Simply download and run EMpire.jar for a list of available sub-commands.
Usage: java -Xmx2G -jar EMpire.jar <Command>
Available <Command> options:
IsoformEM_Footprints | Infer most likely transcripts from ribosome footprint alignments
IsoformEM_Proteomics | Infer most likely isoforms from MS/MS spectra mapping
FootprintFrameAnaysis | Analyse ribosome footprint alignments in terms of fidelity to annotated coding frames
PeptideDigest | Enzymatically digest a protein reference
Relies heavily on general purpose java code in https://github.com/rkitchen/Thunder
Also requires several java libraries:
- commons-io-2.4
- commons-cli-1.2
- commons-lang3-3.3.2
- commons-math3-3.5
- sqlite-jdbc-3.7.2
- sam-1.96