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Microarray-0.45
River stage one • 1 direct dependent • 1 total dependent

Changes for version 0.45

  • Updated Microarray, Microarray::File::Data and Microarray::File::Data:: modules to use a more sensible 'Plug-In' architecture
  • Updated Microarray, Microarray::Image, Microarray::Image::QC_Plots and Microarray::Image::CGH_Plot to correct gdFont issues with latest release of GD
  • Reorganised QC of spot data
    • now performed by the Reporter object, not the Microarray object
    • added method to reject unique spots after QC
    • QC variables are now stored in $ENV
  • Fixed many bugs
  • Added new tests
    • image plotting in Microarray.pm, which also tests some of the Microarray::Image::QC_Plots code as well
    • image plotting in Microarray::Image::CGH_Plot.pm
    • image plotting tests need extra test files downloadable from our web site - see ReadMe
    • Microarray::Reporter
  • Resolved some errors in Perldoc left over from earlier changes to module namespace
  • Other Perldoc changes/updates

Modules

Microarray
A Perl module for creating and manipulating DNA Microarray experiment objects
Microarray::Analysis
A Perl module for analysing microarray data
Microarray::Analysis::CGH
A Perl module for analysing CGH microarray data
Microarray::File
Perl objects for handling microarray file formats
Microarray::File::Clone_Locns
An object oriented Perl module describing a genomic clone location file
Microarray::File::Data
An object oriented Perl module describing microarray data files
Microarray::File::Data::Agilent
A Perl module for managing Agilent microarray files
Microarray::File::Data::BlueFuse
A Perl module for managing BlueFuse 'output' files
Microarray::File::Data::GenePix
A Perl module for managing microarray Axon GenePix data files
Microarray::File::Data::Manor_Output
A Perl module for managing 'Manor' clone and spot level output
Microarray::File::Data::Quantarray
A Perl module for managing Perkin Elmer 'Scanarray' microarray files
Microarray::File::GAL
A Perl module for managing microarray GAL file objects
Microarray::File::Image
Perl objects for handling microarray image file formats
Microarray::Image
A Perl module for creating microarray data plots
Microarray::Image::CGH_Plot
A Perl module for creating CGH-microarray data plots
Microarray::Image::QC_Plots
A Perl module for creating microarray QC/QA plots
Microarray::Reporter
A Perl module for creating and manipulating microarray reporter objects
Microarray::Spot
A Perl module for creating and manipulating microarray spot objects

Provides

agilent_file
in lib/Microarray/File/Data/Agilent.pm
analysis
in lib/Microarray/Analysis.pm
array_reporter
in lib/Microarray/Reporter.pm
array_spot
in lib/Microarray/Spot.pm
bluefuse_file
in lib/Microarray/File/Data/BlueFuse.pm
bluefuse_post_file
in lib/Microarray/File/Data/BlueFuse.pm
cgh_analysis
in lib/Microarray/Analysis/CGH.pm
cgh_plot
in lib/Microarray/Image/CGH_Plot.pm
chromosome_cgh
in lib/Microarray/Analysis/CGH.pm
clone_locn_file
in lib/Microarray/File/Clone_Locns.pm
data_file
in lib/Microarray/File/Data.pm
delimited_file
in lib/Microarray/File.pm
gal_file
in lib/Microarray/File/GAL.pm
genepix_file
in lib/Microarray/File/Data/GenePix.pm
genepix_image
in lib/Microarray/File/Data/GenePix.pm
genome_cgh
in lib/Microarray/Analysis/CGH.pm
genome_cgh_plot
in lib/Microarray/Image/CGH_Plot.pm
heatmap
in lib/Microarray/Image/QC_Plots.pm
intensity_heatmap
in lib/Microarray/Image/QC_Plots.pm
intensity_scatter
in lib/Microarray/Image/QC_Plots.pm
log2_heatmap
in lib/Microarray/Image/QC_Plots.pm
log_file
in lib/Microarray/File.pm
ma_plot
in lib/Microarray/Image/QC_Plots.pm
manor_clone_level
in lib/Microarray/File/Data/Manor_Output.pm
microarray
in lib/Microarray.pm
microarray_file
in lib/Microarray/File.pm
microarray_image_file
in lib/Microarray/File/Image.pm
microarray_text_file
in lib/Microarray/File.pm
plot
in lib/Microarray/Image.pm
quantarray_file
in lib/Microarray/File/Data/Quantarray.pm
quantarray_image
in lib/Microarray/File/Data/Quantarray.pm
ri_plot
in lib/Microarray/Image/QC_Plots.pm
simple_delimited_file
in lib/Microarray/File.pm

Other files