GEOmetadb-package         package:GEOmetadb         R Documentation

_Q_u_e_r_y _N_C_B_I _G_E_O _m_e_t_a_d_a_t_a _f_r_o_m _a _l_o_c_a_l _S_Q_L_i_t_e _d_a_t_a_b_a_s_e

_D_e_s_c_r_i_p_t_i_o_n:

     The NCBI Gene Expression Omnibus (GEO) represents the largest
     public repository of microarray data. However, finding data of
     interest can be challenging using current tools. GEOmetadb is an
     attempt to make access to the metadata associated with samples,
     platforms, and datasets much more feasible. This is accomplished
     by parsing all the NCBI GEO metadata into a SQLite database that
     can be stored and queried locally. GEOmetadb is simply a thin
     wrapper around the SQLite database along with associated
     documentation. Finally, the SQLite database is updated regularly
     as new data is added to GEO and can be downloaded at will for the
     most up-to-date metadata.

_D_e_t_a_i_l_s:


       Package:  GEOmetadb
       Type:     Package
       Version:  1.0.6
       Date:     2008-09-09
       License:  Artistic-2.0

_A_u_t_h_o_r(_s):

     Jack Zhu and Sean Davis

     Maintainer: Jack Zhu <zhujack@mail.nih.gov>

_R_e_f_e_r_e_n_c_e_s:

     http://meltzerlab.nci.nih.gov/apps/geo,
     http://gbnci.abcc.ncifcrf.gov/geo/

_E_x_a_m_p_l_e_s:

     if(file.exists('GEOmetadb.sqlite')) {
       a <- columnDescriptions()[1:5,]
       b <- geoConvert('GPL97','GSM')
     } else {
       print("use getSQLiteFile() to get a copy of the GEOmetadb SQLite file
     and then rerun the example")
     }

