Search Results for: mRNA expression

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...

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...

Differential expression analysis is the process of identifying genes that have a significant difference in expression between two or more groups. For many sequencing experiments, regardless of methodology, differential analysis lays the foundation of the Read More...

The primary means of running differential expression in Seurat is through the FindMarkers function. The main usage for this function is as follows: FindMarkers(object,ident.1= ..., ident.2=..., test.use="wilcox", min.pct = 0.01, logfc. Read More...

2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

04/01/2025 - Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which Read More...

06/02/2015 - This workshop will cover some basic concepts involved in the integration of different types of NGS data in order to obtain a better overall picture of the underlying biology. Specifically, the course will examine Read More...

03/11/2025 - In this class, participants will get hands-on experience with generating and interpreting differential gene expression analysis results from bulk RNA sequencing. In addition, participants will learn to generate common plots used to visualize bulk Read More...

03/04/2025 - Alignment of RNA sequencing data enables researchers to identify where in the genome each sequence came from. However, it does not inform of how many sequences aligned to each genomic feature such as a Read More...

09/11/2024 - Qlucore Omics Explorer is a point-and-click package available to NCI CCR scientists that enables visualization-based analysis of multi-omics data including RNA-seq, scRNA-seq, proteomics, metabolomics, as well as enabling the use of machine learning classification Read More...

One particular critique of differential expression in single cell RNASeq analysis is p-value "inflation," where the p-values get so small that there are far too many genes exist with p-values below 0.05, even after Read More...

RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...

01/19/2022 - For our next CDSL Webinar we will have a guest lecture by  Dr. Russell Rockne from Beckman Research Institute, City of Hope National Medical Center. Abstract: Temporal dynamics of gene expression inform cellular and Read More...

10/12/2021 - Speaker :  Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This Read More...

10/30/2012 - Due to the weather related shutdown of the FEDERAL GOVERNMENT (NIH) this seminar has been POSTPONED ... we will attempt to reschedule at a later date. (10-30-2012)   Topics to be covered   I. Genomic and Read More...

02/24/2025 - AI Club is a weekly meeting that explores various topics relating to AI and deep learning in biomedical sciences, typically in a seminar, workshop, or journal club format. AI Club is intended to be Read More...

10/10/2024 - This introductory lecture will provide an overview of bulk RNA-Seq technology, its various application and shortcomings, as well as detailing the steps involved in analyzing the resulting data. The talk is aimed at those Read More...

06/13/2024 - The schedule for this week consists of one presentation: Lorenz Adlung, UMC Hamburg-Eppendorf, will discuss: scMod: Marrying machine learning and deterministic modelling of longitudinal single-cell data Single-cell-based methods such as flow cytometry or single-cell 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...

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...

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...

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...

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.

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.

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...

CREx News & Updates July 2021   Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Learn more about services from the NHLBI Read More...

Our Team Tatiana S. Karpova Ph.D.Core Headkarpovat@nih.govBuilding 41, Room C615240-760-6637 David A. Ball Ph.D.Core Biologistballa@nih.govBuilding 41, Room B114D240-760-6577 Mohamadreza Fazel, Ph.D.Core Biologistmohamadreza. Read More...

2024 L. Balagopalan, T. Moreno, H. Qin, B. C. Angeles, T. Kondo, J. Yi, K. M. McIntire, N. Alvinez, S. Pallikkuth, M. E. Lee, H. Yamane, A. D. Tran, P. Youkharibache, R. E. Cachau, N. Taylor, Read More...

10/24/2024 - Recent advances in artificial intelligence (AI) have revolutionized the use of hematoxylin and eosin (H&E)-stained tumor slides for precision oncology, enabling data-driven approaches to predict molecular characteristics and therapeutic outcomes. In Read More...

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...

High resolution single cell profiling assays have provided an unprecedented view of many biological systems and processes, but the spatial context in which this biology is occurring is often crucial. Spatial profiling, including spatial transcriptomic Read More...

09/17/2013 - Ingenuity Pathways Analysis (IPA)  is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.   Agenda for Day 1 (Tuesday September 17th) Large Scale ( 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...

09/10/2024 - The training will overview the current status of pathway tools, with focus on software available to NIH community.  It will discuss the biological interoperation of mutation and expression data in the context Read More...

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...

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...

In Seurat (since version 4), differential analysis requires a preprocessing step to appropriately scale the normalized SCTransform assay across samples: adp = PrepSCTFindMarkers(adp) Found 8 SCT models. Recorrecting SCT counts using minimum median counts: 8146 As covered earlier, Read More...

No summary available.

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...

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...

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...

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...

Mass Spectrometry Section of the Collaborative Protein Technology Resource (Bldg. 37) Core Capabilities: Identification of proteins in complexes, organelles, subcellular fractions, or fluids. Global relative protein quantitation. Quantitation by isotopic labeling of cells in culture (SILAC) Read More...

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...

Radiation Oncology Branch is part of CCR. Bioinformatics core is a collaborative resource to support ROB branch and provide service to ROB investigators from NCI and other Institutes access to new technologies, bioinformatics, statistical analysis 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...

