Change Log ============ Version SNAF.git: e23ce39512a1a7f58c74e59b4b7cedc89248b908 (2024.01.15) -------------------------------------------------------------------------- I recommend the user who knew our tool from the official publication to use this version, I have tested and it worked. I will not release new pypi version in the future, but will keep maintaining the github and release new features using specific commits. Version 0.7.0 (2023.05.23) --------------------------- This is a release since the paper's original resubmission, in the past year, we added a ton of new features, main changes are briefly summarized below: #. differential gene analysis, differential splicing analysis, gene enrichment analysis #. hla coverage analysis, for each pHLA, what percentage of the population it can cover (benefit) #. enhanced and more flexible control database, adding two normal cohorts by default, and allowing user to add customized #. improved algorithms for MLE tumor specificity score, and external BayesTS score (https://github.com/frankligy/BayesTS) #. improved output for both T and B antigens #. fix multiple bugs Version 0.6.0 (2022.07.11) ---------------------------- Adding New functionalities: #. report B and T antigen in a more readable format #. allow users to add all info to the frequency table at once #. add long_read mode for B antigen when inferring full-length isoform and update the B viewer codebase as well Version 0.5.2 (2022.04.17) ---------------------------- Fixed multiple bugs: #. scratch folder cleaning issue and multiprocessing conflist issues resolved #. tumor_specificity issue resolved #. fix docstring displacement #. In test folder, contain a complete testing case. Version 0.5.1 (2022.04.16) ---------------------------- Fixed two bugs: #. Weckzueg can not be version 2.1.1, force it to be 2.0.2 #. expose add_coord_frequency_table to snaf namespace Version 0.5.0 (2022.04.06) ---------------------------- Initial release Prior to Version 0.5.0 -------------------------- I started this project since ``Feb 2020`` during my second rotation in Dr. Nathan Salomonis Lab, The initial code base can be seen from the first GitHub repository listed below. The neoantigen has been used in a few manuscript and ongoing project, in which I rename it as ``AltNeo-BT``, the codebase can be seen from the second GitHub repository. * `NeoAntigenWorkflow `_ * `AltNeo-BT `_