A wrapper to FlyBase data
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README.md

rflybase

UPDATE as of 2016-10.15

This package has been rebooted. Access to the flybase Chado database (read only public copy) is done using RPostgreSQL. Functions are based on SQRL queries.

Info

FlyBase provides public read only access to our Chado database. It is not supposed to get intensive traffic. Please read the flybase instruction to downlaod the database for intense use. ftp://ftp.flybase.net/releases/FB2016_04/psql/README

Example of queries: http://gmod.org/wiki/FlyBase_Field_Mapping_Tables

Install

devtools::install_github("ropensci/rflybase")
library("rflybase")

setup connection to flybase database

conn <- fb_connect()

query

library("dplyr")
src <- fb_connect(dplyr = TRUE)
orgs <- src %>% tbl("organism")
orgs %>% filter(genus == "Antheraea")
## # Source:   lazy query [?? x 6]
## # Database: postgres 9.5.7 [flybase@chado.flybase.org:5432/flybase]
##    organism_id abbreviation     genus       species common_name comment
##          <int>        <chr>     <chr>         <chr>       <chr>   <chr>
##  1           8         <NA> Antheraea          jana        <NA>    <NA>
##  2           9         <NA> Antheraea       godmani        <NA>    <NA>
##  3          10         <NA> Antheraea       helferi        <NA>    <NA>
##  4          11         <NA> Antheraea kelimutuensis        <NA>    <NA>
##  5          12         <NA> Antheraea       larissa        <NA>    <NA>
##  6          13         <NA> Antheraea        lampei        <NA>    <NA>
##  7          14         <NA> Antheraea paukstadtorum        <NA>    <NA>
##  8          15         <NA> Antheraea      raffrayi        <NA>    <NA>
##  9          16         <NA> Antheraea    rosemariae        <NA>    <NA>
## 10          17         <NA> Antheraea        roylii        <NA>    <NA>
## # ... with more rows

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for rflybase in R doing citation(package = 'rflybase')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.