rbbt-marq 1.0.0

data/lib/MARQ/score.rb

@@ -0,0 +1,395 @@
+require 'png'
+require 'inline'
+
+module Score
+  def self.combine(up, down)
+    return down if up == 0
+    return up if down == 0
+
+    return up - down
+    if (up > 0) == (down > 0)
+      return 0
+    else
+      up - down
+    end
+  end
+
+  def self.average(list)
+    clean = list.compact
+    clean.inject(0){|acc, e| acc += e}.to_f / clean.length
+  end
+
+  def self.score_area(positions, platform_entries, missing = 0)
+    return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?
+
+    clean_positions = positions.compact.sort
+
+    total_tags      = positions.length + missing
+    extra           = total_tags - clean_positions.length
+
+    top = 0
+    bottom = 0
+
+    clean_positions.each_with_index{|p,i|
+      rel_qt = (i + 1).to_f / total_tags
+      rel_qb = ( i + extra ).to_f / total_tags
+      rel_p  = p.to_f / platform_entries
+
+
+      top    += rel_qt - rel_p if rel_qt > rel_p
+      bottom += rel_p - rel_qb if rel_p > rel_qb
+    }
+
+
+    {
+      :top => top,
+      :bottom => bottom,
+      :score => top > bottom ? top.to_f / total_tags : - bottom.to_f / total_tags, 
+    }
+  end
+
+  def self.score_max_norm(positions, platform_entries, missing = 0)
+    return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?
+
+    clean_positions = positions.compact.sort
+
+    extra           = missing + (positions.length - clean_positions.length)
+    total_tags      = extra + clean_positions.length
+
+    mean = platform_entries / 2
+
+    values_top = [0]
+    values_bottom = [0]
+
+    clean_positions.each_with_index{|p,i| 
+      rel_qt = (i + 1).to_f / total_tags
+      rel_qb = ( i + extra ).to_f / total_tags
+      rel_p  = p.to_f / platform_entries
+
+
+      values_top << (rel_qt - rel_p) * ((p - mean).abs.to_f / mean)**2
+      values_bottom << (rel_p - rel_qb) * ((p - mean).abs.to_f / mean)**2
+    }
+
+    top    = values_top.max
+    bottom = values_bottom.max 
+
+
+    {
+      :score => top > bottom ? top : -bottom, 
+    }
+
+
+  end
+
+  def self.scale_score1(positions, platform_entries)
+
+    mean = platform_entries/2
+    max_top = 0
+    max_bottom = 0
+
+    top_list = []
+    bottom_list = []
+
+    weights = positions.sort.collect{|position| 
+      rel_pos = ((position - mean).abs.to_f / mean);
+      0.3 * rel_pos + 0.7 * Math::exp(30*rel_pos)/Math::exp(30)
+    }
+    weights.unshift(0)
+    total_weights = weights.inject(0){|v,acc| acc += v}
+    weights.collect!{|v| v / total_weights}
+
+    rel_qt = 0
+    rel_qb = 0
+    positions.sort.each_with_index{|position, idx|
+
+      rel_qt += weights[idx + 1] 
+      rel_qb += weights[idx]     
+      rel_p   = position.to_f    / platform_entries
+ 
+      top    = (rel_qt - rel_p);
+      bottom = (rel_p - rel_qb);
+
+      top_list << top
+      bottom_list << bottom
+
+      if (top > max_top) 
+        max_top = top;
+      end
+      if (bottom > max_bottom) 
+        max_bottom = bottom;
+      end
+    }
+
+    p [top_list, bottom_list]
+    if (max_top > max_bottom)
+      return max_top;
+    else
+      return -max_bottom;
+    end           
+  end
+  
+  class << self
+      inline do |builder|
+        builder.c_raw <<-'EOC'
+    double weight(int position, int mean){
+        double rel_pos = (double) abs(position - mean) / mean; 
+        double weight =  0.3 *  0.5 * rel_pos +  0.7 * (exp(30*rel_pos)/exp(30));
+        return(weight);
+    }
+        EOC
+        builder.c <<-'EOC'
+    double fast_score_scale( VALUE positions, int platform_entries, double missing){
+      int idx;
+    
+      int mean = platform_entries / 2;
+
+      VALUE rel_q = rb_ary_new();
+      VALUE rel_l = rb_ary_new();
+      
+      rb_ary_push(rel_q,rb_float_new(0));
+
+      double total_weights = 0;
+      for (idx = 0; idx < RARRAY(positions)->len; idx++){
+        int position = FIX2INT(rb_ary_entry(positions, idx));
+
+        rb_ary_push(rel_l, rb_float_new((double) position / platform_entries));
+
+        total_weights = total_weights + weight(position, mean);
+        rb_ary_push(rel_q,rb_float_new(total_weights));
+      }
+
+      // Add penalty for missing genes
+
+      double penalty = missing * weight( mean * 0.8,mean);
+      total_weights = total_weights + penalty;
+      
+      double max_top, max_bottom;
+      max_top = max_bottom = 0;
+      for (idx = 0; idx < RARRAY(positions)->len; idx++){
+        double top    = RFLOAT(rb_ary_entry(rel_q,idx + 1))->value / total_weights -
+                        RFLOAT(rb_ary_entry(rel_l,idx))->value;
+        double bottom = - (penalty + RFLOAT(rb_ary_entry(rel_q,idx))->value) / total_weights +
+                        RFLOAT(rb_ary_entry(rel_l,idx))->value;
+
+        if (top > max_top) max_top = top;
+        if (bottom > max_bottom) max_bottom = bottom;
+      }
+        
+     if (max_top > max_bottom) return max_top;
+     else                      return -max_bottom;
+    }
+
+        EOC
+
+
+
+        builder.c <<-'EOC'
+    double fast_norm_score( VALUE positions, int total, int extra, int platform_entries){
+      int idx;
+    
+      double mean = (double) platform_entries / 2;
+      double max_top, max_bottom;
+      max_top = max_bottom = 0;
+    
+      for (idx = 0; idx < RARRAY(positions)->len; idx++){
+        double position  = (double) FIX2INT(rb_ary_entry(positions, (long) idx));
+
+
+        double rel_qt = (double) (idx + 1)     / total;
+        double rel_qb = (double) (idx + extra) / total;
+        double rel_p  = position    / platform_entries;
+        
+        double scale = (abs(position - mean) / mean);
+        scale = scale * scale;
+
+        double top    = (rel_qt - rel_p) * scale;
+        double bottom = (rel_p - rel_qb) * scale;
+
+
+        if (top > max_top) max_top = top;
+        if (bottom > max_bottom) max_bottom = bottom;
+      }
+
+      if (max_top > max_bottom) return max_top;
+      else                      return -max_bottom;
+    }
+
+        EOC
+      end
+  end
+  def self.score_scale_fast(positions, platform_entries, missing=0)
+    return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?
