Mercurial > repos > jjohnson > cummerbund

annotate README @ 7:b5562b9a55c7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Use same bias_correction cached param as devteam cuffdiff
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:12:47 -0500
parents 137aab1d9ac1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
1 CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
2 ( http://compbio.mit.edu/cummeRbund/ )
6
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
3 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
4
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
5
6
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
6 Prerequisites for installing cummeRbund:
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
7 The linux package: libxml2-dev
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
8 In ubuntu: sudo apt-get install libxml2-dev
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
9
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
10 R package: ggplot2
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
11 install.packages("ggplot2",dependencies = TRUE)
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
12
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
13 To install cummeRbund on your R server, follow the directions in:
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
14 ( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
15 source("http://bioconductor.org/biocLite.R")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
16 biocLite("cummeRbund")
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
17
6
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
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.
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
19 This cuffdiff builds the cummeRbund database from the cuffdiff output files in the working directory which includes the run.info output,
137aab1d9ac1 Add metadata to datatype: CuffDataDB
Jim Johnson <jj@umn.edu>
parents: 3
diff changeset
20 thus it can populate the replicates information.
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
21
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
22