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annotate README @ 4:57c13cd32044

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Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
author Jim Johnson <jj@umn.edu>
date Fri, 15 Nov 2013 13:42:58 -0600
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children 137aab1d9ac1
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1 CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
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2 ( http://compbio.mit.edu/cummeRbund/ )
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5 Prerequisites for installing cumme=Rbund:
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6 The linux package: libxml2-dev
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7 In ubuntu: sudo apt-get install libxml2-dev
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9 R package: ggplot2
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10 install.packages("ggplot2",dependencies = TRUE)
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12 To install cummeRbund on your R server, follow the directions in:
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13 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
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14 source("http://bioconductor.org/biocLite.R")
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15 biocLite("cummeRbund")
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17 This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an output that can be used directly in cummeRbund.
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f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
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f109453ecfa2 readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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