Overview of possible new prediction algorithms and their installation/run requirements

[susannasiebert]

Name	Our GitHub Issue	Algorithm Repo	Last Update	setup.py	Installation	Manual Dependency	Implementation Notes
PRIME	#1029	https://github.com/GfellerLab/PRIME	10 months ago	N	Download/clone GitHub repo Open the PRIME file and replace lib_path add directory to your PATH	MixMHCpred
DeepHLApan	#1016	https://github.com/jiujiezz/deephlapan	2 years ago	Y	Build from repo's setup.py	None stated	Installation successful with minor modifications. Existing model requires tensorflow 1. Other pVACtools dependencies require tensorflow 2. Attempts to load models into tensorflow 2 were unsuccessful.
BigMHC	#992	https://github.com/KarchinLab/bigmhc	last year	N	Download/clone GitHub repo	None stated	Straightforward installation. Could be made a pvactools package dependency by manually creating a setup.py.
EpiScan	#894	None, Source code available in publication supplemental pdf	?	N	Docker or Web Interface	None stated
APE-Gen	#709	https://github.com/KavrakiLab/APE-Gen	4 years ago	N	Download/clone GitHub repo	Conda	Has dependencies that can only be installed via conda. Because of this it would need to be installed manually by users and can't be made a dependency in pvactools package.
ACME	#703	https://github.com/HYsxe/ACME	2 years ago	N	Download/clone GitHub repo Change cwd to tool Open the binding_prediction.py and main.py file and replace main_dir Paste the peptide sequences and the corresponding MHC alleles in prediction_input.txt	Python 2
PUFFIN	#702	https://github.com/gifford-lab/PUFFIN	2 years ago	N	Download/clone GitHub repo Install dependencies from environment.yml	environment.yml
NetH2pan	#652	None	?	N	Web Interface	None stated
EPIC	#319	https://github.com/BGI2016/EPIP	5 years ago	Y	Build from repo's setup.py	Perl	Installation successful with minor modifications. First tests with own data returns negative prediction values which I'm unsure how to interpret.
MixMHCpred	#240	https://github.com/GfellerLab/MixMHCpred	2 years ago	N	Download/clone GitHub repo Open the MixMHCpred file and replace lib_path add directory to your PATH	None stated	Straightforward installation on Mac. Could be made a pvactools package dependency by manually creating a setup.py. However, on Linux machines C++ code needs to be manually compiled.
MixMHC2pred	#1093	https://github.com/GfellerLab/MixMHC2pred	9 months ago	N	Download/clone GitHub repo	None stated
MHCRank	#1007	https://github.com/ninglab/mhcrank	8 months ago	Y	Download/clone GitHub repo	Train model
DeepImmuno	#1021	https://github.com/frankligy/DeepImmuno	last year	N	Download/clone GitHub repo	various Python packages	Could be made a pvactools package dependency by manually creating a setup.py.
HLAthena	#481	None available	Unknown	N	Web Interface	None stated