Mercurial > repos > jjohnson > cummerbund
comparison README @ 6:137aab1d9ac1
Add metadata to datatype: CuffDataDB
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 18 Nov 2013 16:43:15 -0600 |
parents | f109453ecfa2 |
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5:2bb88bf1c1dd | 6:137aab1d9ac1 |
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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. | 1 CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output. |
2 ( http://compbio.mit.edu/cummeRbund/ ) | 2 ( http://compbio.mit.edu/cummeRbund/ ) |
3 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html ) | |
3 | 4 |
4 | 5 |
5 Prerequisites for installing cumme=Rbund: | 6 Prerequisites for installing cummeRbund: |
6 The linux package: libxml2-dev | 7 The linux package: libxml2-dev |
7 In ubuntu: sudo apt-get install libxml2-dev | 8 In ubuntu: sudo apt-get install libxml2-dev |
8 | 9 |
9 R package: ggplot2 | 10 R package: ggplot2 |
10 install.packages("ggplot2",dependencies = TRUE) | 11 install.packages("ggplot2",dependencies = TRUE) |
12 To install cummeRbund on your R server, follow the directions in: | 13 To install cummeRbund on your R server, follow the directions in: |
13 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html ) | 14 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html ) |
14 source("http://bioconductor.org/biocLite.R") | 15 source("http://bioconductor.org/biocLite.R") |
15 biocLite("cummeRbund") | 16 biocLite("cummeRbund") |
16 | 17 |
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. | 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. |
19 This cuffdiff builds the cummeRbund database from the cuffdiff output files in the working directory which includes the run.info output, | |
20 thus it can populate the replicates information. | |
18 | 21 |
19 | 22 |
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