bioinfo-code-chunks

Random selection of useful code chunks and examples for bioinformatics.

• Author: Michael Jahn, PhD
• Affiliation: Max Planck Unit for the Science of Pathogens (MPUSP), Berlin, Germany
• License: GPL-v3

This repository is a collection of reusable, self-contained code chunks and examples. The goal is to provide code examples for recurring tasks, that require mostly existing packages and therefore do not fulfill the requirements to become a new package.

Structure

• data: raw data tables or files used for examples
• docs: rendered notebooks in html format, for example from R markdown
• output: output files saved for future reference or tests
• pipeline: R markdown or jupyter notebooks with examples
• source: script files

Contents

• Fast gene set enrichment (R)
• Hypergeotric test for gene enrichment (R)
• Quantify overlap between pathways (R)
• Retrieve KEGG pathway information (R)
• Plot sequence logos with logomaker (python)
• Plot coverage tracks (R)
• Plot Circos genomes with pycircos (python)

Run examples

The pipelines collected in this repository are self-contained and executable. For R markdown and jupyter notebooks, the code and the documentation are part of one and the same document. If you want to run the examples yourself, there are two possibilities:

1. copy and paste code chunks from the documents in source/ or pipeline/
2. clone/download the repository, open and re-run notebooks in pipeline/ (see below)

To download the repository on your local drive use git clone in a (linux) terminal:

cd /your-target-folder
git clone https://github.com/m-jahn/bioinfo-code-chunks.git

Open a pipeline with your favorite IDE (Rstudio, jupyterlab, ...) and execute code (chunks) with the Run button. For R markdown notebooks, you can also open an interactive R session and render the document like this:

require(rmarkdown)
rmarkdown::render("document.Rmd")

Import on the fly

It's possible to directly import functions from a github repo into running code. For R code, simply source a function from github like this:

source("https://raw.githubusercontent.com/MPUSP/bioinfo-code-chunks/main/source/get_kegg_pathways.R")