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Repository defuse
Name: defuse
Owner: jjohnson
Synopsis: DeFuse - gene fusion discovery from RNA-Seq data
deFuse - gene fusion discovery using RNA-Seq data

deFuse is a software package for gene fusion discovery using RNA-Seq data. 
The software uses clusters of discordant paired end alignments 
to inform a split read alignment analysis for finding fusion boundaries.  
The software also employs a number of heuristic filters in an attempt 
to reduce the number of false positives and produces 
a fully annotated output for each predicted fusion.

http://sourceforge.net/apps/mediawiki/defuse/

https://bitbucket.org/dranew/defuse
Type: unrestricted
Revision: 15:b67c24d902aa
This revision can be installed: True
Times cloned / installed: 828
Dependencies of this repository

Repository package_boost_1_55 revision 9cc5f2bc9a9c owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_readline_6_2 revision 5313ca2fbce6 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_cairo_1_12_14 revision cd2ed5717e38 owned by devteam (prior install required)
Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision a65217367e4a owned by devteam (prior install required)
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_r_3_1_2 revision 4d2fd1413b56 owned by iuc (prior install required)
Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision a65217367e4a owned by devteam (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
Repository package_libxml2_2_9_1 revision 45b16a3ab504 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_samtools_0_1_19 revision c9bd782f5342 owned by iuc
Repository package_bowtie_1_0_0 revision 9fcaaedbbfd6 owned by iuc
Repository package_gmap_2013_05_09 revision 953f5eb53593 owned by jjohnson

Name Version Type
R 3.1.2 package
ada 2.0.3 package
blat 35x1 package
bowtie 1.0.0 package
defuse 0.6.2 package
gmap 2013-05-09 package
samtools 0.1.19 package

Contents of this repository

Name Description Version Minimum Galaxy Version
identify fusion transcripts 0.6.2.1 16.01
generate a VCF from a DeFuse Results file 0.6.1 16.01
converts a bam file to fastq files. 0.6.2.1 16.01
create a defuse reference from Ensembl and UCSC sources 1.6.1 16.01
create a defuse reference from Ensembl and UCSC sources 0.6.2.1 16.01
verify fusions with trinity 0.6.1 16.01

Name Version Data Tables
data_manager_defuse_reference 0.0.1 defuse_reference

extension type mimetype subclass
defuse.conf galaxy.datatypes.data:Text True
defuse.results.tsv galaxy.datatypes.tabular:Tabular True

Categories
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis