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Search Results for: scRNA-Seq

Total Results Found: 111

Total Results Found: 111

Introduction to scRNA-Seq with R (Seurat)

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Bioinformatics

04/24/2024 - This seminar provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat.  In this seminar, attendees will learn about options for analyzing scRNA-Seq data, resources for learning R, how Read More...

Getting Started with scRNA-Seq Seminar Series: The data

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Bioinformatics

In this tutorial, we will continue to use data from Nanduri et al. 2022, Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins , published in Nature Communications . As a reminder, Read More...

Getting Started with scRNA-Seq Seminar Series: The data

Web Page

Bioinformatics

In this tutorial, we will continue to use data from Nanduri et al. 2022, Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins , published in Nature Communications . As a reminder, Read More...

Getting Started with scRNA-Seq Seminar Series: References

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Bioinformatics

The following resources were instrumental in designing this lesson: https://www.sc-best-practices.org/introduction/analysis_tools.html#single-cell-analysis-frameworks-and-consortia https://satijalab.org/seurat/articles/essential_commands https://github.com/hbctraining/scRNA-seq_online/blob/master/lessons/03_SC_ Read More...

Getting Started with scRNA-Seq Seminar Series: Commenting

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Bioinformatics

You can annotate your code by starting annotations with # . Comments to the right of # will be ignored by R. Use # ---- to create navigable code sections. For report generation, use R Markdown or Quarto .

Getting Started with scRNA-Seq Seminar Series: Contacts

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Bioinformatics

Who can you contact with questions? NCI CCR Single Cell Analysis Facility (SCAF) provides single cell support to NCI-CCR Researchers. NCI CCR Bioinformatics Training and Education Program (BTEP) provides bioinformatics training support. Contact BTEP via Read More...

Getting Started with scRNA-Seq Seminar Series: SCTransform

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Bioinformatics

Rather than relying on the above steps ( NormalizeData() , FindVariableFeatures() , and ScaleData() ), we are going to proceed with a newer method ( SCtransform ) instead. This method uses Pearson residuals for transformation, which better accounts for the overall Read More...

Getting Started with scRNA-Seq Seminar Series: The Data

Web Page

Bioinformatics

In this tutorial, we are using data from Nanduri et al. 2022, Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins , published in Nature Communications . The raw count matrices are Read More...

Getting Started with scRNA-Seq Seminar Series: Load the packages

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Bioinformatics

library(tidyverse) # dplyr and ggplot2; CRAN library(Seurat) # Seurat toolkit; CRAN library(hdf5r) # for data import; CRAN library(patchwork) # for plotting; CRAN library(presto) # for differential expression; Github library(glmGamPoi) # for sctransform; Bioconductor library( Read More...

NCI Genomic Data Commons (GDC)
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...

NCI Genetics Branch: OMICS Technology Facility
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...

CCR Sequencing Facility
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...

CCR Collaborative Bioinformatics Resource (CCBR)
Bethesda, MD

Collaborative

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

NIH Intramural Sequencing Center (NISC)
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...

January 2022 Newsletter

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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...

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...

CCR Genomics Core
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...