Mercurial > repos > jjohnson > cummerbund
annotate README @ 5:2bb88bf1c1dd
Add tool_data_table_conf.xml.sample
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 15 Nov 2013 14:13:14 -0600 |
| parents | f109453ecfa2 |
| children | 137aab1d9ac1 |
| rev | line source |
|---|---|
| 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 | |
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f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
21 |
|
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
22 |