plethy: management of whole body plethysmography data in R.
Identifieur interne : 000E25 ( PubMed/Corpus ); précédent : 000E24; suivant : 000E26plethy: management of whole body plethysmography data in R.
Auteurs : Daniel Bottomly ; Beth Wilmot ; Shannon K. McweeneySource :
- BMC bioinformatics [ 1471-2105 ] ; 2015.
English descriptors
- KwdEn :
- Animals, Birds, Computer Graphics, Coronavirus (genetics), Genome, Viral, Genomics, Influenza A virus (genetics), Influenza in Birds (virology), Mice, Mice, Inbred C57BL, Models, Statistical, Orthomyxoviridae Infections (virology), Phenotype, Plethysmography, Whole Body, Respiration (genetics), Severe Acute Respiratory Syndrome (virology), Software.
- MESH :
- genetics : Coronavirus, Influenza A virus, Respiration.
- virology : Influenza in Birds, Orthomyxoviridae Infections, Severe Acute Respiratory Syndrome.
- Animals, Birds, Computer Graphics, Genome, Viral, Genomics, Mice, Mice, Inbred C57BL, Models, Statistical, Phenotype, Plethysmography, Whole Body, Software.
Abstract
Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known as plethysmographs that can measure thoracic movement. One such approach (the Buxco platform) performs unrestrained whole body plethysmography on mice which infers thoracic movements from pressure differences from the act of inhalation and exhalation. While proprietary software is available to perform basic statistical analysis as part of machine's bundled software, it is desirable to be able to incorporate these analyses into high-throughput pipelines and integrate them with other data types, as well as leverage the wealth of analytic and visualization approaches provided by the R statistical computing environment.
DOI: 10.1186/s12859-015-0547-7
PubMed: 25924931
Links to Exploration step
pubmed:25924931Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">plethy: management of whole body plethysmography data in R.</title><author><name sortKey="Bottomly, Daniel" sort="Bottomly, Daniel" uniqKey="Bottomly D" first="Daniel" last="Bottomly">Daniel Bottomly</name><affiliation><nlm:affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. bottomly@ohsu.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Wilmot, Beth" sort="Wilmot, Beth" uniqKey="Wilmot B" first="Beth" last="Wilmot">Beth Wilmot</name><affiliation><nlm:affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. wilmotb@ohsu.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Mcweeney, Shannon K" sort="Mcweeney, Shannon K" uniqKey="Mcweeney S" first="Shannon K" last="Mcweeney">Shannon K. Mcweeney</name><affiliation><nlm:affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. mcweeney@ohsu.edu.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25924931</idno><idno type="pmid">25924931</idno><idno type="doi">10.1186/s12859-015-0547-7</idno><idno type="wicri:Area/PubMed/Corpus">000E25</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E25</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">plethy: management of whole body plethysmography data in R.</title><author><name sortKey="Bottomly, Daniel" sort="Bottomly, Daniel" uniqKey="Bottomly D" first="Daniel" last="Bottomly">Daniel Bottomly</name><affiliation><nlm:affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. bottomly@ohsu.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Wilmot, Beth" sort="Wilmot, Beth" uniqKey="Wilmot B" first="Beth" last="Wilmot">Beth Wilmot</name><affiliation><nlm:affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. wilmotb@ohsu.edu.</nlm:affiliation></affiliation></author><author><name sortKey="Mcweeney, Shannon K" sort="Mcweeney, Shannon K" uniqKey="Mcweeney S" first="Shannon K" last="Mcweeney">Shannon K. Mcweeney</name><affiliation><nlm:affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. mcweeney@ohsu.edu.</nlm:affiliation></affiliation></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Birds</term><term>Computer Graphics</term><term>Coronavirus (genetics)</term><term>Genome, Viral</term><term>Genomics</term><term>Influenza A virus (genetics)</term><term>Influenza in Birds (virology)</term><term>Mice</term><term>Mice, Inbred C57BL</term><term>Models, Statistical</term><term>Orthomyxoviridae Infections (virology)</term><term>Phenotype</term><term>Plethysmography, Whole Body</term><term>Respiration (genetics)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Software</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term><term>Influenza A virus</term><term>Respiration</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Influenza in Birds</term><term>Orthomyxoviridae Infections</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Birds</term><term>Computer Graphics</term><term>Genome, Viral</term><term>Genomics</term><term>Mice</term><term>Mice, Inbred C57BL</term><term>Models, Statistical</term><term>Phenotype</term><term>Plethysmography, Whole Body</term><term>Software</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known as plethysmographs that can measure thoracic movement. One such approach (the Buxco platform) performs unrestrained whole body plethysmography on mice which infers thoracic movements from pressure differences from the act of inhalation and exhalation. While proprietary software is available to perform basic statistical analysis as part of machine's bundled software, it is desirable to be able to incorporate these analyses into high-throughput pipelines and integrate them with other data types, as well as leverage the wealth of analytic and visualization approaches provided by the R statistical computing environment.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">25924931</PMID><DateCompleted><Year>2015</Year><Month>09</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><PubDate><Year>2015</Year><Month>Apr</Month><Day>29</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>plethy: management of whole body plethysmography data in R.</ArticleTitle><Pagination><MedlinePgn>134</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12859-015-0547-7</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known as plethysmographs that can measure thoracic movement. One such approach (the Buxco platform) performs unrestrained whole body plethysmography on mice which infers thoracic movements from pressure differences from the act of inhalation and exhalation. While proprietary software is available to perform basic statistical analysis as part of machine's bundled software, it is desirable to be able to incorporate these analyses into high-throughput pipelines and integrate them with other data types, as well as leverage the wealth of analytic and visualization approaches provided by the R statistical computing environment.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">This manuscript describes the plethy package which is an R/Bioconductor framework for pre-processing and analysis of plethysmography data with emphasis on larger scale longitudinal experiments. The plethy package was designed to facilitate quality control and exploratory data analysis. We provide a demonstration of the features of plethy using a dataset assessing the respiratory effects over time of SARS and Influenza infection in mice.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The plethy package provides functionality for users to import, perform quality assessment and exploratory data analysis in a manner that allows interoperability with existing modelling tools. Our package is implemented in R and is freely available as part of the Bioconductor project http://www.bioconductor.org/packages/release/bioc/html/plethy.html .</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bottomly</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. bottomly@ohsu.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wilmot</LastName><ForeName>Beth</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. wilmotb@ohsu.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McWeeney</LastName><ForeName>Shannon K</ForeName><Initials>SK</Initials><AffiliationInfo><Affiliation>Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. mcweeney@ohsu.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>1U19AI100625</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U54 AI081680</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>5P30CA069533</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>5U54AI081680</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>UL1 RR024140</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U19 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MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001717" MajorTopicYN="N">Birds</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003196" MajorTopicYN="Y">Computer Graphics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017934" MajorTopicYN="N">Coronavirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009980" MajorTopicYN="N">Influenza A virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005585" MajorTopicYN="N">Influenza in Birds</DescriptorName><QualifierName UI="Q000821" 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