Adam Sorbie's repositories
Supervised_Classification_Haller_Lab
R script for performing supervised classification of microbiota profiles
Coleman_Lobner_ATF6_Dysbiosis_Gastroenterology_2018
machine learning in R
2017-03-29-Software_Carpentry_Munich_Teaching_Material
Teaching Material of the Software Carpentry Munich 2017-03-29
adamsorbie.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
BenakisLab
Scripts and pipelines used for microbiota and metabolome analysis
intro-to-HPC-course-2020
Introduction to HPC/working on the LRZ linux cluster
Stroke_Microbiota_reproducibility
Repository for Sorbie, Jimenez and Benakis, iScience 2022
unix_shell_course-2020-02-14
Short Unix course 2020
applied-computational-genomics
Applied Computational Genomics Course at UU: Spring 2020
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
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
Gut_brain_axis_course-Bioinformatic_analysis
The microbiome-gut-brain axis: Concepts and methods in experimental stroke research – Bioinformatic analysis
helper_scripts
Collection of scripts used for converting data types, data import etc
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
Spike-in_analysis
This repo contains a python script to facilitate processing of 16S sequencing data with Spikes to calculate absolute abundance.
Supervised_classification_AV_AVI
Phenotype prediction in AV and AVI mouse lines based on microbiota abundance and alpha diversity
tsnemicrobiota
t-distributed stochastic neighbor embedding for microbiota data