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Search Results for: Hu Mik Beta 1

Total Results Found: 40

Total Results Found: 40

Microbiome Analysis with QIIME2: Beta diversity

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Bioinformatics

Beta diversity is between sample diversity. This is useful for answering the question, how different are these microbial communities? Image modified from https://www.genome.gov/genetics-glossary/Microbiome Beta diversity is measured using distance and 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...

Microbiome Analysis with QIIME2: Learning Objectives

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Bioinformatics

Understand the difference between alpha and beta diversity Introduce several alpha diversity metrics Understand what rarefaction is and why it is important Introduce the debate regarding rarefaction and other methods of normalization Often many questions 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: Practice Lesson 6

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Bioinformatics

This practice lesson is associated with Lesson 6 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will view beta diversity results and determine whether our two conditions (old vs young) demonstrate significant differences Read More...

Biopharmaceutical Development Program (BDP)
Frederick, MD

Collaborative

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...

Microbiome Analysis with QIIME2: Other notable plugins

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Bioinformatics

DEICODE compositional beta diversity with biplots performs a Robust Aitchison PCA q2-clawback can improve taxonomic classifications uses taxonomic weights based on environment q2-picrust2 functional prediction from 16S rRNA data q2-sidle a new Read More...

Microbiome Analysis with QIIME2: Phylogeny

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Bioinformatics

In addition to clasifying our organisms, we also want to reconstruct their phylogenetic relationships by generating a phylogenetic tree. We often assume that phylogenetic closeness can elucidate commonalities in phenotypic properties / functions, so it is Read More...

BTEP Coding Club: Advantages of clusterProfiler

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Bioinformatics

ORA and GSEA support Functionality for multiple ontology and pathway databases Allows user defined databases and annotations, which is particularly useful for non-model organisms Easily compare functional profiles between treatments integrates the tidy philosophy complementary Read More...

Microbiome Analysis with QIIME2: What have we done?

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Bioinformatics

Using a small subset of data: Imported raw fastq files using qiime tools import . Data was paired-end CASAVA format. Checked for primers using qiime cutadapt trim-paired . Denoised with qiime dada2 denoise-paired and generated summaries of Read More...

Microbiome Analysis with QIIME 2

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Bioinformatics

10/19/2022 - Welcome to the Microbiome Analysis with QIIME 2 course series!                   This course series was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME 2 platform. Attendees will learn how to Read More...

Big Data In Immunology - sharing, dissemination, and repurposing

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Bioinformatics

12/04/2020 - Register Meeting ID: 161 756 1452 Passcode: 586729 One tap mobile +16692545252,,1617561452#,,,,,,0#,,586729# US (San Jose) +16468287666,,1617561452#,,,,,,0#,,586729# US (New York) Dial by your location +1 669 254 5252 US (San Jose) +1 646 828 7666 US (New York) Meeting ID: 161 756 1452 Passcode: 586729 Find your local number: https://nih.zoomgov.com/ Read More...

Single Cell RNA-Seq Trajectory Analysis in Partek Flow

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Bioinformatics

06/24/2020 - Join us for a webinar:  How to Analyze Single Cell RNA-Seq Data: Point, Click, Done Register:  https://www.partek.com/webinar/how-to-analyze-single-cell-rna-seq-data-point-click-done/ Single cell mRNA sequencing allows for the identification of different cell subtypes Read More...

BTEP Coding Club: Using Excel

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Bioinformatics

These questions can be answered in excel. However, the data would need to be reshaped. To see what I mean, let's take a brief look at the data in Excel. Notice that there are Read More...

Class Documents

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Bioinformatics

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...

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: Course Overview

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Bioinformatics

This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim sequences, denoise Read More...

Microbiome Analysis with QIIME2: Home

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Bioinformatics

Course Overview This course was designed to teach the basics of targeted amplicon data processing and analysis using the QIIME2 platform. Attendees will learn how to format data and metadata, import data, demultiplex sequences, trim 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...

Galaxy for Immunological and Infectious Disease Research

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Bioinformatics

09/04/2020 - Speakers: Dave Clements, Galaxy Community Manager, Johns Hopkins University, Steven Weaver, Senior Programmer Analyst, Temple University Galaxy is an open web-based platform for data integration and analysis in the life sciences. Galaxy makes sophisticated Read More...

ChIP-Seq Data Analysis Workshop (2-day)

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Bioinformatics

11/18/2014 - Day 1 - AM (9:30-12:30)  Introductory Lecture ( Peter FitzGerald, PhD - CCR, NCI ) Introduction Historical Perspective and Technical Variations Experimental methodology Comparison to ChIP-Chip Data Analysis Experimental Design Quality Control  Peak Calling (Different methodologies) Major Read More...

BTEP Coding Club: Reduce redundancy

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Bioinformatics

Because of the nature of GO, organized as a directed acyclic graph, parent terms can show enrichment due to over represented child terms. To reduce redundancy among enriched terms, clusterProfiler uses a simplify() function that Read More...

BTEP Coding Club: Return to R

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Bioinformatics

Let's reshape the data. I will rely heavily on dplyr functions to perform these tasks. First, I want to isolate the alpha chain and beta chain data. #isolate alpha and beta dfTRA< Read More...

BTEP Coding Club: Using <code>?enrichGO()</code>

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Bioinformatics

GO enrichment refers specifically to gene ontology. The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. --- https://www.ebi.ac.uk/ols/ Read More...

BTEP Coding Club: GSEA with GO

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Bioinformatics

As mentioned, clusterProfiler also includes GSEA functions for specific functional databases. For example, we can look at the enrichment of terms from the Gene Ontology Consortium (GO) using gseGO(). For this function, we need to Read More...

BTEP Video Archive of Past Classes

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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...

BTEP Coding Club: Results

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Bioinformatics

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