Source code for Generating Medical Subject Heading Over-Representation Profiles
Python Shell Perl R
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direct_gd_predict
gene_parse
mesh_parse Added author and nr-chem build targets Sep 30, 2012
profile_gd_predict Merge ../digenei5 Sep 30, 2012
pubmed_parse Added author and nr-chem build targets Sep 30, 2012
sh Fixed extra space Mar 29, 2011
sql Added author and nr-chem build targets Sep 30, 2012
txt Added author and nr-chem build targets Sep 30, 2012
util Mode change Jan 6, 2011
ChangeLog Mode change Jan 6, 2011
LICENSE Mode change Jan 6, 2011
Makefile Added alternative gene subsets (e.g. Jaspar TFs) Jun 22, 2011
README.top Mode change Jan 6, 2011
config.default.mk Added author and nr-chem build targets Sep 30, 2012
startMake.sh Some updates for SGE with hard vmem limits Feb 23, 2012

README.top

Quick Start

1. Unpack source files into directory (or clone the git repository)
2. Copy ./config.default.mk to ./config.mk
3. Edit ./config.mk to point to pubmed and Entrez files
4. Make a subdirectory ./tmp/ if it does not exist

Top level README file

List of directory contents
(WIP)

mesh_parse/	parse the NIH Medical Subject Heading XML files