Tools BASE Plug-ins
BASE Plug-ins
LCB has created plugins for BASE and the LCB Datawarehouse. Since it is based on open-source code, the product is open-source as well. Note that the code requires a recent installation of BASE and other software as described in the included README file. They are NOT meant to be run as stand-alone applications.

Plug-in: plugins060918.zip (75k)
Date: 2006-09-18
Version: 5.01
Creator: Adam Ameur
Support: LCBDWH Team
Description: Please see all the details in the README file.

Plug-in: plugins.tar.gz (28k)
Date: 2005-11-14
Version: 4.01
Creator: Adam Ameur
Support: LCBDWH Team
Description: Please see all the details in the README and change.log files provided within this plug-in distribution.

Plug-in: R-plugins_lcb_v1.01.tar.gz (13k)
Date: 2004-03-17
Version: 1.01
Creator: Ola Spjuth
Support: LCBDWH Team
Description: Please see all the details in the readme.txt and change.log files provided within this plug-in distribution.

Plug-in: R-plugins_lcb_v0.93.tar.gz (10k)
Date: 2003-09-29
Creator: Ola Spjuth
Description:
  • R: Arrayplots
    Creates several types of plots using LIMMA and SMA
    Featured plots: Imageplot, Boxplot, Background plots, MA-plot with print-tip loess curves, Densityplots, Overall Boxplots
    Options to filter out flagged spots of desired value and/or subtract local background
  • R: Normalizations
    Normalization using R functions from Bioconductor(LIMMA) and SMA.
    Featured normalization methods: None, Median, Loess, Printtiploess, Composite, RobustSplines
    Options to filter out flagged spots of desired value and/or subtract local background
  • R: Normalization between arrays
    Normalization between arrays (scaling) using R functions from Bioconductor(LIMMA).
  • R: B-statistics
    Calculates B-statistics, t-statistics, and p-value for ranking genes
    Produces graphs and a ranked list of reporters based on B-statistics using Bioconductor(LIMMA)and SMA.
    Features plots: QQT plot, B-stat plot with geneNames, B-stat plot with reporterID
  • R: B-statistics with dupcor
    Calculates B-statistics, t-statistics, and p-value for ranking genes with correction of duplicates (dupcor)
    Produces graphs and a ranked list of reporters based on B-statistics using Bioconductor(LIMMA)and SMA.
    Features plots: QQT plot, B-stat plot with geneNames, B-stat plot with reporterID

    Files included Description
    base_R.plPerl-script for executing R-scripts from BASE
    parse.basefile.R Functions for reading/writing BASEfiles within R
    arrayplots.R R-script for constructing various Array plots
    rnorm.R R-script using Bioconductor(LIMMA) functions to normalize 2ch arrays
    rnorm.betw.arr.RR-script using Bioconductor(LIMMA) functions to normalize between arrays
    bstat.RR-script using Bioconductor(LIMMA) functions to rank genes by B-statistics
    bstat.dupcor.R R-script using Bioconductor(LIMMA) functions to rank genes by B-statistics with duplicate correction (dupcor)
    arrayplots.basePlugin definition file
    rnorm.basePlugin definition file
    rnorm.btw.arr.base Plugin definition file
    bstat.base Plugin definition file
    bstat.dupcor.basePlugin definition file
    readme.txtThis file


    Plug-in: base_r-plugins_lcb_v081.tar.gz (6k)
    Date: 2003-08-14
    Creator: Ola Spjuth

    Files included Description
    base_R.pl Perl-script for executing R-scripts from BASE
    parse.basefile.R Functions for reading/writing BASEfiles
    arrayplots.R R-script for constructing various Array plots
    rnorm.R R-script using Bioconductor(LIMMA) functions to normalize 2ch arrays
    arrayplots.base Plugin definition file
    rnorm.base Plugin definition file

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