Command Line Interface

Commands can be invoked via the command line using mieaa SUBCOMMAND.Help and options for all subcommands can be view with mieaa SUBCOMMAND -h

Commands may require specifying whether the input is from a list of strings or a file (see -m/M in Mutually exclusive options, below).In such cases, the the lowercase flag letter specifies a string/list, and uppercase specifies a file.

Supported Species

  • hsa - Homo sapiens
  • mmu - Mus musculus
  • rno - Rattus norvegicus
  • ath - Arabidopsis thaliana
  • bta - Bos taurus
  • cel - Caenorhabditis elegans
  • dme - Drosophila melanogaster
  • dre - Danio rerio
  • gga - Gallus gallus
  • ssc - Sus scrofa

Specifying precursorsFor subcommands where you need to specify precursor or mature, mature is always assumed unless the --precursor (-p) flag is set.

Mutually exclusive optionsEach subcommand requires either --mirna-set (-m) or --mirna-set-file (-M) to be specified. Enrichment analyses also require similarly behaving arguments for categories (-c or -C), and optionally for reference sets (-r or -R) in the case of ORA.

  • mieaa SUBCOMMAND --mirna-set MIRNA [MIRNA ...]
  • mieaa SUBCOMMAND --mirna-set MIRNAS_STRING
  • mieaa SUBCOMMAND --mirna-set-file MIRNA_FILE

Subcommands

to_precursor

Convert miRNA -> precursor

  • mieaa to_precursor [-m | -M] [OPTIONS]
$ mieaa to_precursor -m hsa-miR-20b-5p hsa-miR-144-5p --tabsep --unique
$ mieaa to_precursor -m 'hsa-miR-20b-5p,hsa-miR-144-5p' --newline -o precursors.txt
$ mieaa to_precursor -M mirnas.txt --outfile precursors.txt

to_mirna

Converting between precursor -> miRNA

  • mieaa to_mirna [-m | -M] [OPTIONS]
$ mieaa to_mirna -m hsa-mir-20b hsa-mir-144 --tabsep --unique
$ mieaa to_mirna -m 'hsa-mir-20b,hsa-mir-144' --newline -o mirnas.txt
$ mieaa to_mirna -M precursors.txt --outfile mirnas.txt

convert_mirbase

Converting miRBase version

  • mieaa convert_mirbase FROM_VERSION [-m | -M] [OPTIONS]
$ mieaa convert_mirbase 16 -m hsa-miR-642b,hsa-miR-550b
$ mieaa convert_mirbase 16 --to 22 -m hsa-miR-642b hsa-miR-550b
$ mieaa convert_mirbase 16  -M version_16.txt -o version_22.txt

gsea

Gene Set Enrichment Analysis (GSEA)

  • mieaa gsea SPECIES [-m | -M] [-c | -C] [OPTIONS]

Species must be specified using their three letter identifier, e.g. hsa, mmu, rno The category flags (-c -C) behave identically to the miRNA set flags (-m -M).

$ mieaa gsea hsa --precursors -M precursors.txt -C categories.txt -o results.csv
$ mieaa gsea hsa -p -M precursors.txt -c HMDD MNDR > results.csv
$ mieaa gsea mmu -M mirnas.txt -C categories.txt --adjustment none
$ mieaa gsea rno -M mirnas.txt -C categories.txt -a bonferroni --json -o results.json

ora

Over-representation Analysis (ORA)

  • mieaa ora SPECIES [-m | -M] [-c | -C] [OPTIONS]

Species must be specified using their three letter identifier, e.g. hsa, mmu, rno. The category flags (-c -C) and reference set flags (-r -R) behave identically to the miRNA set flags (-m -M).

$ mieaa ora hsa --precursors -M precursors.txt -C categories.txt > results.csv
$ mieaa ora hsa -p -M precursors.txt -c HMDD MNDR -o results.csv
$ mieaa ora hsa -p -M precursors.txt -C categories.txt -R reference.txt
$ mieaa ora mmu -M mirnas.txt -C categories.txt --adjustment none
$ mieaa ora rno -M mirnas.txt -C categories.txt -a bonferroni --json -o results.json