First, build the method-based summary file using the (method)_to_pairwise_summary.pl

Then, generate a venn of all comparisons using: venn_pairwise_summaries.pl --minFC 2 

# stats for agreement between methods.
venn_pairwise_summaries.pair_stats.pl  venn.min2fold.summary > venn.min2fold.summary.stats

# get those features where at least 2 DE progs agree:
c venn.min2fold.summary | perl -lane '@x = split(/,/, $F[3]); if (scalar @x > 1) { print;}' > venn.min2fold.summary.min2progsAgree 

# pull those corresponding records from the original pairwise summary files:
extract_venn_agree_from_summaries.pl venn.min2fold.summary.min2progsAgree EBSeq.pairwise.gene.post0.05.dat edgeR.genes.pairwise_summary.FDR0.05.dat MMDIFF.gene.pairwise_summary.PostProb0.2.dat > venn.min2fold.summary.min2progsAgree.all_summaries

# generate the multi-sample DE classifications:
pairwise_DE_summary_to_DE_classification.pl  venn.min2fold.summary.min2progsAgree.all_summaries
    generates: .class, .graph, and .class.prioritized


# get counts of enrichment categories (up and down)
add_counts_to_classes.pl venn.min2fold.summary.min2progsAgree.all_summaries.class > venn.min2fold.summary.min2progsAgree.all_summaries.class.wCounts.