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2017-03-29-software_carpentry_munich_teaching_material

Teaching Material of the Software Carpentry Munich 2017-03-29

2018-01-23-intermediate_scientific_computing_skills_munich

Scientific Computing Skills - Intermediate Workshop Munich (2018-01-23)

adamsorbie.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

atf6_public_data

av_kinetic

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

bash_script_one_liners

Useful BASH scripts and one liners for working with Microbiome/NGS data

benakislab

Scripts and pipelines used for microbiota and metabolome analysis

bio_tools

Simple scripts useful for molecular biology

biotools

A list of useful bioinformatics resources

coleman_lobner_atf6_dysbiosis_gastroenterology_2018

machine learning in R

comparative_genomics

Comparative genomic analysis of related taxa of those enriched in ATF6 mice with tumors

denovo_to_picrust

Pipeline for using de-novo picked otus with PICRUSt

dive-into-machine-learning

Dive into Machine Learning with Python Jupyter notebook and scikit-learn!

ggmp-regional-variations

gut_brain_axis_course-bioinformatic_analysis

The microbiome-gut-brain axis: Concepts and methods in experimental stroke research – Bioinformatic analysis

handson-ml

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.

helper_scripts

Collection of scripts used for converting data types, data import etc

intro-to-hpc-course-2020

Introduction to HPC/working on the LRZ linux cluster

introtojulia

A Deep Introduction to Julia for Data Science and Scientific Computing

microbiome

Scripts for microbiome analysis

microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages. Apart for some simple scripts, this package has a single function generates a HTML report with preliminary QC, Alpha Diversity, Ordination and Composition analysis of OTU tables.

microbiota_analysis_templates

Rmarkdown and other analysis templates from the Benakis Lab

neuroimmunological-methods-in-stroke-research-course-2023

Data analysis part of the 2023 Neuroimmunolgical methods in stroke research at the ISD

neuroimmunological-methods-in-stroke-research-course-2024

Data analysis part of the 2024 Neuroimmunolgical methods in stroke research at the ISD

oneliners

Useful bash one-liners for bioinformatics.

otu-project

plotting

Collection of Python and R Scripts for commonly used plots