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TOPIC: Python

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Ben Tully edited this page Aug 4, 2020 · 20 revisions

Suggested prerequisites for this topic

If the user is interested in natively installing python on their computer, please see https://www.python.org/downloads/

Otherwise, see: Introduction to using Jupiter notebooks via MyBinder.org

Overview

Lesson 1 -- Introduction to Python

Introductory material

Date posted: 14 April 2020 Author(s): Ashley B. Cohen
Instructor(s): Ashley B. Cohen

  • Exploring the features of Binder
  • Running a simple script
  • Typing python commands in a terminal environment

Video presentation

Interactive material

Date posted: 14 April 2020 Author(s): Ashley B. Cohen
Instructor(s): Ashley B. Cohen

Content | Video presentation | Binder

Lesson 2 -- Immutable Data types

Introductory material

Date posted: 30 April 2020 Author(s): Dr. Ben Tully
Instructor(s): Dr. Ben Tully

  • Set and determine the datatype of a variable using python methods
  • Apply some of the built-in python string functions to manipulate the way that text is displayed in print statements

Content | Video presentation

Interactive material

Date posted: 30 April 2020
Author(s): Dr. Ben Tully
Instructor(s): Dr. Ben Tully

Content | Binder

Lesson 3 -- Mutable Data types

Interactive material

Part 1 - Strings and Lists

Date posted: 12 May 2020
Author(s): Ashley Cohen
Instructor(s): Ashley Cohen

Content | Video Presentation | Binder

Interactive material

Part 2 - Dictionaries

Date posted: 12 May 2020
Author(s): Dr. Ben Tully
Instructor(s): Dr. Ben Tully

Content | Video Presentation | Binder

Lesson 4 -- Live Coding Demo 1

Interactive material

Parsing the header line of a FASTA file

Date posted: 14 May 2020
Author(s): Ashley Cohen
Instructor(s): Ashley Cohen

Content | Video Presentation | Binder

Lesson 5 -- Live Coding Demo 2

Interactive material

Parsing the columns of the GenBank Assembly file

Date posted: 23 May 2020
Author(s): Dr. Ben Tully
Instructor(s): Dr. Ben Tully

Content | Video Presentation | Binder

Lesson 6 -- Live Coding Demo 3

Interactive material

Aggregating taxon and combining OTU count data

Date posted: 6 June 2020
Author(s): Ashley Cohen
Instructor(s): Ashley Cohen

Content | Video Presentation | Binder

Lesson 7 -- Introduction to Pandas dataframes

Interactive material

Date posted: 22 June 2020
Author(s): Ashley Cohen
Instructor(s): Ashley Cohen

  • A library developed for handling multi-dimensional data sets, which are stored as DataFrame python objects

Content | Video Presentation | Binder

Lesson 8 -- Pandas dataframes II

Interactive material

Date posted: 7 July 2020
Author(s): Ashley Cohen
Instructor(s): Ashley Cohen

  • clean up the metadata table
  • clean up the OTU table
  • filter the OTU table
  • Examine the abundances of OTUs in relationship to relevant categorical metadata

Content | Video Presentation | Binder

Lesson 9 -- Ordinations Part I

Interactive material

Date posted: 3 August 2020
Author(s): Ashley Cohen
Instructor(s): Ashley Cohen

  • Distance metrics - Jaccard & Bray-Curtis
  • Ordination analysis
  • Principle Coordinates Analysis

Content | Video Presentation | Binder

Extended Resources and Publications

Tools:

Basic:

Advanced:

Home -- Topics -- Unix -- R -- Amplicons -- Metagenomics -- Functional Annotation -- Transcriptomics -- Networks -- Python -- Reproducibility Challenge -- BVCN Conference 2021 -- Infrastructure Used -- Jupyter -- MyBinder -- Get Involved!

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