miARma-Seq statistics

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Popular tool citations

chevron_left Gene set enrichment analysis Known transcript quantification miRNA target prediction Normalization Differential expression Bioinformatics workflows Read quality control Adapter trimming Spliced read alignment chevron_right
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Associated diseases

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miARma-Seq specifications

Information


Unique identifier OMICS_13537
Name miARma-Seq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output format SAM, BAM, PDF, TSV, XLS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, Python, R
Computer skills Advanced
Version 1.5.1
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

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Publication for miARma-Seq

miARma-Seq in publications

 (3)
PMCID: 5826934
PMID: 29483516
DOI: 10.1038/s41598-018-21517-4

[…] was isolated from mvs or cells using trizol. next generation sequencing was performed in an illumina hiseq. 2500 (illumina, san diego, ca). data normalization and analysis were conducted with the miarma-seq tool (see supplemental materials). briefly, sequence quality was assessed with fastqc; sequence reads were aligned with bowtie2 to the ncbi rattus norvegicus annotation release 105 […]

PMCID: 5666336
PMID: 29104512
DOI: 10.7150/ijbs.21502

[…] gsm1923402, gsm1923401, gsm1923403 . these data were obtained from hepg2 cells, which were treated with same experimental procedures as rna-seq. the number of reads of each mirna was counted by miarma-seq (v1.5) . the differential expression analysis was performed with the same standard as rna-seq procedure via edger , ., the mirna binding sites between all differential expressed rnas, […]

PMCID: 5384238
PMID: 28387377
DOI: 10.1038/srep46101

[…] mrna experiments were downloaded from the controlled-access cancer genomics hub. these samples were analysed following the protocol proposed previously and using a pipeline for ngs studies called miarma-seq. briefly, this tool brings together well-established software in a single bundle, allowing a complete analysis of the raw data. quality analysis, adapter removal, read alignment, read […]


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miARma-Seq institution(s)
Bioinformatics Unit, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain; Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario de Valme, Instituto de Biomedicina de Sevilla (IBIS), Seville, Spain
miARma-Seq funding source(s)
This work was supported by the European Union grant FP7-REGPOT-2012-2013-1.

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