Stars
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
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
❄️🐻 Climate change and cross-species viral transmission
Predicting the mammalian viral sharing network
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
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Computes affinity between two entities based on their co-occurrence
Make Interactive Complex Heatmaps
The Microbiome Interpretable Temporal Rule Engine