|
0
|
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/ )
|
|
|
3
|
|
|
4
|
|
|
5 Prerequisites for installing cumme=Rbund:
|
|
|
6 The linux package: libxml2-dev
|
|
|
7 In ubuntu: sudo apt-get install libxml2-dev
|
|
|
8
|
|
|
9 R package: ggplot2
|
|
|
10 install.packages("ggplot2",dependencies = TRUE)
|
|
|
11
|
|
|
12 To install cummeRbund on your R server, follow the directions in:
|
|
|
13 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
|
|
|
14 source("http://bioconductor.org/biocLite.R")
|
|
|
15 biocLite("cummeRbund")
|
|
|
16
|
|
|
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
|
|
|
19
|
|
|
20
|
