antarctica: Specificity results from Antarctic cryoconite holes

In darcyj/specificity.shiny: Interactive Visualization for package `specificity`

Description

A dataset containing a specs list (a named list of outputs from specificity::phy_or_env_spec), and taxonomic information for each feature (bacterial OTU) within the specs list.

Usage

antarctica

Format

A list containing 2 objects:

antarctica_specs_list:

A list of outputs from specificity::phy_or_env_spec(), with entries for Nitrogen ("N"), Phosphorus ("P"), geographic distance ("Geo"), fungal beta-diversity ("Fungi"), and algal beta-diversity ("Algae").

antarctica_taxonomy:

data.frame object containing taxonomic information for the species in antarctica_specs_list. Columns are as follows:

Columns in antarctica_taxonomy:

id:

species identity. corresponds to rownames in antarctica_specs_list.

eval:

e-value from BLAST, which was used to assign taxonomy from the greengenes database.

hit:

identity of the closest match within the greengenes database.

k:

kingdom-level taxonomy

p:

phylum-level taxonomy

c:

class-level taxonomy

o:

order-level taxonomy

f:

family-level taxonomy

g:

genus-level taxonomy

s:

species-level taxonomy

Source

Sommers et al. (2019) Comparison of microbial communities in the sediments and water columns of frozen cryoconite holes in the McMurdo Dry Valleys, Antarctica. Front Microbiol 10(65) https://doi.org/10.3389/fmicb.2019.00065

darcyj/specificity.shiny documentation built on Dec. 19, 2021, 8:11 p.m.