Load bioinformatics datasets into a local database
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vignette/sets
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DESCRIPTION
LICENSE
NAMESPACE
README.md

README.md

Once ingredients have been procured, they are shelved in the pantry ready for use.

Bioinformatics datasets are provided by a wide range of groups, in a wide range formats, and are rapidly changing. This is an opinionated guide to collect and curate data sets. It sets up a local database of datasets that can be used for an integrated analysis.

to install:

  1. Install a postgres database (http://www.postgresql.org/)

1a. Create the json file ~/.pantry_login that will be passed to dplyr::src_postgres to login ot the database. For example:

{ "dbname" : "<database name", "host" : "", "user" : "", "password" : "", "port" : }

  1. Install the package

install.packages("devtools")

devtools::install_github("momeara/BioChemPantry")

usage:

  1. Install datasets

library(BioChemPantry)

  1. Use datasets

    library(plyr) library(dplyr) library(BioChemPantry) pantry <- get_pantry(schema=)

    tbl <- pantry %>% schema_tbl("")

    a dplyr table