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Nick Youngblut's Projects

screenpro2 icon screenpro2

Genome-scale or custom CRISPR screen analysis for single gene or combinatorial libraries.

seq_tools icon seq_tools

Miscellaneous tools for working with sequences

seqdb_tools icon seqdb_tools

commands for interacting with public sequence databases

sgepy icon sgepy

SGE job submission & monitoring

sharchaea icon sharchaea

Sharchaea: the top predator of the microbial world

sipsim icon sipsim

A toolset for simulating high resolution stable isotope probing data

sipsimr icon sipsimr

Simulate High Resolution Stable Isotope Probing Datasets (associated R scripts)

snakemakenb icon snakemakenb

Create snakemake rules to run Jupyter/Ipython Notebooks

spede icon spede

A python application for MALDI-TOF MS dereplication

staged-recipes icon staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

strainfacts icon strainfacts

Factorize metagenotypes to infer strains and their abundances

strainscan icon strainscan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

tmhmm.py icon tmhmm.py

A transmembrane helix finder in Python 3.

traitar3 icon traitar3

From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)

veba icon veba

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

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