Name: Galaxy
Owner: modENCODE-DCC
Description: modENCODE Galaxy on Amazon Cloud
Created: 2012-12-09 21:44:49.0
Updated: 2016-04-29 15:47:58.0
Pushed: 2014-11-13 14:31:16.0
Size: 87312
Language: Shell
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| Björn Grüning | 2014-11-12 23:04:33.0 | 13 |
| Quang Trinh | 2014-11-13 14:31:16.0 | 116 |
| ziruzhou | 2012-12-13 16:44:23.0 | 7 |
| rssetia | 2013-06-21 21:10:24.0 | 13 |
| Fei-Yang Jen | 2013-04-17 16:58:11.0 | 208 |
Other Committers
| User | Most Recent Commit | # Commits | |
|---|---|---|---|
| root | root@domu-12-31-38-04-79-f7.compute-1.internal | 2013-01-15 14:15:55.0 | 1 |
| root | root@ip-10-126-34-127.ec2.internal | 2013-07-08 17:20:20.0 | 1 |
| Ubuntu | ubuntu@domu-12-31-38-07-45-32.compute-1.internal | 2012-12-23 12:58:57.0 | 1 |
| Ziru Zhou | zzhou@olm-zzhou.local | 2012-12-19 21:08:03.0 | 23 |
This GitHub repository contains tools and scripts put together by members of the modENCODE DCC team:
Alumini:
We would like to thank Bjoern Gruening (bjoern.gruening@gmail.com) for updating many of our scripts to take advantages of the newer Tool Shed features. Please send your comments/questions to modENCODE DCC at help@modencode.org.
README file on how to launch an instance of Galaxy on Amazon Cloud.
README file on how to use the ENCODE/modENCODE uniform processing/peak calling pipeline ( macs2, IDR, and IDR-plot ) in Galaxy on Amazon Cloud.
README file on how to use the ENCODE/modENCODE uniform processing/peak calling workflows ( macs2, IDR, and IDR-plot ) in Galaxy on Amazon Cloud.
README files on how to use Amazon Cloud AMI or Bionimbus Cloud to run the uniform processing/peak calling pipeline from the command line
The tools listed below are also on Galaxy Toolshed
modENCODE_DCC_tools/bamedit - merging, splitting, filtering, and QC of BAM files
modENCODE_DCC_tools/idr - Reproducibility and automatic thresholding of ChIP-seq data, written by Anshul Kundaje ( https://sites.google.com/site/anshulkundaje/projects/idr )
modENCODE_DCC_tools/macs - model-based analysis of ChIP-Seq (1.4.1), written by Tao Liu
modENCODE_DCC_tools/macs2 - model-based analysis of ChIP-Seq (2.0.10.2), written by Tao Liu ( https://github.com/taoliu/MACS )
modENCODE_DCC_tools/peakranger - multi-purpose, ultrafast ChIP-Seq peak caller, written by Xin Feng ( http://ranger.sourceforge.net/ )
modENCODE_DCC_tools/spp - cross-correlation analysis package ( http://code.google.com/p/phantompeakqualtools/ )