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Edited wrappers for R scripts #81

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Edited wrappers for R scripts #81

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Commits on Apr 8, 2017

  1. edited wrapper for enrichment to use the r script; renamed wrapper ac… 

    …cordingly
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  2. added r script to perform overrepresentation and gse analysis (using … 

    …clusterProfiler package)
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  3. modified name of second column from weight to value

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  4. minor change

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  5. added r script to perform overrepresentation and gse analysis with KE… 

    …GG (using clusterProfiler package)
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  6. added r script to perform overrepresentation and gse analysis with KE… 

    …GG (using clusterProfiler package)
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  7. edited wrapper to remove pacman package from requirements

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  8. edited wrapper to remove pacman package from requirements

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  9. renamed and modified wrapper to compile networw with STRINGdb which n… 

    …ow calls the r script directly (instead of calling r script from MultiPEN)
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  10. r script to use STRINGdb to compile a network from a list of genes

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  11. renamed and modified wrapper to compile networw with STRINGdb which n… 

    …ow calls the r script directly (instead of calling r script from MultiPEN)
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  12. removed duplicated wrapper

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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  13. edit Rscript-STRINGdb-network.xml file: minor edits to help section

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 8, 2017
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Commits on Apr 10, 2017

  1. edited Rscript-enrichment-GO.xml to add references to gene ontology

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 10, 2017
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  2. edited Rscript-enrichment-GO.xml to add references to KEGG

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 10, 2017
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  3. edited Rscript-STRINGdb-network.xml to expand help on input for speci… 

    …es code
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 10, 2017
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  4. edited compileNetworkStringDB.R: added licence information, reference… 

    …s, description of inputs and how to run Rscript
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 10, 2017
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Commits on Apr 17, 2017

  1. modified IDs to be lower case

    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 17, 2017
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  2. modified MultiPEN-feature-selectiom.xml to include string with option… 

    …al parameters for log2 transform, z-scores, decision threshold, max number of iterations
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 17, 2017
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  3. modified MultiPEN-feature-selectiom.xml to include string with option… 

    …al parameters for log2 transform, z-scores, decision threshold, max number of iterations; optional string is also added at the end of all output file name
    @PerlaTroncosoRey
    PerlaTroncosoRey committed Apr 17, 2017
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Commits on Jul 10, 2017

  1. Update Rscript-enrichment-KEGG.xml

    @wjurkowski
    wjurkowski authored Jul 10, 2017
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  2. Update MultiPEN-feature-selection.xml

    @wjurkowski
    wjurkowski authored Jul 10, 2017
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  3. fixes to R script and MultiPEN wrappers

    @wjurkowski
    wjurkowski committed Jul 10, 2017
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  4. fixes to R script wrapper

    @wjurkowski
    wjurkowski committed Jul 10, 2017
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Commits on Aug 18, 2017

  1. Fixes for stringdb-network tool

    @nsoranzo
    nsoranzo committed Aug 18, 2017
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  2. Rename tool XML file same as tool id

    @nsoranzo
    nsoranzo committed Aug 18, 2017
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  3. Fix file permissions

    @nsoranzo
    nsoranzo committed Aug 18, 2017
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