[embed]https://youtu.be/yTl1Q0D7aZ0[/embed] 10x Genomics' supports multiple cancer research areas from single nucleotide and structural variant detection to single cell whole transcriptome gene expression analysis of thousands of individual Read More...

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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx NCI CLIA Molecular Diagnostics Laboratory (CMDL) The NCI CMDL is available to assist all 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...

Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...

09/26/2019 - Qlucore Omics Explorer is an interactive analysis and visualization tool that helps the user to find groups, structures, variable networks and discriminating variables. You can use your own data and analyze public data. Omics Read More...

06/19/2017 - Harvesting the Wealth of TCGA Data The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA Read More...

09/01/2016 - This 2-day workshop, including a BYOD (Bring Your Own Data) exercise, will provide an introduction and hands-on training for Cytoscape, which is an open source software platform for visualizing  networks and integrating these networks Read More...

01/07/2016 - REGISTRATION IS FULL FOR THIS WORKSHOP (25 ATTENDEES; 6 WAITLIST) The Cancer Genome Atlas (TCGA) is a large-scale study that has cataloged genomic data accumulated for many different types of cancers, and includes mutations, copy number Read More...

03/18/2014 - The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA and miRNA gene expression, and DNA Read More...

The reference genome is a completely assembled sequence that we can compare other sequences to. For high throughput sequencing, we need the known sequences so that we can find out where in the genome each Read More...

The reference genome is a completely assembled sequence (ie. the order in which the nucleotides are arranged is known). For high throughput sequencing, the known sequence help scientists find out where in the genome each Read More...

There are a number of core facilities available to NCI researchers. See more information from the Office of Science and Technology Resources. We most commonly see data from the following cores: CCR Sequencing Facility (CCR-SF) Read More...

The reference genome is a completely assembled sequence (ie. the order in which the nucleotides are arranged is known). For high throughput sequencing, the known sequence help scientists find out where in the genome each Read More...

Note This is not an exhaustive list. cBioPortal cBioPortal is a platform for exploratory and interactive visualization, analysis, and download of cancer genomics data. With cBioPortal You can quickly view genomic alterations across a set Read More...

06/03/2025 - Class Description Introduction to RNA-Seq data analysis Step-by-step live demonstration of RNA-Seq analysis using the Galaxy platform   What You’ll Learn: How to independently carry out the basic gene expression Read More...

05/19/2025 - Immunotherapy has the potential to revolutionize the way we treat cancer, but a key challenge has been finding ways to tailor that therapy to the right patient at the right time. Attend this webinar, Read More...

05/07/2025 - Join Dr. Eytan Ruppin, NCI investigator in the Center for Cancer Research, as he discusses Path2Space, a new and unpublished deep learning approach that predicts spatial gene expression directly from histopathology slides. Spatial Read More...

04/10/2025 - TumorDecon is a computational tool at an early stage of contributing to the intersection of bioinformatics and oncology. The goal of TumorDecon is to estimate the percentages of various immune cells from gene expression Read More...

04/08/2025 - Reactome is a free, open-source, curated and peer-reviewed pathway database that includes bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. This lesson will showcase the capabilities of Reactome in garnering biological Read More...

04/02/2025 - Please note: Registration is required to get the Meeting Link for this event. Please pre-register. The Human Tumor Atlas Network (HTAN) is a National Cancer Institute (NCI)-funded initiative to construct 3-dimensional atlases of Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

03/12/2025 - Clustering is one of the fundamental unsupervised machine learning algorithms. It is often used to group quantitative proteomic or RNAseq expression data to suggest sub-types of a particular cancer. This presentation covers building a Read More...

02/18/2025 - This class will introduce basic experimental and analytical considerations for bulk RNA sequencing, a technique that is used to profile gene expression at the tissue level. Information taught serves as the foundation for participants Read More...

10/30/2024 - In this session of the BTEP Coding Club, Emily Clough, PhD, GEO Curator, will explore updates to analysis tools available within the Gene Expression Omnibus (GEO), a public repository for gene expression and epigenomics Read More...

10/09/2024 - This session will give an overview of the NCI Cancer Research Data Commons and the variety of available cancer data such as RNA expression and protein abundance. These data are hosted in openly accessible Read More...

07/19/2024 - The molecular mechanisms underlying many types of cancer involve aberrances in trans-acting factors and their binding to cis-regulatory elements to regulate gene expression. Techniques such as ChIP-seq, DNase-seq, and ATAC-seq are commonly used to Read More...

06/27/2024 - During this presentation, you will learn about the GenePattern ecosystem, an environment for accessible, reproducible research that has been serving the needs of the cancer genomics community since 2004. GenePattern hosts hundreds of genomics analysis Read More...

Single cell RNASeq is a remarkably powerful tool for analyzing populations of cells that can be recovered from various experiments. Clustering and cell type annotation can be used to distinguish different populations with a level Read More...

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...