+
+    clean_positions = positions.compact.sort
+    missing = missing + positions.length - clean_positions.length
+
+    {
+      :score => fast_score_scale(clean_positions,  platform_entries, missing)
+    }
+  end
+
+
+  def self.score_norm_fast(positions, platform_entries, missing = 0)
+    return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?
+
+    clean_positions = positions.compact.sort
+
+    extra           = missing + (positions.length - clean_positions.length)
+    total_tags      = extra + clean_positions.length
+
+    {
+      :score => fast_norm_score(clean_positions, total_tags, extra, platform_entries)
+    }
+  end
+
+  def self.score_max(positions, platform_entries, missing = 0)
+    return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?
+
+    clean_positions = positions.compact.sort
+
+    extra           = missing + (positions.length - clean_positions.length)
+    total_tags      = extra + clean_positions.length
+
+
+    values = [0]
+
+    clean_positions.each_with_index{|p,i| 
+      
+      up   = (i + 1).to_f / total_tags
+      down = p.to_f       / platform_entries
+
+      values << up - down
+    }
+
+    top    = values.max
+    bottom = values.min + ((extra - 1).to_f/ total_tags)
+
+
+    {
+      :score => top.abs > bottom.abs ? top : bottom, 
+    }
+  end
+
+  class << self
+    alias_method :score, :score_scale_fast
+  end
+
+
+  def self.score_up_down(up, down, total, missing_up = 0, missing_down = 0)
+    up = score(up, total, missing_up)
+    down = score(down, total, missing_down)
+
+    {:up =>  up[:score], :down => down[:score], :score => combine(up[:score], down[:score])}
+  end
+
+  def self.permutations(genes, total, times = 10000)
+    scores = []
+    times.times{
+      positions = Array.new(genes){ (rand * total).to_i }
+      scores << score(positions, total)[:score]
+    }
+    scores
+  end
+
+  def self.pvalues(scores, up, down, total, options = {})
+    times = options[:times]|| 1000
+
+    permutations_up = permutations(up, total, times)
+    permutations_down = permutations(down, total, times )
+    permutations = permutations_up.zip(permutations_down).collect{|p| combine(*p).abs }.sort
+
+    scores.collect{|score| 
+      num = permutations.count_smaller(score.abs)
+      (times - num).to_f / times
+    }
+  end
+
+  COLORS = {
+    :red =>   PNG::Color::Red,
+    :green => PNG::Color::Green,
+    :white => PNG::Color::White,
+    :black => PNG::Color::Black,
+
+  }
+
+  def self.draw_hits(hits, total, filename = nil, options = {})
+
+    size = options[:size] || total
+    bg_color = options[:bg_color] || :white
+    width = options[:width] || 20
+    sections = options[:sections] || []
+
+    size = [size, total].min
+
+    hits = hits.collect{|h| h - 1}
+    if size < total
+      hits = hits.collect{|h| (h.to_f * size / total).to_i}
+    end
+
+    canvas = PNG::Canvas.new size, width, COLORS[bg_color]
+
+    sections.each{|color, info|
+      start = info[0]
+      finish = info[1]
+      (start..finish).each{|x|
+        (0..width - 1).each{|y|
+          canvas[x,y] = COLORS[color]
+        }
+      }
+    }
+
+    hits.each{|hit|
+      canvas.line hit, 0, hit , width - 1, PNG::Color::Black
+    }
+
+    png = PNG.new canvas
+
+    if filename
+      png.save filename
+    else
+      png.to_blob
+    end
+  end
+end
+
+if __FILE__ == $0
+  size = 1000
+  positions=%w(10 30 200).collect{|v| v.to_i}
+  np = positions.collect{|p| size - p}
+  p Score.score(positions, size )
+  p Score.score(np, size )
+
+
+  p Score.scale_score1(positions,  size )
+  p Score.scale_score1(np,  size )
+
+  require 'benchmark'
+
+
+  p = (0..100).collect{ (rand * 1000).to_i}
+  puts Benchmark.measure{
+    1000.times{|i|
+      Score.score_max_norm(p, 1000);
+    }
+  }
+  puts Benchmark.measure{
+    1000.times{|i|
+      Score.score_max_norm_fast(p, 1000);
+    }
+  }
+
+
+  per_list = []
+  1000.times{
+    per_list << Array.new(200){(rand * 1000).to_i}
+  }
+
+  require 'benchmark'
+  puts Benchmark.measure{
+    per_list.each{|p|
+      Score.score_max_norm(p, 1000);
+    }
+  }
+
+end

data/tasks/install.rake

@@ -0,0 +1,21 @@
+require 'MARQ'
+
+$datadir = MARQ.datadir
+$scriptdir = File.join(MARQ.rootdir, '/install_scripts')
+
+task 'GEO' do |t|
+    directory = "#{$datadir}/GEO"
+    FileUtils.mkdir_p(directory)
+    %w(Rakefile series).each{|f|
+      FileUtils.cp_r File.join($scriptdir, "GEO/#{ f }"), directory 
+    }
+    FileUtils.mkdir(File.join(directory, "platforms")) unless File.exist? File.join(directory, "platforms")
+end
+
+task 'CustomDS' do |t|
+    directory = "#{$datadir}/CustomDS"
+    FileUtils.mkdir_p(directory)
+    Dir.glob($scriptdir + '/CustomDS/*').each{|f|
+      FileUtils.cp_r  f, directory 
+    }
+end

metadata

@@ -0,0 +1,588 @@
+--- !ruby/object:Gem::Specification 
+name: rbbt-marq
+version: !ruby/object:Gem::Version 
+  version: 1.0.0
+platform: ruby
+authors: 
+- Miguel Vazquez
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-11-10 00:00:00 +01:00
+default_executable: marq_config
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rbbt
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: rake
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: simpleconsole
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: DBcache
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: DRbServe
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+description: Find microarray experiments with similar or opposite signature to a given query. This gem contains the library, SOAP web server and web portal for the system.
+email: miguel.vazquez@fdi.ucm.es
+executables: 
+- marq_config
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- R/CustomDS.R
+- R/GEO.R
+- R/MA.R
+- bin/marq_config
+- install_scripts/CustomDS/Rakefile
+- install_scripts/GEO/Rakefile
+- install_scripts/GEO/platforms/GPL100.yaml
+- install_scripts/GEO/platforms/GPL1002.yaml
+- install_scripts/GEO/platforms/GPL1007.yaml
+- install_scripts/GEO/platforms/GPL101.yaml
+- install_scripts/GEO/platforms/GPL1010.yaml
+- install_scripts/GEO/platforms/GPL1073.yaml
+- install_scripts/GEO/platforms/GPL1074.yaml
+- install_scripts/GEO/platforms/GPL1090.yaml
+- install_scripts/GEO/platforms/GPL1104.yaml
+- install_scripts/GEO/platforms/GPL118.yaml
+- install_scripts/GEO/platforms/GPL1205.yaml
+- install_scripts/GEO/platforms/GPL1211.yaml
+- install_scripts/GEO/platforms/GPL1213.yaml
+- install_scripts/GEO/platforms/GPL1219.yaml
+- install_scripts/GEO/platforms/GPL1223.yaml
+- install_scripts/GEO/platforms/GPL1226.yaml
+- install_scripts/GEO/platforms/GPL1229.yaml
+- install_scripts/GEO/platforms/GPL1230.yaml
+- install_scripts/GEO/platforms/GPL1231.yaml
+- install_scripts/GEO/platforms/GPL1232.yaml
+- install_scripts/GEO/platforms/GPL1260.yaml
+- install_scripts/GEO/platforms/GPL1261.yaml
+- install_scripts/GEO/platforms/GPL127.yaml
+- install_scripts/GEO/platforms/GPL128.yaml
+- install_scripts/GEO/platforms/GPL1290.yaml
+- install_scripts/GEO/platforms/GPL1292.yaml
+- install_scripts/GEO/platforms/GPL1293.yaml
+- install_scripts/GEO/platforms/GPL1294.yaml
+- install_scripts/GEO/platforms/GPL1295.yaml
+- install_scripts/GEO/platforms/GPL13.yaml
+- install_scripts/GEO/platforms/GPL1310.yaml
+- install_scripts/GEO/platforms/GPL1313.yaml
+- install_scripts/GEO/platforms/GPL1323.yaml
+- install_scripts/GEO/platforms/GPL1331.yaml
+- install_scripts/GEO/platforms/GPL1352.yaml
+- install_scripts/GEO/platforms/GPL1355.yaml
+- install_scripts/GEO/platforms/GPL1382.yaml
+- install_scripts/GEO/platforms/GPL1387.yaml
+- install_scripts/GEO/platforms/GPL1397.yaml
+- install_scripts/GEO/platforms/GPL14.yaml
+- install_scripts/GEO/platforms/GPL1412.yaml
+- install_scripts/GEO/platforms/GPL1415.yaml
+- install_scripts/GEO/platforms/GPL1420.yaml
+- install_scripts/GEO/platforms/GPL144.yaml
+- install_scripts/GEO/platforms/GPL1449.yaml
+- install_scripts/GEO/platforms/GPL1458.yaml
+- install_scripts/GEO/platforms/GPL1523.yaml
+- install_scripts/GEO/platforms/GPL1524.yaml
+- install_scripts/GEO/platforms/GPL1528.yaml
+- install_scripts/GEO/platforms/GPL153.yaml
+- install_scripts/GEO/platforms/GPL1530.yaml
+- install_scripts/GEO/platforms/GPL1535.yaml
+- install_scripts/GEO/platforms/GPL155.yaml
+- install_scripts/GEO/platforms/GPL163.yaml
+- install_scripts/GEO/platforms/GPL168.yaml
+- install_scripts/GEO/platforms/GPL169.yaml
+- install_scripts/GEO/platforms/GPL1704.yaml
+- install_scripts/GEO/platforms/GPL1708.yaml
+- install_scripts/GEO/platforms/GPL1739.yaml
+- install_scripts/GEO/platforms/GPL1740.yaml
+- install_scripts/GEO/platforms/GPL1749.yaml
+- install_scripts/GEO/platforms/GPL177.yaml
+- install_scripts/GEO/platforms/GPL1790.yaml
+- install_scripts/GEO/platforms/GPL1792.yaml
+- install_scripts/GEO/platforms/GPL181.yaml
+- install_scripts/GEO/platforms/GPL1818.yaml
+- install_scripts/GEO/platforms/GPL1820.yaml
+- install_scripts/GEO/platforms/GPL1823.yaml
+- install_scripts/GEO/platforms/GPL1826.yaml
+- install_scripts/GEO/platforms/GPL183.yaml
+- install_scripts/GEO/platforms/GPL1831.yaml
+- install_scripts/GEO/platforms/GPL1833.yaml
+- install_scripts/GEO/platforms/GPL1872.yaml
+- install_scripts/GEO/platforms/GPL1911.yaml
+- install_scripts/GEO/platforms/GPL1914.yaml
+- install_scripts/GEO/platforms/GPL1928.yaml
+- install_scripts/GEO/platforms/GPL1942.yaml
+- install_scripts/GEO/platforms/GPL1945.yaml
+- install_scripts/GEO/platforms/GPL1964.yaml
+- install_scripts/GEO/platforms/GPL198.yaml
+- install_scripts/GEO/platforms/GPL1981.yaml
+- install_scripts/GEO/platforms/GPL200.yaml
+- install_scripts/GEO/platforms/GPL2006.yaml
+- install_scripts/GEO/platforms/GPL201.yaml
+- install_scripts/GEO/platforms/GPL2011.yaml
+- install_scripts/GEO/platforms/GPL2026.yaml
+- install_scripts/GEO/platforms/GPL205.yaml
+- install_scripts/GEO/platforms/GPL207.yaml
+- install_scripts/GEO/platforms/GPL2136.yaml
+- install_scripts/GEO/platforms/GPL220.yaml
+- install_scripts/GEO/platforms/GPL226.yaml
+- install_scripts/GEO/platforms/GPL24.yaml
+- install_scripts/GEO/platforms/GPL246.yaml
+- install_scripts/GEO/platforms/GPL247.yaml
+- install_scripts/GEO/platforms/GPL2507.yaml
+- install_scripts/GEO/platforms/GPL2529.yaml
+- install_scripts/GEO/platforms/GPL2531.yaml
+- install_scripts/GEO/platforms/GPL254.yaml
+- install_scripts/GEO/platforms/GPL2569.yaml
+- install_scripts/GEO/platforms/GPL257.yaml
+- install_scripts/GEO/platforms/GPL2598.yaml
+- install_scripts/GEO/platforms/GPL260.yaml
+- install_scripts/GEO/platforms/GPL2614.yaml
+- install_scripts/GEO/platforms/GPL2622.yaml
+- install_scripts/GEO/platforms/GPL2623.yaml
+- install_scripts/GEO/platforms/GPL2660.yaml
+- install_scripts/GEO/platforms/GPL2670.yaml
+- install_scripts/GEO/platforms/GPL2677.yaml
+- install_scripts/GEO/platforms/GPL2700.yaml
+- install_scripts/GEO/platforms/GPL2721.yaml
+- install_scripts/GEO/platforms/GPL2727.yaml
+- install_scripts/GEO/platforms/GPL273.yaml
+- install_scripts/GEO/platforms/GPL2763.yaml
+- install_scripts/GEO/platforms/GPL2824.yaml
+- install_scripts/GEO/platforms/GPL284.yaml
+- install_scripts/GEO/platforms/GPL287.yaml
+- install_scripts/GEO/platforms/GPL2872.yaml
+- install_scripts/GEO/platforms/GPL288.yaml
+- install_scripts/GEO/platforms/GPL2883.yaml
+- install_scripts/GEO/platforms/GPL289.yaml
+- install_scripts/GEO/platforms/GPL2895.yaml
+- install_scripts/GEO/platforms/GPL2897.yaml
+- install_scripts/GEO/platforms/GPL2902.yaml
+- install_scripts/GEO/platforms/GPL2987.yaml
+- install_scripts/GEO/platforms/GPL2995.yaml
+- install_scripts/GEO/platforms/GPL3039.yaml
+- install_scripts/GEO/platforms/GPL3050.yaml
+- install_scripts/GEO/platforms/GPL3084.yaml
+- install_scripts/GEO/platforms/GPL3113.yaml
+- install_scripts/GEO/platforms/GPL317.yaml
+- install_scripts/GEO/platforms/GPL319.yaml
+- install_scripts/GEO/platforms/GPL32.yaml
+- install_scripts/GEO/platforms/GPL3222.yaml
+- install_scripts/GEO/platforms/GPL3295.yaml
+- install_scripts/GEO/platforms/GPL3305.yaml
+- install_scripts/GEO/platforms/GPL3306.yaml
+- install_scripts/GEO/platforms/GPL3307.yaml
+- install_scripts/GEO/platforms/GPL333.yaml
+- install_scripts/GEO/platforms/GPL3341.yaml
+- install_scripts/GEO/platforms/GPL3349.yaml
+- install_scripts/GEO/platforms/GPL339.yaml
+- install_scripts/GEO/platforms/GPL340.yaml
+- install_scripts/GEO/platforms/GPL3408.yaml
+- install_scripts/GEO/platforms/GPL341.yaml
+- install_scripts/GEO/platforms/GPL3415.yaml
+- install_scripts/GEO/platforms/GPL3423.yaml
+- install_scripts/GEO/platforms/GPL3440.yaml
+- install_scripts/GEO/platforms/GPL3457.yaml
+- install_scripts/GEO/platforms/GPL3504.yaml
+- install_scripts/GEO/platforms/GPL3506.yaml
+- install_scripts/GEO/platforms/GPL355.yaml
+- install_scripts/GEO/platforms/GPL3558.yaml
+- install_scripts/GEO/platforms/GPL3607.yaml
+- install_scripts/GEO/platforms/GPL368.yaml
+- install_scripts/GEO/platforms/GPL3695.yaml
+- install_scripts/GEO/platforms/GPL371.yaml
+- install_scripts/GEO/platforms/GPL3834.yaml
+- install_scripts/GEO/platforms/GPL4006.yaml
+- install_scripts/GEO/platforms/GPL4055.yaml
+- install_scripts/GEO/platforms/GPL409.yaml
+- install_scripts/GEO/platforms/GPL4191.yaml
+- install_scripts/GEO/platforms/GPL4226.yaml
+- install_scripts/GEO/platforms/GPL4371.yaml
+- install_scripts/GEO/platforms/GPL4567.yaml
+- install_scripts/GEO/platforms/GPL4685.yaml
+- install_scripts/GEO/platforms/GPL483.yaml
+- install_scripts/GEO/platforms/GPL49.yaml
+- install_scripts/GEO/platforms/GPL50.yaml
+- install_scripts/GEO/platforms/GPL500.yaml
+- install_scripts/GEO/platforms/GPL507.yaml
+- install_scripts/GEO/platforms/GPL51.yaml
+- install_scripts/GEO/platforms/GPL513.yaml
+- install_scripts/GEO/platforms/GPL519.yaml
+- install_scripts/GEO/platforms/GPL52.yaml
+- install_scripts/GEO/platforms/GPL529.yaml
+- install_scripts/GEO/platforms/GPL53.yaml
+- install_scripts/GEO/platforms/GPL5356.yaml
+- install_scripts/GEO/platforms/GPL538.yaml
+- install_scripts/GEO/platforms/GPL54.yaml
+- install_scripts/GEO/platforms/GPL543.yaml
+- install_scripts/GEO/platforms/GPL544.yaml
+- install_scripts/GEO/platforms/GPL545.yaml
+- install_scripts/GEO/platforms/GPL546.yaml
+- install_scripts/GEO/platforms/GPL547.yaml
+- install_scripts/GEO/platforms/GPL549.yaml
+- install_scripts/GEO/platforms/GPL550.yaml
+- install_scripts/GEO/platforms/GPL56.yaml
+- install_scripts/GEO/platforms/GPL560.yaml
+- install_scripts/GEO/platforms/GPL564.yaml
+- install_scripts/GEO/platforms/GPL57.yaml
+- install_scripts/GEO/platforms/GPL570.yaml
+- install_scripts/GEO/platforms/GPL571.yaml
+- install_scripts/GEO/platforms/GPL576.yaml
+- install_scripts/GEO/platforms/GPL58.yaml
+- install_scripts/GEO/platforms/GPL5823.yaml
+- install_scripts/GEO/platforms/GPL59.yaml
+- install_scripts/GEO/platforms/GPL5915.yaml
+- install_scripts/GEO/platforms/GPL5947.yaml
+- install_scripts/GEO/platforms/GPL61.yaml
+- install_scripts/GEO/platforms/GPL64.yaml
+- install_scripts/GEO/platforms/GPL6419.yaml
+- install_scripts/GEO/platforms/GPL6424.yaml
+- install_scripts/GEO/platforms/GPL65.yaml
+- install_scripts/GEO/platforms/GPL6574.yaml
+- install_scripts/GEO/platforms/GPL6649.yaml
+- install_scripts/GEO/platforms/GPL67.yaml
+- install_scripts/GEO/platforms/GPL6720.yaml
+- install_scripts/GEO/platforms/GPL7054.yaml
+- install_scripts/GEO/platforms/GPL737.yaml
+- install_scripts/GEO/platforms/GPL738.yaml
+- install_scripts/GEO/platforms/GPL74.yaml
+- install_scripts/GEO/platforms/GPL75.yaml
+- install_scripts/GEO/platforms/GPL76.yaml
+- install_scripts/GEO/platforms/GPL764.yaml
+- install_scripts/GEO/platforms/GPL772.yaml
+- install_scripts/GEO/platforms/GPL782.yaml
+- install_scripts/GEO/platforms/GPL783.yaml
+- install_scripts/GEO/platforms/GPL784.yaml
+- install_scripts/GEO/platforms/GPL80.yaml
+- install_scripts/GEO/platforms/GPL81.yaml
+- install_scripts/GEO/platforms/GPL82.yaml
+- install_scripts/GEO/platforms/GPL83.yaml
+- install_scripts/GEO/platforms/GPL85.yaml
+- install_scripts/GEO/platforms/GPL86.yaml
+- install_scripts/GEO/platforms/GPL87.yaml
+- install_scripts/GEO/platforms/GPL870.yaml
+- install_scripts/GEO/platforms/GPL875.yaml
+- install_scripts/GEO/platforms/GPL884.yaml
+- install_scripts/GEO/platforms/GPL887.yaml
+- install_scripts/GEO/platforms/GPL89.yaml
+- install_scripts/GEO/platforms/GPL890.yaml
+- install_scripts/GEO/platforms/GPL891.yaml
+- install_scripts/GEO/platforms/GPL90.yaml
+- install_scripts/GEO/platforms/GPL91.yaml
+- install_scripts/GEO/platforms/GPL92.yaml
+- install_scripts/GEO/platforms/GPL920.yaml
+- install_scripts/GEO/platforms/GPL922.yaml
+- install_scripts/GEO/platforms/GPL924.yaml
+- install_scripts/GEO/platforms/GPL93.yaml
+- install_scripts/GEO/platforms/GPL96.yaml
+- install_scripts/GEO/platforms/GPL968.yaml
+- install_scripts/GEO/platforms/GPL97.yaml
+- install_scripts/GEO/platforms/GPL98.yaml
+- install_scripts/GEO/platforms/GPL981.yaml
+- install_scripts/GEO/platforms/GPL99.yaml
+- install_scripts/GEO/platforms/GPL999.yaml
+- install_scripts/GEO/series/GSE10018.yaml
+- install_scripts/GEO/series/GSE1002.yaml
+- install_scripts/GEO/series/GSE10066.yaml
+- install_scripts/GEO/series/GSE10073.yaml
+- install_scripts/GEO/series/GSE10091.yaml
+- install_scripts/GEO/series/GSE101.yaml
+- install_scripts/GEO/series/GSE10100.yaml
+- install_scripts/GEO/series/GSE10101.yaml
+- install_scripts/GEO/series/GSE10102.yaml
+- install_scripts/GEO/series/GSE10267.yaml
+- install_scripts/GEO/series/GSE10268.yaml
+- install_scripts/GEO/series/GSE10279.yaml
+- install_scripts/GEO/series/GSE103.yaml
+- install_scripts/GEO/series/GSE104.yaml
+- install_scripts/GEO/series/GSE10514.yaml
+- install_scripts/GEO/series/GSE10521.yaml
+- install_scripts/GEO/series/GSE10554.yaml
+- install_scripts/GEO/series/GSE1073.yaml
+- install_scripts/GEO/series/GSE10860.yaml
+- install_scripts/GEO/series/GSE10930.yaml
+- install_scripts/GEO/series/GSE10933.yaml
+- install_scripts/GEO/series/GSE10944.yaml
+- install_scripts/GEO/series/GSE10947.yaml
+- install_scripts/GEO/series/GSE10948.yaml
+- install_scripts/GEO/series/GSE11061.yaml
+- install_scripts/GEO/series/GSE11071.yaml
+- install_scripts/GEO/series/GSE11111.yaml
+- install_scripts/GEO/series/GSE11236.yaml
+- install_scripts/GEO/series/GSE11282.yaml
+- install_scripts/GEO/series/GSE11377.yaml
+- install_scripts/GEO/series/GSE11380.yaml
+- install_scripts/GEO/series/GSE11397.yaml
+- install_scripts/GEO/series/GSE11412.yaml
+- install_scripts/GEO/series/GSE11452.yaml
+- install_scripts/GEO/series/GSE11620.yaml
+- install_scripts/GEO/series/GSE11621.yaml
+- install_scripts/GEO/series/GSE11651.yaml
+- install_scripts/GEO/series/GSE11754.yaml
+- install_scripts/GEO/series/GSE11799.yaml
+- install_scripts/GEO/series/GSE11856.yaml
+- install_scripts/GEO/series/GSE11878.yaml
+- install_scripts/GEO/series/GSE11983.yaml
+- install_scripts/GEO/series/GSE12004.yaml
+- install_scripts/GEO/series/GSE12055.yaml
+- install_scripts/GEO/series/GSE12061.yaml
+- install_scripts/GEO/series/GSE12104.yaml
+- install_scripts/GEO/series/GSE12138.yaml
+- install_scripts/GEO/series/GSE12150.yaml
+- install_scripts/GEO/series/GSE12684.yaml
+- install_scripts/GEO/series/GSE12685.yaml
+- install_scripts/GEO/series/GSE1365.yaml
+- install_scripts/GEO/series/GSE1404.yaml
+- install_scripts/GEO/series/GSE1492.yaml
+- install_scripts/GEO/series/GSE15222.yaml
+- install_scripts/GEO/series/GSE1553.yaml
+- install_scripts/GEO/series/GSE1617.yaml
+- install_scripts/GEO/series/GSE1688.yaml
+- install_scripts/GEO/series/GSE1693.yaml
+- install_scripts/GEO/series/GSE1752.yaml
+- install_scripts/GEO/series/GSE1753.yaml
+- install_scripts/GEO/series/GSE1754.yaml
+- install_scripts/GEO/series/GSE1758.yaml
+- install_scripts/GEO/series/GSE1759.yaml
+- install_scripts/GEO/series/GSE1760.yaml
+- install_scripts/GEO/series/GSE1763.yaml
+- install_scripts/GEO/series/GSE1915.yaml
+- install_scripts/GEO/series/GSE1927.yaml
+- install_scripts/GEO/series/GSE1941.yaml
+- install_scripts/GEO/series/GSE1942.yaml
+- install_scripts/GEO/series/GSE1944.yaml
+- install_scripts/GEO/series/GSE1975.yaml
+- install_scripts/GEO/series/GSE20.yaml
+- install_scripts/GEO/series/GSE2107.yaml
+- install_scripts/GEO/series/GSE2159.yaml
+- install_scripts/GEO/series/GSE2246.yaml
+- install_scripts/GEO/series/GSE2263.yaml
+- install_scripts/GEO/series/GSE2267.yaml
+- install_scripts/GEO/series/GSE23.yaml
+- install_scripts/GEO/series/GSE2329.yaml
+- install_scripts/GEO/series/GSE2330.yaml
+- install_scripts/GEO/series/GSE2349.yaml
+- install_scripts/GEO/series/GSE2412.yaml
+- install_scripts/GEO/series/GSE2419.yaml
+- install_scripts/GEO/series/GSE2420.yaml
+- install_scripts/GEO/series/GSE2434.yaml
+- install_scripts/GEO/series/GSE2526.yaml
+- install_scripts/GEO/series/GSE2579.yaml
+- install_scripts/GEO/series/GSE2806.yaml
+- install_scripts/GEO/series/GSE2831.yaml
+- install_scripts/GEO/series/GSE2832.yaml
+- install_scripts/GEO/series/GSE29.yaml
+- install_scripts/GEO/series/GSE3006.yaml
+- install_scripts/GEO/series/GSE3043.yaml
+- install_scripts/GEO/series/GSE3122.yaml
+- install_scripts/GEO/series/GSE3130.yaml
+- install_scripts/GEO/series/GSE3151.yaml
+- install_scripts/GEO/series/GSE3160.yaml
+- install_scripts/GEO/series/GSE3190.yaml
+- install_scripts/GEO/series/GSE3205.yaml
+- install_scripts/GEO/series/GSE3206.yaml
+- install_scripts/GEO/series/GSE3315.yaml
+- install_scripts/GEO/series/GSE3335.yaml
+- install_scripts/GEO/series/GSE34.yaml
+- install_scripts/GEO/series/GSE3470.yaml
+- install_scripts/GEO/series/GSE35.yaml
+- install_scripts/GEO/series/GSE3503.yaml
+- install_scripts/GEO/series/GSE3683.yaml
+- install_scripts/GEO/series/GSE3684.yaml
+- install_scripts/GEO/series/GSE3685.yaml
+- install_scripts/GEO/series/GSE3686.yaml
+- install_scripts/GEO/series/GSE3687.yaml
+- install_scripts/GEO/series/GSE3802.yaml
+- install_scripts/GEO/series/GSE3803.yaml
+- install_scripts/GEO/series/GSE3804.yaml
+- install_scripts/GEO/series/GSE3805.yaml
+- install_scripts/GEO/series/GSE3813.yaml
+- install_scripts/GEO/series/GSE3814.yaml
+- install_scripts/GEO/series/GSE3815.yaml
+- install_scripts/GEO/series/GSE3817.yaml
+- install_scripts/GEO/series/GSE3818.yaml
+- install_scripts/GEO/series/GSE3819.yaml
+- install_scripts/GEO/series/GSE3820.yaml
+- install_scripts/GEO/series/GSE3821.yaml
+- install_scripts/GEO/series/GSE3844.yaml
+- install_scripts/GEO/series/GSE3853.yaml
+- install_scripts/GEO/series/GSE3935.yaml
+- install_scripts/GEO/series/GSE3969.yaml
+- install_scripts/GEO/series/GSE4049.yaml
+- install_scripts/GEO/series/GSE4144.yaml
+- install_scripts/GEO/series/GSE4261.yaml
+- install_scripts/GEO/series/GSE4295.yaml
+- install_scripts/GEO/series/GSE4398.yaml
+- install_scripts/GEO/series/GSE4719.yaml
+- install_scripts/GEO/series/GSE4720.yaml
+- install_scripts/GEO/series/GSE4721.yaml
+- install_scripts/GEO/series/GSE4807.yaml
+- install_scripts/GEO/series/GSE4826.yaml
+- install_scripts/GEO/series/GSE4934.yaml
+- install_scripts/GEO/series/GSE5027.yaml
