and support research on brain and behavior, with the goal of Read More...
Web Page
October 6, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NIH Center For Human Immunology, Inflammation, And Autoimmunity (CHI) CHI is a Read More...
Web Page
September 8, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight Trans-NIH Intramural Sequencing Center (NISC) NISC is a multi-disciplinary genomics facility that Read More...
Bethesda, MD
Collaborative
The Mass Spectrometry Unit of the Collaborative Protein Technology Resource uses mass spectrometry for the study of proteins. We perform collaborative experiments with CCR researchers in areas such as: interactomes, quantitative global proteome analyses, and Read More...
Web Page
Bioinformatics
Here, we will start with the data stored in a Seurat object. For instructions on data import and creating the object, see an Introduction to scRNA-Seq with R (Seurat) and Getting Started with Seurat: QC Read More...
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Bioinformatics
Biostar Class - Sequencing Instruments Below are a list of links and resources mentioned in the BIOSTAR Sequencing Instruments class given on 06/10/20 and 06/11/20 Sequencing Technologies - Company Web Sites Illumina PacBio Oxford Nanopore 10X Genomics Read More...
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Bioinformatics
Lesson 14 Practice Objectives Here, we will practice using the Integrative Genome Viewer (IGV) to visualize the hcc1395 RNA sequencing alignment results. About the data and launching IGV We were introduced to the hcc1395 RNA sequencing Read More...
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Bioinformatics
Below, you will find questions and answers brought up in the course polls for the BTEP Bioinformatics for Beginners course series that took place from September 13th, 2022 to December 13th, 2022. Question 1 : Normalization - when to Read More...
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Bioinformatics
BTEP Bioinformatics for Beginners (September 13th, 2022 - December 13th, 2022) Questions and Answers Below, you will find questions and answers brought up in the course polls for the BTEP Bioinformatics for Beginners course series that took Read More...
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...
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Bioinformatics
Lesson 10: Introducing the FASTQ file and assessing sequencing data quality Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 9 Review In the previous lesson, we explored the reference genomes and Read More...
Web Page
Bioinformatics
In lesson 9, we learned that reference genomes came in the form of FASTA files, which essentially store nucleotide sequences. In this lesson, we will learn about the FASTQ file, which is the file format that Read More...
Web Page
Bioinformatics
Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...
Web Page
Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...
Web Page
Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...
Web Page
Bioinformatics
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...
Bethesda, MD
Collaborative
The goals of the Bioinformatics Training and Education Program within NCI/CCR are: To make researchers aware of the bioinformatics resources available to them, To provide training and guidance on these resources regularly and at Read More...
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...
Web Page
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
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...
Web Page
Back Services: Biophysics Facility offers MP as an open-access instrument. First-time users must complete a short training session before gaining access to the instrument training calendar. Training includes mass distribution analysis of a Read More...
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...
Bloomington, IN
Repositories
Trans NIH Facility
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...
Web Page
CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More. New Resources on CREx NIMH Human Brain Collection Core (HBCC) The HBCC obtains human brain tissue, hair, and blood Read More...
Web Page
CREx News & Updates January 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NCI ANTIBODY CHARACTERIZATION LABORATORY (ACL) The ACL specializes in rigorously validating antibodies for signaling and Read More...
Rockville, MD
Repositories
Trans NIH Facility
Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status, and enzyme activity levels. You can choose to search for a Read More...
Bethesda, MD
Core Facility
The Flow Cytometry Core (LGI) offers established technologies to support studies using flow cytometry and cell sorting. Established Technologies Applications that run on FACS Caliburs include: Immunophenotyping (up to 4-color), Intracellular markers, including cytokines and 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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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Technology Event Biophysical Methods for Protein Interactions Monday, May 15 – Friday, May 19, 2023 This workshop will review the strategies of Read More...
Rockville, MD
Collaborative
We are a bioinformatics team within the Center for Biomedical Informatics and Information Technology’s (CBIIT’s) Cancer Informatics Branch (CIB)—soon to be referred to as the Informatics and Data Science (IDS) Program. Headed Read More...
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...
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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...
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The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management 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...
Bethesda, MD
Collaborative
Repositories
The National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...
Frederick, Maryland
Core Facility
CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...
Bethesda, MD
Core Facility
The Biophysics Core’s mission is to provide support in the study of macromolecular interactions, dynamics, and stability by offering consultations, training, professional collaborations, and instrument access. General Services: Multi-technique molecular interaction studies, Kinetic and Read More...
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Back Services: Biophysics Facility offers ITC calorimeters as open-access instruments. First-time users must complete a short training session before gaining access to the instrument reservation calendar. Training includes performing a test experiment and Read More...
Frederick, MD
Core Facility
The Clinical Support Laboratory offers processing, tracking, and testing of a broad range of clinical samples. Support can begin at the early stages of clinical trial development to aid in developing a comprehensive strategy for Read More...
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Supplemental Technology Award Review System (STARS) Overview STARS Request Form STARS System The Supplemental Technology Award Review System (STARS) is a web-based interface for submission and review of S&S supplement requests by CCR 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...
Bethesda, MD
Core Facility
The Genomics and Pharmacology Facility is part of the NCI's Center for Cancer Research (CCR), within the Developmental Therapeutics Branch. Its mission is to manage and assess molecular interaction data obtained through multiple platforms, increase Read More...
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Confocal
A typical HTI screening project at HiTIF can be subdivided in 5 phases: Pre-Development The investigator contacts the Facility Head to inquire about the current availability of instrumentation time and manpower for the project to be Read More...
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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...
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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
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...
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Bioinformatics
Managing Bioinformatics Projects with Jupyter Lab Learning Objectives After this class, participants will have obtained the foundation needed to start using Jupyter Lab as an all-in-one place to maintain code, output, and other description of Read More...