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Search Results for: low abundance

Total Results Found: 122

Total Results Found: 122

Microbiome Analysis with QIIME2: Differential abundance testing

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Bioinformatics

Differential abundance testing examines which taxa are significantly different in abundance between conditions. However, challenges such as sparsity, compositionality, and library size differences make this challenging to determine.

R Introductory Series: Reshaping for plotting

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Bioinformatics

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

R Introductory Series: Reshaping for plotting

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Bioinformatics

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

Bioinformatics for Beginners 2022: Remember

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Bioinformatics

RNASEQ looks at steady state mRNA levels which is the sum of transcription and degradation Protein levels are assumed to be driven by mRNA levels RNASEQ can measure relative abundance not absolute abundance RNASEQ is Read More...

Past Seminars

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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...

Microbiome Analysis with QIIME2: Methods of filtering

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Bioinformatics

Frequency based filtering, contingency based filtering, metadata based filtering qiime feature-table filter-samples Filter samples based on total number of sequences (e.g., --p-min-frequency 1000 ) Filter samples with a minimal number of features (e.g., --p-min-features 10 ) Metadata Read More...

NanoString GeoMX Digital Spatial Profiler

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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...

Microbiome Analysis with QIIME2: Course Wrap-Up

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Bioinformatics

Lesson 7: Course Wrap-Up Learning Objectives Introduce the QIIME2 microbiome workflow for Biowulf Review key concepts Showcase additional plugins QIIME 2 on Biowulf As mentioned previously, QIIME 2 is installed on Biowulf. To see available versions use module Read More...

Bioinformatics for Beginners 2022: RNA-SEQ Overview

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Bioinformatics

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...

R Introductory Series: Facets

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Bioinformatics

A way to add variables to a plot beyond mapping them to an aesthetic is to use facets or subplots. There are two primary functions to add facets, facet_wrap() and facet_grid() . If faceting Read More...

Data Wrangling with R: Facets

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Bioinformatics

A way to add variables to a plot beyond mapping them to an aesthetic is to use facets or subplots. There are two primary functions to add facets, facet_wrap() and facet_grid() . If faceting Read More...

Microbiome Analysis with QIIME2: Rarefaction

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Bioinformatics

To rarefy or not to rarefy? Feature tables are composed of sparse and compositional data. Measuring microbial diversity using 16S rRNA sequencing is dependent on sequencing depth. By chance, a sample that is more deeply Read More...

Bioinformatics for Beginners 2022: Replicates

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Bioinformatics

Technical Replicates It’s generally accepted that they are not necessary because of the low technical variation in RNASeq experiments Biological Replicates (Always useful) Not strictly needed for the identification of novel transcripts and transcriptome Read More...

Bioinformatics for Beginners 2022: Read Choices

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Bioinformatics

For any NGS experiment you will have to make choices about the following sequencing options. Unfortunately, there is and inverse relationship between accuracy and cost. Read Depth More depth needed for lowly expressed genes Detecting Read More...

Data Visualization with R: Scaling

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Bioinformatics

Prior to sending our data into the heatmap generating algorithm, it is a good idea to sacle. There are several reasons for doing this Variables in the data might not have the same units, thus Read More...

Data Visualization with R: Scaling

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Bioinformatics

Prior to sending our data into the heatmap generating algorithm, it is a good idea to sacle. There are several reasons for doing this Variables in the data might not have the same units, thus 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...

Mass Photometer (MP) – Refeyn OneMP

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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...

Fluorescence – PTI/Horiba QuantaMaster

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Back Services: Biophysics Facility offers fluorometers as open-access instruments.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3226 Description: Some substances reemit light after Read More...

DCTD Tumor Repository
Frederick, MD

Repositories

Trans NIH Facility

The Developmental Therapeutics Program (DTP) within NCI's Division of Cancer Treatment and Diagnostics (DCTD), has maintained a low temperature repository of transplantable in vivo-derived tumors and in vitro-established tumor cell lines from various species. This Read More...

NCI LASP Animal Diagnostic Lab (ADL)
Frederick, MD

Core Facility

The Animal Diagnostic Laboratory (ADL) provides a full range of diagnostic capabilities, including microbiological cultures on various culture medium, microscopic screening for parasites such as mites and pinworms, molecular detection of pathogens, serological evaluation of 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...

NCI at Frederick Central Repository
Frederick, MD

Collaborative

Repositories

The Central Repository provides the research community at the NCI with various cryogenic services, including low-temperature storage from +4° C to -196° C, controlled-rate freezing, computerized inventory and distribution of samples. The Central Repository is operated Read More...

