/bioinformatics-projects

A Collection of Bioinformatics Projects

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

bioinformatics-projects

Here, I am sharing scripts and methods I used for some of the Bioinformatics projects.

Table of Contents

  1. Project 1 - 16s Microbiome Data Analysis Qiime 1
    1. Loading Qiime meta data to Phyloseq library
    2. Prevalence filtering
    3. Filtering and Normalization
      1. TSS: Total-Sum Scaling
      2. Rarefying
      3. CSS: Cumulative-Sum Scaling
    4. Abundance Plot
      1. Violine plots and Bargraphs
    5. MetagenomeSeq
      1. CSS Normalized Viloline plot and Bargraphs
      2. Presence-absence testing
      3. Unique OTUs or features
      4. HeatMaps and PCA plots
  2. Project 2 - In Silico Restriction Enzyme Digestion
  3. Project 3 - Random GGplots
  4. Project 4 - Microbiome Data Analysis Qiime 2