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miARma_pipelineV1.7.2.tar.bz2 (115.5 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| Examples_miARma_miRNAs.tar.bz2 | 2016-03-28 | 137.1 MB | |
| Examples_miARma_circRNAs.tar.bz2 | 2016-03-15 | 765.7 MB | |
| Examples_miARma_mRNAs.tar.bz2 | 2016-03-15 | 189.4 MB | |
| Totals: 3 Items | 1.1 GB | 0 | |
miARma WebPage
miARma web page that includes guides, installation details and examples has been moved to http://miarmaseq.com
miARma
miARma is a fully customizable pipeline for NGS transcriptome analyses. Including gene/transcripts, miRNAs and circRNAs expression measurements. Created at Computational Biology and Bioinformatics Group (CbBio) Institute of Biomedicine of Seville. IBIS (Spain) Modified and Updated at Bioinformatics Unit at IPBLN-CSIC (Institue for Parasitology and Biomedicine Lopez-Neyra, CSIC). Granada (Spain). Copyright (c) 2017 IBIS & IPBLN. All rights reserved.
miARma 1.7.2 release (18/Dec/17)
Minor bugs fixed.
- New Ensembl BiomaRt URL used
- Order columns from ReadCount section without checking samples names
- Fixed a bug in the TargetPrediction
miARma 1.7.1 release (21/Aug/17)
Minor bugs fixed eg. * No aligned reads in hisat2 paired end analysis added.
Added stuff: * Unaligned files are compressed * miRDeeparam added to include parameters to miRDeep execution
miARma 1.7.0 release (09/Aug/17)
- Hisat v2.1.0 has been included as a mRNA aligner.
- STAR v020201 has been included as a mRNA aligner.
1. Included in miARma
Quality Software
Trimming Softare
Aligners
Entity Quantification
Others
2. Pre-requisites
miARma-Seq is a tool that provides an easy and common interface to various analysis software. It also intends to reduce to the minimum the number of dependencies. Nevertheless, some basic programs listed below must be correctly installed:
- Perl v5.6.0 or higher.
- Java JDK v.1.6. or higher.
- R environment v.3.2 or higher.
- Bioconductor v.1.3 or higher.