+- install_scripts/GEO/series/GSE5070.yaml
+- install_scripts/GEO/series/GSE5238.yaml
+- install_scripts/GEO/series/GSE5267.yaml
+- install_scripts/GEO/series/GSE5281.yaml
+- install_scripts/GEO/series/GSE5290.yaml
+- install_scripts/GEO/series/GSE5376.yaml
+- install_scripts/GEO/series/GSE5575.yaml
+- install_scripts/GEO/series/GSE5835.yaml
+- install_scripts/GEO/series/GSE5836.yaml
+- install_scripts/GEO/series/GSE5837.yaml
+- install_scripts/GEO/series/GSE5938.yaml
+- install_scripts/GEO/series/GSE600.yaml
+- install_scripts/GEO/series/GSE6018.yaml
+- install_scripts/GEO/series/GSE6066.yaml
+- install_scripts/GEO/series/GSE6067.yaml
+- install_scripts/GEO/series/GSE6068.yaml
+- install_scripts/GEO/series/GSE6070.yaml
+- install_scripts/GEO/series/GSE6071.yaml
+- install_scripts/GEO/series/GSE6072.yaml
+- install_scripts/GEO/series/GSE6101.yaml
+- install_scripts/GEO/series/GSE6111.yaml
+- install_scripts/GEO/series/GSE6190.yaml
+- install_scripts/GEO/series/GSE6277.yaml
+- install_scripts/GEO/series/GSE6331.yaml
+- install_scripts/GEO/series/GSE6346.yaml
+- install_scripts/GEO/series/GSE6358.yaml
+- install_scripts/GEO/series/GSE6405.yaml
+- install_scripts/GEO/series/GSE6450.yaml
+- install_scripts/GEO/series/GSE6687.yaml
+- install_scripts/GEO/series/GSE6705.yaml
+- install_scripts/GEO/series/GSE6801.yaml
+- install_scripts/GEO/series/GSE6847.yaml
+- install_scripts/GEO/series/GSE6870.yaml
+- install_scripts/GEO/series/GSE7103.yaml
+- install_scripts/GEO/series/GSE7140.yaml
+- install_scripts/GEO/series/GSE7188.yaml
+- install_scripts/GEO/series/GSE7261.yaml
+- install_scripts/GEO/series/GSE7337.yaml
+- install_scripts/GEO/series/GSE7338.yaml
+- install_scripts/GEO/series/GSE7362.yaml
+- install_scripts/GEO/series/GSE7369.yaml
+- install_scripts/GEO/series/GSE7525.yaml
+- install_scripts/GEO/series/GSE7537.yaml
+- install_scripts/GEO/series/GSE7645.yaml
+- install_scripts/GEO/series/GSE7660.yaml
+- install_scripts/GEO/series/GSE7820.yaml
+- install_scripts/GEO/series/GSE79.yaml
+- install_scripts/GEO/series/GSE8035.yaml
+- install_scripts/GEO/series/GSE8088.yaml
+- install_scripts/GEO/series/GSE8089.yaml
+- install_scripts/GEO/series/GSE8111.yaml
+- install_scripts/GEO/series/GSE8237.yaml
+- install_scripts/GEO/series/GSE8326.yaml
+- install_scripts/GEO/series/GSE8399.yaml
+- install_scripts/GEO/series/GSE850.yaml
+- install_scripts/GEO/series/GSE8506.yaml
+- install_scripts/GEO/series/GSE8542.yaml
+- install_scripts/GEO/series/GSE8558.yaml
+- install_scripts/GEO/series/GSE8559.yaml
+- install_scripts/GEO/series/GSE8613.yaml
+- install_scripts/GEO/series/GSE8629.yaml
+- install_scripts/GEO/series/GSE8729.yaml
+- install_scripts/GEO/series/GSE8761.yaml
+- install_scripts/GEO/series/GSE8765.yaml
+- install_scripts/GEO/series/GSE8805.yaml
+- install_scripts/GEO/series/GSE8825.yaml
+- install_scripts/GEO/series/GSE8895.yaml
+- install_scripts/GEO/series/GSE8897.yaml
+- install_scripts/GEO/series/GSE8898.yaml
+- install_scripts/GEO/series/GSE8900.yaml
+- install_scripts/GEO/series/GSE8982.yaml
+- install_scripts/GEO/series/GSE920.yaml
+- install_scripts/GEO/series/GSE960.yaml
+- install_scripts/GEO/series/GSE961.yaml
+- install_scripts/GEO/series/GSE962.yaml
+- install_scripts/GEO/series/GSE963.yaml
+- install_scripts/GEO/series/GSE964.yaml
+- install_scripts/GEO/series/GSE965.yaml
+- install_scripts/GEO/series/GSE966.yaml
+- install_scripts/GEO/series/GSE993.yaml
+- lib/MARQ.rb
+- lib/MARQ/CustomDS.rb
+- lib/MARQ/GEO.rb
+- lib/MARQ/ID.rb
+- lib/MARQ/MADB.rb
+- lib/MARQ/annotations.rb
+- lib/MARQ/fdr.rb
+- lib/MARQ/main.rb
+- lib/MARQ/rankproduct.rb
+- lib/MARQ/score.rb
+- tasks/install.rake
+- LICENSE
+- README.rdoc
+has_rdoc: true
+homepage: http://github.com/mikisvaz/rbbt-marq
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: MicroArray Rank Query
+test_files: []
+