EMpire

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

Depedencies

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