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branch: master

Feb 03, 2014

  1. al2na

    readme typo on master fixed

    authored February 03, 2014

Nov 26, 2013

  1. al2na

    Update DESCRIPTION

    authored November 26, 2013

Nov 20, 2013

  1. al2na

    Update DESCRIPTION

    working description
    authored November 20, 2013

Nov 18, 2013

  1. al2na

    Update README.md

    authored November 19, 2013
  2. al2na

    Merge branch 'master' into development

    merging with master
    authored November 19, 2013
  3. al2na

    changed readme

    authored November 19, 2013
  4. al2na

    replaced by development

    authored November 19, 2013
  5. al2na

    readme changed

    authored November 19, 2013
  6. al2na

    desc and readme changed

    authored November 19, 2013
  7. al2na

    changes to help

    authored November 18, 2013
  8. al2na

    -legend is optional for multiHeatMatrix

    authored November 18, 2013
  9. al2na

    -multiHeatMatrix does work when group is a factor

    - xlabels overlap with the tickmarks less
    - new argument, common.scale multiHeatMatrix
    authored November 18, 2013
  10. al2na

    -heatMatrix does return the clusters when kmeans=TRUE

    authored November 18, 2013
  11. al2na

    changes

    -version bump
    -heatMeta was not working with SM not it is
    -plotMeta works with xcoords when input is SM
    authored November 18, 2013

Nov 15, 2013

  1. al2na

    multiHeatMatrix now does return the correct order when Kmeans=TRUE an…

    …d order=TRUE
    authored November 15, 2013
  2. al2na

    Merge pull request #52 from frenkiboy/development

    Big one updated
    authored November 15, 2013
  3. frenkiboy

    readAnnotate.R:

    	- examples are done
    authored November 15, 2013
  4. frenkiboy

    scoreMatrixList.R:

    	- fixed the binMatrix for ScoreMatrixList
    authored November 15, 2013

Nov 14, 2013

  1. frenkiboy

    readAnnotate.R:

    	- added examples
    
    Vignette:
    	- removed par statements
    authored November 14, 2013
  2. frenkiboy

    Vignette:

    	- unable to position the wrapfigure
    authored November 14, 2013
  3. frenkiboy

    Vignette draft is done

    authored November 14, 2013

Nov 12, 2013

  1. frenkiboy

    Vignette in beta version.

    authored November 13, 2013
  2. frenkiboy

    readAnnotate.R:

    	- show:AnnotationByFeature, made the messages more understandable
    authored November 12, 2013
  3. frenkiboy

    readAnnotate.R:

    	- sorted the whitespace in the function
    authored November 12, 2013
  4. frenkiboy

    readAnnotate.R:

    	- annotateWithFeature: feature.name taken by default from
    	a variable
    authored November 12, 2013
  5. frenkiboy

    readAnnotate.R:

    	- plotGeneAnnotation now works with cluster=TRUE
    authored November 12, 2013
  6. frenkiboy

    NAMESPACE:

    	- randomEnrichment -> RandomEnrichment
    	- annotationByFeature -> AnnotationByFeature
    	- annotationByGeicParts -> AnnotationByGeneParts
    
    genomation-classes.R:
    	- randomEnrichment -> RandomEnrichment
    
    getRandomEnrichment.R:
    	- randomEnrichment -> RandomEnrichment
    	- getRandomEnrichment returned a list not an object
    authored November 12, 2013
  7. frenkiboy

    readAnnotate.R:

    genomation-classes.R:
    	- changed annotationByGenicParts -> AnnotationByGeneParts
    	- changed annotationByFeature -> AnnotationByFeature
    authored November 12, 2013
  8. frenkiboy

    readAnnotate.R:

    	annotateWithFeatureFlank
    	- sorted out chr -> chrs
    	- feature -> target in intersect.chr=TRUE
    	annotateWithFeature
    	- sorted out chr -> chrs
    	- feature -> target in intersect.chr=TRUE
    authored November 12, 2013
  9. frenkiboy

    NAMESPACE:

    	- added plotGeneAnnotation
    
    readAnnotate.R:
    	PlotGenicAnnotation
    	- plotGenicAnnotation -> plotGeneAnnotation
    	- plotGeneAnnotation works
    	- added intersect.chr to annotateWithGeneParts
    	- changed the GRangeList.obj variable to feature
    authored November 12, 2013
  10. frenkiboy

    genomation-classes.R:

    	- changed the order of annotationByGenicParts and
    	  annotationByFeature
    
    readAnnotate.R:
    	- annotateWithFeature: added intersect.chr
    authored November 12, 2013
  11. frenkiboy

    Moved the class definition from readAnnotate.R to genomation-classes.R

    authored November 12, 2013

Nov 11, 2013

  1. frenkiboy

    plotMatrix.R:

    	- changed GAGE -> CAGE typo
    
    tried to compile the vignette - did not work
    authored November 11, 2013
  2. frenkiboy

    scoreMatrixList.R:

    	- changed & -> && when testing for the file
    authored November 11, 2013
  3. frenkiboy

    DESCRIPTION:

    	- sorted the whitespace
    
    plotMatrix:
    	- removed the ifelse from the arguments and put it into function
    	  body
    
    readData:
    	- corrected meta.col -> meta.cols in readGeneric
    
    scoreMatrixList.R:
    	- changed target->targets
    authored November 11, 2013
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