miARma-Seq

miARma is a fully customizable pipeline for NGS transcriptome analyses. Including gene/transcripts, miRNAs and circRNAs expression measurements.

Info

Members (researchers): Eduardo Andres Leon

Research Groups: Computational Biomedicine and Health Data Science

Contact Email: eduardo.andres@csic.es

Tool Repository: https://github.com/eandresleon/miARma-seq

Documentation: https://github.com/eandresleon/miARma-seq/blob/main/mRNA_miARma_doc_1.1.pdf

Publications DOI: https://doi.org/10.1038/srep25749, https://doi.org/10.1016/j.ymeth.2018.09.002

Institution: Instituto de Parasitología y Biomedicina López Neyra (IPBLN)

Application domain:

Expression Profiling, RNA Sequencing (RNA-seq), Transcriptomics

Technical details
Type of application
  • Command line tool (mainly perl + R)
Software compatibility
  • Linux
  • Mac
Hardware requirements
Programming language
  • BASH
  • Perl
  • R
Type of containerization
  • Docker
  • None
Wrapper type
  • None
Input file formats
  • bam
  • gff
  • gtf
  • Other
  • sam
Output file formats
  • html
  • pdf
  • tsv
Compatibility with other tools
  • miRGate