Metagenomic profile analysis of Mt. Erebus, Antarctica ...
This is a R markdown script and all necessary data to reproduce an analysis of publicly available and unrestricted metagenomes from the Integrated Microbial Genomes System (IMG-DOE). This analysis was used to place pfam-based functional profiles of microbial communities from Tramway Ridge, Mt. Erebu...
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Online Access: | https://dx.doi.org/10.5281/zenodo.10928973 https://zenodo.org/doi/10.5281/zenodo.10928973 |
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ftdatacite:10.5281/zenodo.10928973 2024-06-09T07:39:55+00:00 Metagenomic profile analysis of Mt. Erebus, Antarctica ... Herbold, Craig 2024 https://dx.doi.org/10.5281/zenodo.10928973 https://zenodo.org/doi/10.5281/zenodo.10928973 en eng Zenodo https://dx.doi.org/10.5281/zenodo.10928974 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 metagenome microbial ecology Ecosystems Microbiology FOS Biological sciences CreativeWork article Workflow 2024 ftdatacite https://doi.org/10.5281/zenodo.1092897310.5281/zenodo.10928974 2024-05-13T11:15:17Z This is a R markdown script and all necessary data to reproduce an analysis of publicly available and unrestricted metagenomes from the Integrated Microbial Genomes System (IMG-DOE). This analysis was used to place pfam-based functional profiles of microbial communities from Tramway Ridge, Mt. Erebus, Antarctica in context of other metagenomic datasets. Jaccard Presence-absence patterns were chosen to calculate dissimilarity because for many datasets, abundance information is not available. This also meant that the dataset needed to be filtered for both total length and total number of pfams detected to avoid a saturation effect, where the number of pfams detected approaches unity in extremely deeply sequenced or sufficiently large metagenomes. Finally, samples with a large median dissimilarity to all samples were removed. This dataset was classified by environment and examined for bulk distance (boxplots / Tukey's test) and relational distance between individual samples (PcoA and tSNE). ... Article in Journal/Newspaper Antarc* Antarctica DataCite Metadata Store (German National Library of Science and Technology) Tramway Ridge ENVELOPE(167.100,167.100,-77.517,-77.517) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
metagenome microbial ecology Ecosystems Microbiology FOS Biological sciences |
spellingShingle |
metagenome microbial ecology Ecosystems Microbiology FOS Biological sciences Herbold, Craig Metagenomic profile analysis of Mt. Erebus, Antarctica ... |
topic_facet |
metagenome microbial ecology Ecosystems Microbiology FOS Biological sciences |
description |
This is a R markdown script and all necessary data to reproduce an analysis of publicly available and unrestricted metagenomes from the Integrated Microbial Genomes System (IMG-DOE). This analysis was used to place pfam-based functional profiles of microbial communities from Tramway Ridge, Mt. Erebus, Antarctica in context of other metagenomic datasets. Jaccard Presence-absence patterns were chosen to calculate dissimilarity because for many datasets, abundance information is not available. This also meant that the dataset needed to be filtered for both total length and total number of pfams detected to avoid a saturation effect, where the number of pfams detected approaches unity in extremely deeply sequenced or sufficiently large metagenomes. Finally, samples with a large median dissimilarity to all samples were removed. This dataset was classified by environment and examined for bulk distance (boxplots / Tukey's test) and relational distance between individual samples (PcoA and tSNE). ... |
format |
Article in Journal/Newspaper |
author |
Herbold, Craig |
author_facet |
Herbold, Craig |
author_sort |
Herbold, Craig |
title |
Metagenomic profile analysis of Mt. Erebus, Antarctica ... |
title_short |
Metagenomic profile analysis of Mt. Erebus, Antarctica ... |
title_full |
Metagenomic profile analysis of Mt. Erebus, Antarctica ... |
title_fullStr |
Metagenomic profile analysis of Mt. Erebus, Antarctica ... |
title_full_unstemmed |
Metagenomic profile analysis of Mt. Erebus, Antarctica ... |
title_sort |
metagenomic profile analysis of mt. erebus, antarctica ... |
publisher |
Zenodo |
publishDate |
2024 |
url |
https://dx.doi.org/10.5281/zenodo.10928973 https://zenodo.org/doi/10.5281/zenodo.10928973 |
long_lat |
ENVELOPE(167.100,167.100,-77.517,-77.517) |
geographic |
Tramway Ridge |
geographic_facet |
Tramway Ridge |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
https://dx.doi.org/10.5281/zenodo.10928974 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_doi |
https://doi.org/10.5281/zenodo.1092897310.5281/zenodo.10928974 |
_version_ |
1801383068810870784 |