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