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Need all_fasta.loc for cummerbund
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:39:39 -0500
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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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3 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
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6 Prerequisites for installing cummeRbund:
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7 The linux package: libxml2-dev
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8 In ubuntu: sudo apt-get install libxml2-dev
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10 R package: ggplot2
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11 install.packages("ggplot2",dependencies = TRUE)
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13 To install cummeRbund on your R server, follow the directions in:
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14 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
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15 source("http://bioconductor.org/biocLite.R")
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16 biocLite("cummeRbund")
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18 This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an SQLite data base output that can be used directly in cummeRbund.
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19 This cuffdiff builds the cummeRbund database from the cuffdiff output files in the working directory which includes the run.info output,
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20 thus it can populate the replicates information.
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