Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

Image processing in Python

Python module utilizing libCZI for reading Zeiss CZI files.

Read Carl Zeiss image files (CZI).

libCZI is an Open Source Cross-Platform C++ library to read and write CZI.

Algorithms package for generating model metagenomes with specified properties

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Cross Validation (CV) of DNA barcodes reference databases (refDB) using blast

This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.

🍄 Qiime2 ITS classifiers for the UNITE database

Ready-made Taxonomic Weights Repository

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

A "batteries-included" distribution of ImageJ 🔋

Materials for my R programming course

SPAdes Genome Assembler

De novo assembler for single molecule sequencing reads using repeat graphs

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

Accurate sample inference from amplicon data with single nucleotide resolution

Scripts written for the "Finding Hidden Messages in DNA (Bioinformatics I)" course offered by UCSanDiego on Coursera.org