Calculate assocations between genes and traits

Actually sort files on your FAT drives

Facilities to access (ex)FAT and NTFS filesystems and disk images with Python 3

Generate summary graphics from sl1p or dada2 output

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models

Python package for scraping recipes data

ASMAPP assembly appraisal workflow. Built in snakemake, ASMAPP performs many basic and intermediate assembly appraisal tasks.

Open source code for AlphaFold 2.

Data and scripts associated with manuscript on Tree Metrics of Cophylogeny

SPAdes Genome Assembler

Call TMHMM from R, to predict transmembrane helices in proteins

A set of functions to visualise genotypes based on a VCF

NOVOPlasty - The organelle assembler and heteroplasmy caller

colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures

Plot microbiome time series in parallel

❄️🐻 Climate change and cross-species viral transmission

Predicting the mammalian viral sharing network

Generating large pangenome for Aspergillus fumigatus

A listing of the commands, protocols and other notes that I take on a daily basis

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

De novo assembler for single molecule sequencing reads using repeat graphs

Tool to plot synteny and structural rearrangements between genomes

Maximum Likelihood Amplicon Pipeline

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

R package to facilitate making plots as circles

Computes affinity between two entities based on their co-occurrence

Make Interactive Complex Heatmaps

The Microbiome Interpretable Temporal Rule Engine