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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Overview of possible new prediction algorithms and their installation/run requirements #1056

Open susannasiebert opened 7 months ago

susannasiebert commented 7 months ago
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