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Repository trinityrnaseq
Name: trinityrnaseq
Owner: jjohnson
Synopsis: De novo assembly of rna-seq data coupled with downstream analyses
Trinity incorporated into Galaxy in addition to enabling downstream analyses of transcript expression, differential expression, and transcript functional annotations.
Link to this repository: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/trinityrnaseq/09c1e388c20c
Clone this repository: hg clone https://testtoolshed.g2.bx.psu.edu/repos/jjohnson/trinityrnaseq
Type: unrestricted
Revision: 9:09c1e388c20c
This revision can be installed: True
Times cloned / installed: 556
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
Repository package_trinityrnaseq_2013_08_14 revision df23c0ef83a6 owned by jjohnson
Repository package_samtools_0_1_19 revision a0ab0fae27e5 owned by iuc
Repository package_bowtie_1_0_0 revision e682af6a72cd owned by jjohnson
Repository package_hmmer_3_0 revision a44693e3a2c4 owned by iuc
Repository package_rsem_1_1_17 revision 7d060ea51c6f owned by jjohnson

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
bowtie 1.0.0 package
hmmer 3.0 package
rsem 1.1.17 package
samtools 0.1.19 package
trinityrnaseq 2013_08_14 package

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
De novo assembly of RNA-Seq data Using Trinity 0.0.2 any
run RSEM to estimate transcript abundances 0.0.2 any
Pre-process RNA-seq data to reduce coverage of highly covered areas 0.0.2 any
Trinity Transcripts to Candidate Peptides 0.0.2 any

Categories
Assembly - Tools for working with assemblies
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis