.. UiTeiLab documentation master file, created by sphinx-quickstart on Tue Jun 1 12:03:58 2021. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. ###################### Welcome to UiTei-Lab!! ###################### .. figure:: http://ui-tei.rnai.jp/assets/images/top_211021_gifversion2.gif :alt: Members-in-UiTei-Laboratory :target: http://ui-tei.rnai.jp/ |GitHub version| |Install This Package| |GitHub repo size| |license| |実習wiki| |程研HP| |Documentation| |twitter badge| |Open in Colab| ************************************************* Basic Laboratory Work in Life Science Experiments ************************************************* In this lecture, we will perform bioinformatics experiments such as **"Sequencing"**, **"Biochemical Reaction Simulation"**, and **"Gene Expression Profiling"** (← Our Lab is in charge of this). This lecture is for students in , department of Bioinformatics and Systems Biology or department of Biophysics and Biochemistry. Please refer to `Lecture's Wiki `__ or `Repository's Wiki `__ to check the schedule. Wet Experiment (MicroArray) =========================== .. graphviz:: _graphviz/graphviz_MicroArrayOverview.dot :class: popup-img ******* Package ******* You can install this package with the following command etc. .. code:: sh $ pip install "git+https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments.git" This package is for facilitating the lecture, so it contains many utility functions, such as data handling and anonymous questions. However, it also contains functions to easily plot **MAplot** and **XYplot** . If you want to know how to use those plotting functions, please refer to the followings. +------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------+ | module | Notebook | documentation | +============+=============================================================================================================================================================================================================================================+===============================+ | plotly | :fa:`home` `notebook/Local/Main-Lecture-Material-plotly.ipynb `_ | :doc:`teilab.plot.plotly` | +------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------+ | matplotlib | :fa:`home` `notebook/Local/Main-Lecture-Material-matplotlib.ipynb `_ | :doc:`teilab.plot.matplotlib` | +------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------+ Package Contents ================ .. toctree:: :maxdepth: 6 teilab ************ Installation ************ I recommend you to use `Pyenv `__ and `Poetry `__ to set up the required environment. .. code:: sh $ git clone https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments.git $ cd TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments $ pyenv install 3.8.9 $ pyenv local 3.8.9 $ python -V Python 3.8.9 $ poetry install If you want to use Jupyter Notebook with this environment, check `this notebook `__. Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` .. |GitHub version| image:: https://badge.fury.io/gh/iwasakishuto%2FTeiLab-BasicLaboratoryWork-in-LifeScienceExperiments.svg :target: https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments .. |Install This Package| image:: https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments/workflows/Install%20This%20Package/badge.svg :target: https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments/blob/master/.github/workflows/install_this_package.yml .. |GitHub repo size| image:: https://img.shields.io/github/repo-size/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments :target: https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments .. |license| image:: https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000 :target: https://github.com/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments/blob/master/LICENSE .. |実習wiki| image:: https://img.shields.io/badge/website-wiki-9ecca4 :target: http://ui-tei.rnai.jp/microarray/doku.php?id=2021 .. |程研HP| image:: https://img.shields.io/badge/website-HP-9ecca4 :target: http://ui-tei.rnai.jp/ .. |Documentation| image:: https://img.shields.io/badge/Documentation-portfolio-1f441e?style=flat-radius :target: https://iwasakishuto.github.io/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments/index.html .. |twitter badge| image:: https://img.shields.io/badge/twitter-Ask%20Author-1da1f2?style=flat-radius&logo=twitter :target: https://www.twitter.com/messages/compose?recipient_id=1042783905697288193&text=2021年度の生命科学基礎実験を受講しているものですが、 .. |Open in Colab| image:: https://img.shields.io/badge/2022S-open%20in%20Colab-3d80bc?style=flat-radius&logo=google-colab :target: https://colab.research.google.com/github/iwasakishuto/TeiLab-BasicLaboratoryWork-in-LifeScienceExperiments/blob/main/notebook/Colaboratory/microarray2022S.ipynb