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bio-ml

Command lines for the BIO-ML resources

biobakery

bioBakery tools for meta'omic profiling

blobology

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)

buildshiny

How to build a Shiny App

co-occurrence

R scripts for performing co-occurrence analyses

complete-python-3-bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

genomics

A collection of scripts and notes related to genomics and bioinformatics

growth_curves

isoseq_sa3nup

Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

lrasmanuscript

Reproducible Analyses accompanying DADA2 + PacBio Manuscript

machine-learning-with-r-cookbook

Code repository for Machine Learning with R Cookbook, published by Packt Publishing

mailspring

:love_letter: A beautiful, fast and maintained fork of @Nylas Mail by one of the original authors.

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

microbiome_evolution

Scripts for analyzing evolutionary dynamics in large cohorts of human gut metagenomes

microbiome_helper

An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.

microbiomeseq

An R package for microbial community analysis in an environmental context

mmvec

Neural networks for microbe-metabolite interaction analysis

omeclust

multi-resolution clustering of omics data

oneliners

Useful bash one-liners for bioinformatics.

pcgr

Personal Cancer Genome Reporter (PCGR)

physalia-workshop

Stab at a github.io page for the Physalia Workshop

randomforest-microbe

Presentation and code for running random forests with microbial community

regularization_learning_networks

Implementation of RLNs, as described in https://arxiv.org/abs/1805.06440

rep-cookbook

Replication Cookbook for FGFP GWAS

samsa

Programs and documentation for the SAMSA pipeline, version 1.0

sib_longreadsworkshop_zh18

Course material "Bioinformatics of Long Read Sequencing", edition Zürich 2018

single-cell-training

Website hosted at https://sib-swiss.github.io/single-cell-training/latest/

spieceasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

stomamicrobiota

Plasticity of the adult human small intestinal stoma microbiota