Zobrazeno 1 - 10
of 120
pro vyhledávání: '"Grice EA"'
Autor:
Hannigan GD, not provided Meisel JS, not provided Tyldsley AS, not provided Zheng Q, not provided Hodkinson BP, not provided SanMiguel AJ, not provided Minot S, not provided Bushman FD, not provided Grice EA
This collection contains protocolsfor the computational analysis performed in the paper"The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome".Geoffrey Hannigan an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::844b81df0cbd19dfc6a66a497fac92e5
https://doi.org/10.17504/protocols.io.ekubcww
https://doi.org/10.17504/protocols.io.ekubcww
This section outlines the analyses we used in our replication cycle section of our report. We first predict how many contigs are potentially of the temperate replication cycle and display this information using a Euler diagram. We then use a relative
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0bf71112cef8c021bd7fd17d3548585f
https://doi.org/10.17504/protocols.io.ejfbcjn
https://doi.org/10.17504/protocols.io.ejfbcjn
This protocolsoutlines our definitions of core operational protein families (OPFs), potential auxiliary metabolic genes (AMGs), sharing of genes across anatomical sites, and Bray-Curtis dissimilarity of the OPFs by anatomical site. Based on methods f
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6d80ae58ba91e58d5483d9fbbe97dd28
https://doi.org/10.17504/protocols.io.ejkbckw
https://doi.org/10.17504/protocols.io.ejkbckw
This protocoloutlines how to generate tables to analyze CRISPR interactions. Based on methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enri
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d533cd3ce1e9a4fbe3e1152b01064f8f
https://doi.org/10.17504/protocols.io.ejqbcmw
https://doi.org/10.17504/protocols.io.ejqbcmw
This protocol outlines the analysis used to plot MEGAN taxonomic assignments. Based on the methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d7368e8cff631370a45f04c0d9270a6c
https://doi.org/10.17504/protocols.io.ejdbci6
https://doi.org/10.17504/protocols.io.ejdbci6
This protocoloutlines the beta-diversity analysis that we performed on the whole metagenome samples. We measured the signifiance of the dissimilarity between samples that were grouped by biological occlusion status, microenvironment (sebaceous, moist
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::62ac770b66fa5c94d87464f9285a9788
https://doi.org/10.17504/protocols.io.ejebcje
https://doi.org/10.17504/protocols.io.ejebcje
This protocoloutlines the analysis used to plot MetaPhlAn taxonomic assignments. Based on methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7081df81fd171504a2c3f3d09de5297e
https://doi.org/10.17504/protocols.io.ejbbcin
https://doi.org/10.17504/protocols.io.ejbbcin
This protocoloutlines the analysis used to plot KEGG functional annotation.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::bbc6e20be13791243d019e10b9b2242e
https://doi.org/10.17504/protocols.io.ejibcke
https://doi.org/10.17504/protocols.io.ejibcke
This protocoloutlines our analysis of the potential antibiotic resistance genes found within the skin virome. We start by visualizing the relative abundances of the top 10 antibiotic resistance categories (according to the CARD). We then quantify the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5e972805ff718188a24212b8987d6ca1
https://doi.org/10.17504/protocols.io.ejnbcme
https://doi.org/10.17504/protocols.io.ejnbcme
This protocoloutlines the Bray-Curtis dissimilarity NMDS ordination and significance analysis of our manuscript. Here we will look at the clustering of the virome samples using our reference independent OTU table based on contig hits. We will compare
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2e07dd409cc0c9c5edfc06f7970c14d2
https://doi.org/10.17504/protocols.io.einbcde
https://doi.org/10.17504/protocols.io.einbcde