apredeus/old_genequery

Old stand-alone application and web-server for GeneQuery, as well as source code for binary files. Preprocessing is available elsewhere.

Perl GeneQuery

This is the old version of our GeneQuery tool -both stand-alone used for bootstrapping and other applications, and web-server.

C code

The repository includes C code used to make two necessary binary files: fisher_test_right and normal_pval_left

Compiling commands:

gcc -std=c99 -O2 normal.c normal_pval_left.c -o normal_pval_left -lm

gcc -std=c99 -O2 fisher.c fisher_test_right.c -o fisher_test_right -lm

Perl requirements

CGI, File::Temp, HTML::Table

Necessary data

The datais of substantial size and thus are not deposited here (but are available upon request).

Includes:

• pre-made images for heatmaps - one per GSE
• databases in GSEXXX_GPLYYYModule#Gene_entrez_id format (1 line per gene)
• 3-column annotation for each GPL that's on the list - tab-separated probe ID, gene symbol, and Entrez ID