In addition to the Heatmap and the FeaturePlot shown previously, two other options easily accessible through Seurat are the Dot Plot and Violin Plot. The dot plot can visualize relative expression level and expression fraction. Read More...

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 have already been filtered Read More...

It is next standard to scale and center the features in the data set prior to dimension reduction or visualization via heatmap. Scaling the data will keep highly expressed genes from dominating our analysis. This Read More...

Now that we have loaded the package, we can import our data. Generally, in R programming, functions that involve data import begin with "read / Read". Seurat includes a number of read functions for Read More...

library(tidyverse) # dplyr and ggplot2 library(Seurat) # Seurat toolkit library(hdf5r) # for data import library(patchwork) # for plotting library(presto) # for differential expression library(glmGamPoi) # for sctransform Warning: package 'glmGamPoi' was built under R 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...

Now, that we have clusters, we can use differential expression analysis to uncover markers that define our clusters. These markers can be used to assign cell types to our clusters. First, because we are working Read More...

No summary available.

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...

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...

The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...

CREx News & Updates July 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Click below to learn how easy it is to navigate the CREx platform. These short videos will Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH Read More...

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...

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...

CREx News & Updates October 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CPTR Read More...

The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...

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...

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...

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...

The facilities at AIM are available for use by the entire NIH intramural research community. While we welcome users with any size imaging project, AIM specializes in large, yearlong (or longer), collaborative research efforts with Read More...

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...

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...

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...

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...

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...

Anaconda ( https://www.anaconda.com/ ) is a package manager and distributor for a wide array of data science software. Package managers are ideal for scientists who conduct analysis on a personal computer as they eliminate Read More...

03/21/2025 - Partek Flow is a point-and-click software for analyzing multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. Input options include FASTQ, BAM, or expression tables, thus enabling scientists Read More...

03/20/2025 - Please note: Registration is required to get the Meeting Link for this event. Please pre-register. BTEP and the Single Cell and Spatial Transcriptomics Interest Group jointly present: Quantifying spatiotemporal dynamics during embryogenesis is crucial Read More...

03/18/2025 - This class is not hands-on and will demonstrate to participants the use of IGV for visualizing alignment results from Next Generation Sequencing using RNA as an example. After this class, participants will be able Read More...

BTEP strives to maintain links to resources that should be of interest to CCR Bioinformatics Community.  Some of the resources to will be accessible through more than one of these lists, but since the lists Read More...

Register now for an upcoming seminar on January 22, 2025 , “Revealing Tumor-Promoting Signals in Breast Cancer Subtypes: A NIDAP Analysis of Single-Cell Data” . This one-hour talk will feature guest speaker and NIDAP developer, Josh Meyer, who will Read More...

12/12/2024 - This class will introduce bulk RNA sequencing analysis using Qiagen software. Participants will learn how to process FASTQ files and obtain differential expression using CLC Genomics Workbench as well as extract biological insight using Read More...

What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...

11/19/2024 - Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is a point-and-click software hosted on Biowulf, the NIH Read More...

10/16/2024 - Dear Colleagues,   Thanks to advances in single-cell genomics, researchers can construct large-scale organ atlases, giving you more accurate ways to study genetic mutations and alterations related to drug responses and disease. These Read More...

09/13/2024 - Reverse-phase protein arrays (RPPAs) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and develop novel cancer therapies.   To facilitate community-based investigation of the large-scale protein expression data generated by Read More...

07/11/2024 - Please join us for this special event featuring three speakers on the topic of Single-Cell Spatial Transcriptomics. George Zaki, Ph.D., Director, Applied Scientific Computing, BACS, The Frederick National Lab for Cancer Research, NCI/ Read More...

06/12/2024 - Join us for an engaging training session where we will examine the similarities and differences between machine learning and statistical differential gene expression (DGE) analysis using Qlucore Omics Explorer. Qlucore Omics Explorer is a Read More...

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...

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...

Transformed data will be available in the SCT assay, which is set as the default after running sctransform. During normalization, we can also remove confounding sources of variation, for example, mitochondrial mapping percentage The glmGamPoi Read More...

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...

The role of cell clustering is to identify cells with similar transcriptomic profiles by computing Euclidean distances across genes . However, scRNA-Seq experiments include highly dimensional data, with each cell associated with the expression of thousands Read More...

Many experiments look to compare to distinct populations, and scRNASeq is no exception. The two populations being compared can vary wildly from experiment to experiment; some look to draw comparisons based on the experimental condition, Read More...

As we can see above, the glimpse command shows the metadata that can be used to classify the cells. Within Seurat, the metadata is used to define the "identity" of the dataset. This Read More...

Following Cell Ranger and/or other pre-processing tools, you will have a gene-by-cell counts table for each sample. The three most popular frameworks for analyzing these count matrices include: R ( Seurat ). Seurat, brought to you Read More...

From the paper where this data was obtained, the following (incomplete) list of gene markers was obtained: Mmp3: preadipocytes Mki67: proliferating cells Fabp4: differentiating beige adipocytes and differentiated beige adipocytes Scd1: differentiated beige adipocytes Ucp1: Read More...

No summary available.