Software &amp; Techniques

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Confocal

Software Image Acquisition Commercial imaging systems of LRBGE Optical Microscopy Core are controlled by acquisition software specifically designed for the appropriate microscope, such as ZEN (Zeiss confocal microscopes), Nikon Elements (Nikon), Imspector (Abberior). Custom-built HILO Read More...

Microbiome Analysis with QIIME2: Beta Diversity

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Bioinformatics

Lesson 6 . Learning Objectives Introduce several beta diversity metrics Discover different ordination methods Learn about statistical methods that are applicable Beta diversity Beta diversity is between sample diversity. This is useful for answering the question, how Read More...

Bioinformatics for Beginners 2022: Alignment

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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...

Bioinformatics for Beginners 2022: B4b 2022 rnaseq jw

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Bioinformatics

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...

NIH Artificial Intelligence Symposium

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Bioinformatics

05/16/2025 - This one-day in-person NIH AI Symposium will bring together researchers from a broad range of disciplines to share their AI-related research, with the goal of disseminating the newest AI research, providing an opportunity to Read More...

Microscopy Image Analysis and Quantification Using MATLAB

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Bioinformatics

04/10/2025 - This one hour online training introduces participants to the tools and techniques for analyzing and quantifying microscopy images using MATLAB&rsquo;s low-code algorithms. Participants will learn how to preprocess images, segment regions Read More...

Microbiome Analysis with QIIME2: Statistics

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Bioinformatics

Some typical statitstical tests applied to beta diversity metrics include the following: Adonis (PERMANOVA) Similar to a MANOVA, but is permutational and non-parametric. Sensitive to group dispersion, so it is worth running alongside a beta-dispersion Read More...

Microbiome Analysis with QIIME2: Course Outline

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Bioinformatics

Work through DNAnexus? Find a nice cancer data set for 16S and shotgun Divide into two workshops or courses? Course structure or workshop structure? Amplicon processing and analysis (5 week course) (4 weeks) 1. Talk by Greg Caparaso? 1. Read More...

Microbiome Analysis with QIIME2: Microbiome Course

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Bioinformatics

Microbiome Course Course Outline Work through DNAnexus? Find a nice cancer data set for 16S and shotgun Divide into two workshops or courses? Course structure or workshop structure? Amplicon processing and analysis (5 week course) (4 weeks) 1. Read More...

Microbiome Analysis with QIIME2: Practice Lesson 4

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Bioinformatics

This practice lesson is associated with Lesson 4 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will work on filtering our feature table and representative sequences, classify our features, and generate a phylogenetic Read More...

Turning discovery into health with the spatial biology community

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Bioinformatics

10/03/2023 - Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Significant advances in the field now allow high-parameter data collection (60+ targets); however, considerable expertise and capital are needed to validate Read More...

Data Visualization with R: Using factors

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Bioinformatics

class(a1$dose) ## [1] "numeric" As it turns out, dose is really an experimental factor, so if we specify factor(dose) it will be interpreted as a categorical or discrete. Before fixing the x Read More...

Data Visualization with R: row-wise scaling

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Bioinformatics

Scaling is important during cluster analysis because it reduces the influence that variables with high magnitude values will have on distance. (https://medium.com/analytics-vidhya/why-is-scaling-required-in-knn-and-k-means-8129e4d88ed7). A common method for scaling is Read More...

STRIDES Initiative
Bethesda, MD

Trans NIH Facility

The Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative The STRIDES Initiative aims to help NIH and its institutes, centers, and offices (ICOs) accelerate biomedical research by reducing barriers in utilizing Read More...

CCR Genomics Technology Laboratory (GTL)
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...

Isothermal Titration Calorimetry (ITC) – iTC200

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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...

NIH AgingResearchBiobank
Bethesda, Maryland

Core Facility

Repositories

The AgingResearchBiobank was officially launched in January 2019 with a mission to provide a state-of-the-art inventory system for the storage, maintenance, and distribution of de-identified biospecimens and associated phenotypic, clinical, and imaging data from numerous NIA-funded 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...

Multi-Angle Light Scattering (MALS)

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

Bioinformatics for Beginners 2022: 18. BLAST copy

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Bioinformatics

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment and create a directory for today's work. conda activate bioinfo mkdir blast cd blast What is Read More...

Data Visualization with R: Lesson 4

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Bioinformatics

/* Whole document: */ body{ font-family: Times; font-size: 16pt; } Stat Transformations: Bar plots, box plots, and histograms Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar Read More...

Data Visualization with R: Lesson5

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Bioinformatics

Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn how to work with the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify to Read More...