Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update

Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update

Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access...

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Bibliographic Details
Main Authors: Afgan, E. (Author), Blankenberg, D. (Author), Bouvier, D. (Author), Clements, D. (Author), Hillman-Jackson, J. (Author), Lariviere, D. (Author), Nekrutenko, A. (Author), Ostrovsky, A. (Author), Schatz, M.C (Author), Taylor, J. (Author), Team, T.G (Author)
Format: Article
Language:English
Published: Blackwell Publishing Inc. 2021
Subjects:
article
bioinformatics
biologist
biology
chromatin immunoprecipitation sequencing
computational biology
Computational Biology
data analysis
Data Analysis
exon
Galaxy
genome
Genome
genomics
Genomics
human
Humans
jumping
single cell RNA seq
single nucleotide polymorphism
software
Software
web application
Online Access:View Fulltext in Publisher
Description
Summary:Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web-based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high-capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping-off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Finding human coding exons with highest SNP density. Basic Protocol 2: Calling peaks for ChIP-seq data. Basic Protocol 3: Compare datasets using genomic coordinates. Basic Protocol 4: Working with multiple alignments. Basic Protocol 5: Single cell RNA-seq. © 2021 Wiley Periodicals LLC
ISBN:26911299 (ISSN)
DOI:10.1002/cpz1.31

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