Title: | PR2 database with shiny web interface |
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Description: | PR2 database See https://pr2-database.org |
Authors: | Daniel Vaulot [cre, aut] |
Maintainer: | Daniel Vaulot <[email protected]> |
License: | MIT + file LICENSE |
Version: | 5.0.0 |
Built: | 2024-12-09 04:46:11 UTC |
Source: | https://github.com/pr2database/pr2database |
The PR2 database is provided as a data frame.
This is a join between the following tables:
pr2_main
pr2_taxonomy
pr2_sequence
pr2_metadata
pr2_traits
pr2_silva
euribo
The metadata contains different types of fields
gb_ : originating from the GenBank entry
eukref_ : annotated by the Eukref project
pr2_ : annotated by pr2 such latitude and longitude
eukribo_: information from the EukRibo database
Description of fields: https://pr2-database.org/documentation/pr2-fields
pr2_database()
pr2_database()
A data frame
# Read the whole database my_pr2 <- pr2_database() # Select a specific genus pr2_ostreo <- pr2_database() pr2_ostreo <- dplyr::filter(pr2_ostreo , genus == "Ostreococcus") pr2_ostreo <- dplyr::select(pr2_ostreo, pr2_accession, species) head(pr2_ostreo)
# Read the whole database my_pr2 <- pr2_database() # Select a specific genus pr2_ostreo <- pr2_database() pr2_ostreo <- dplyr::filter(pr2_ostreo , genus == "Ostreococcus") pr2_ostreo <- dplyr::select(pr2_ostreo, pr2_accession, species) head(pr2_ostreo)
The PR2 database taxonomy is provided as a data frame with the number of sequences for each taxon
pr2_taxonomy()
pr2_taxonomy()
A data frame
# Read the whole database taxonomy my_pr2_taxo <- pr2_taxonomy() # Select a specific genus my_pr2_taxo <- dplyr::filter( my_pr2_taxo , genus == "Ostreococcus") head(my_pr2_taxo)
# Read the whole database taxonomy my_pr2_taxo <- pr2_taxonomy() # Select a specific genus my_pr2_taxo <- dplyr::filter( my_pr2_taxo , genus == "Ostreococcus") head(my_pr2_taxo)
Allows to interact with the PR2 database:
* Select and visualize taxonomy * Select and download sequences based on length and sample type
run_app( onStart = NULL, options = list(), enableBookmarking = NULL, uiPattern = "/", ... )
run_app( onStart = NULL, options = list(), enableBookmarking = NULL, uiPattern = "/", ... )
onStart |
A function that will be called before the app is actually run.
This is only needed for |
options |
Named options that should be passed to the |
enableBookmarking |
Can be one of |
uiPattern |
A regular expression that will be applied to each |
... |
arguments to pass to golem_opts. See '?golem::get_golem_options' for more details. |