Mercurial > repos > jjohnson > cummerbund

comparison README @ 6:137aab1d9ac1

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add metadata to datatype: CuffDataDB
author Jim Johnson <jj@umn.edu>
date Mon, 18 Nov 2013 16:43:15 -0600
parents f109453ecfa2
children
comparison
equal deleted inserted replaced
5:2bb88bf1c1dd 6:137aab1d9ac1
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
20
21
22