Mercurial > repos > miller-lab > genome_diversity

comparison rank_pathways.xml @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
parents 184d14e4270d
children
comparison
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30:4188853b940b 31:a631c2f6d913
51 51
52 <outputs> 52 <outputs>
53 <data name="output" format="tabular" /> 53 <data name="output" format="tabular" />
54 </outputs> 54 </outputs>
55 55
56 <requirements>
57 <requirement type="package" version="0.2.5">mechanize</requirement>
58 <requirement type="package" version="1.8.1">networkx</requirement>
59 <requirement type="package" version="0.1.4">fisher</requirement>
60 </requirements>
61
62
56 <tests> 63 <tests>
57 <test> 64 <test>
58 </test> 65 </test>
59 </tests> 66 </tests>
60 67
62 69
63 **Dataset formats** 70 **Dataset formats**
64 71
65 The query dataset has a column containing ENSEMBL transcript codes for 72 The query dataset has a column containing ENSEMBL transcript codes for
66 the gene set of interest, while the background dataset has one column 73 the gene set of interest, while the background dataset has one column
67 with ENSEMBL transcript codes and another with GO terms, for some larger 74 with ENSEMBL transcript codes and another with KEGG pathways, for some larger
68 universe of genes. 75 universe of genes.
69 76
70 All of the input and output datasets are in tabular_ format. The input 77 All of the input and output datasets are in tabular_ format. The input
71 dataset (i.e. query) to rank by "percentage of genes affected" has a 78 dataset (i.e. query) to rank by "percentage of genes affected" has a
72 column containing ENSEMBL transcript codes for the gene set of interest, 79 column containing ENSEMBL transcript codes for the gene set of interest,