Mercurial > repos > mvdbeek > dapars

annotate README.md @ 6:1cc6c9e327fb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mvdbeek/dapars commit deab588a5d5ec7022de63a395fbd04e415ba0a42-dirty
author mvdbeek
date Thu, 29 Oct 2015 17:15:54 -0400
parents bb84ee2f2137
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
1 DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
2 ======
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
3
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
4 **Current version**: 0.9.1
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
5
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
6 [**Full Documentations**](http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html)
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
7 Description
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
8 -----
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
9 The dynamic usage of the 3’untranslated region (3’UTR) resulting from alternative polyadenylation (APA) is emerging as a pervasive mechanism for regulating mRNA diversity, stability and translation. Though RNA-seq provides the whole-transcriptome information and a lot of tools for analyzing gene/isoform expression are available, very few tool focus on the analysis of 3'UTR from standard RNA-seq. DaPars is the first de novo tool that directly infers the dynamic alternative polyadenylation (APA) usage by comparing standard RNA-seq. Given the annotated gene model, DaPars can infer the de novo proximal APA sites as well as the long and short 3'UTR expression levels. Finally, the dynamic APA usages between two conditions will be identified.
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
10
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
11
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
12
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
13 ![Flowchart](http://farm6.staticflickr.com/5533/12003068763_87e68075f6.jpg)
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
14 ![Cancer](http://farm8.staticflickr.com/7459/8858567224_4b0f0214cf.jpg)
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
15
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
16
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
17
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
18 Citation
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
19 -----
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
20 *Please cite the following articles if you use DaPars in your research*:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
21 * Masamha, C.P., Xia, Z., Yang, J., Albrecht, T.R., Li, M., Shyu, A., Li, W., Wagner, E.J. 2014. CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression. Nature, 510:412-416.
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
22
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
23 * Xia, Z., Donehower, L.A., Wheeler, D.A., Cooper, T.A., Neilson, J.R., Wagner E.J., Li, W. 2014. Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3'-UTR Landscape Across 7 Tumor Types. Nature Communications, 5:5274.
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
24
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
25 Mailing list
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
26 -----------
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
27 If you have questions, requests, or bugs to report, please email the [DaPars mailing list](https://groups.google.com/forum/#!forum/DaPars)
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
diff changeset
28