{ "info": { "author": "tadahaya mizuno", "author_email": "tadahaya@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "Copyright (c) 2018 Tadahaya Mizuno\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\nDescription-Content-Type: UNKNOWN\nDescription: ========\n OLSAPY\n ========\n \n OLSAPY: Orthogonal Linear Separation Analysis in Python\n =======================================================\n * OLSA is an analysis method of omics data to decompose the complex effects of a perturbagen into basic components.\n * OLSAPY is a package for OLSA in python.\n * OLSA can be applied to any kinds of omics data such as RNA-seq, proteome, and so on.\n \n Dependency\n =======================================================\n * python 3.6\n * requirements: numpy, pandas, scipy\n \n Setup\n =======================================================\n ::\n \n pip install olsapy\n \n Usage\n =======================================================\n 1. prepare a profile matrix with variables in rows and samples in columns as a csv file\n 2. import necessary modules as follows:\n \n ::\n \n from olsapy import olsa as ol\n \n 3. generate a DataClass object as follows:\n \n ::\n \n dat = ol.DataClass()\n \n 4. load the prepared data file into the generated object as follows:\n \n ::\n \n dat.load()\n \n 5. run OLSA and obtain a Result object as follows:\n \n ::\n \n res = ol.olsa(dat)\n \n 6. export each result as csv files as follows:\n \n ::\n \n res.export()\n \n 7. each result can be extracted as a dataframe if necessary as follows:\n \n ::\n \n dataframe = res.rsm()\n \n * a sample code for running OLSA described below:\n \n ::\n \n from olsapy import olsa as ol\n \n filein = ''\n \n #run OLSA simply\n dat = ol.DataClass() #generate a DataClass object\n dat.load(filein) #load data\n res = ol.olsa(dat) #run OLSA and obtain a Result object\n res.export() #save data\n \n #run OLSA with some options\n df = res.rsm() #.rsm(), etc. extract stored data in a Result object as a dataframe\n dat2 = ol.DataClass()\n dat2.load_df(df) #load dataframe into a DataClass object\n res2 = ol.olsa(dat2,accumulation=0.5) #accumulation determines the vectors subjected to varimax rotation\n res2.export(CM=True,TS=False) #results to be exported can be chosen.\n \n Licence\n =======================================================\n This software is released under the MIT License, see LICENSE.\n \n Authors\n =======================================================\n Setsuo Kinoshita, Shotaro Maedera, and Tadahaya Mizuno\n \n References\n =======================================================\n http://www.ilincs.org/ilincs/\n \n Bug Report\n =======================================================\n If you would like to report any bugs about olsapy, don't hesitate to create an issue on github here, or email me: tadahaya@gmail.com\nKeywords: olsa,usspca,profiling,omics,bioinformatics,profile data,transcriptome\nPlatform: UNKNOWN\nClassifier: Development Status :: 5 - Production/Stable\nClassifier: Environment :: Win32 (MS Windows)\nClassifier: Framework :: IPython\nClassifier: Intended Audience :: Science/Research\nClassifier: Operating System :: Microsoft :: Windows :: Windows 10\nClassifier: Programming Language :: Python :: 3.6\nClassifier: Topic :: Scientific/Engineering :: Bio-Informatics\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/tadahaya222/OLSApy", "keywords": "", "license": "The MIT License (MIT)", "maintainer": "", "maintainer_email": "", "name": "olsapy", "package_url": "https://pypi.org/project/olsapy/", "platform": "", "project_url": "https://pypi.org/project/olsapy/", "project_urls": { "Homepage": "https://github.com/tadahaya222/OLSApy" }, "release_url": "https://pypi.org/project/olsapy/1.0.1/", "requires_dist": [ "numpy", "scipy", "pandas" ], "requires_python": "", "summary": "a package for orthogonal linear separation analysis (OLSA)", "version": "1.0.1" }, "last_serial": 4128148, "releases": { "1.0.1": [ { "comment_text": "", "digests": { "md5": "8b70c59cccbae4b964fd0cee54a75490", "sha256": "b0c02d50cc3efa136f9093ce90947b99ac5a6b20b249c217cd03f0f0875c3fe0" }, "downloads": -1, "filename": "olsapy-1.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "8b70c59cccbae4b964fd0cee54a75490", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 12021, "upload_time": "2018-08-02T11:03:54", "url": "https://files.pythonhosted.org/packages/a3/f9/9ef19977d92ea7e4f1c22673c62986aef6c5466d782cfc84b8c6fa07a2a9/olsapy-1.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "885e0b5ace0b356112c4c4ccfb898abd", "sha256": "e383249531d5152aca525d55c59a590f5dc4283e7f3f25ba6ed5627a36d3dfea" }, "downloads": -1, "filename": "olsapy-1.0.1.tar.gz", "has_sig": false, "md5_digest": "885e0b5ace0b356112c4c4ccfb898abd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9456, "upload_time": "2018-08-02T11:03:55", "url": "https://files.pythonhosted.org/packages/34/5e/c630de19f92a034a3eb0865247bd123c6b9c3e15226145da2f407cb7c5c6/olsapy-1.0.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "8b70c59cccbae4b964fd0cee54a75490", "sha256": "b0c02d50cc3efa136f9093ce90947b99ac5a6b20b249c217cd03f0f0875c3fe0" }, "downloads": -1, "filename": "olsapy-1.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "8b70c59cccbae4b964fd0cee54a75490", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 12021, "upload_time": "2018-08-02T11:03:54", "url": "https://files.pythonhosted.org/packages/a3/f9/9ef19977d92ea7e4f1c22673c62986aef6c5466d782cfc84b8c6fa07a2a9/olsapy-1.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "885e0b5ace0b356112c4c4ccfb898abd", "sha256": "e383249531d5152aca525d55c59a590f5dc4283e7f3f25ba6ed5627a36d3dfea" }, "downloads": -1, "filename": "olsapy-1.0.1.tar.gz", "has_sig": false, "md5_digest": "885e0b5ace0b356112c4c4ccfb898abd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9456, "upload_time": "2018-08-02T11:03:55", "url": "https://files.pythonhosted.org/packages/34/5e/c630de19f92a034a3eb0865247bd123c6b9c3e15226145da2f407cb7c5c6/olsapy-1.0.1.tar.gz" } ] }