Compare different differential abundance and expression methods
An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
OTU co-occurrence network inferrence base on null model for HPC
Building an interactive dashboard to explore the Belly Button Biodiversity dataset using JavaScript, D3, Plotly, HTML and CSS.
Rsearch: An R Interface to VSEARCH supporting visualization and parameter tuning
This bash script is used to generate a one page KRONA html from a rarified multi samples OTU table.
A Julia pipeline with WebUI for amplicon metabarcoding from raw paired-end Illumina reads to filtered, taxonomy-annotated ASV/OTU tables.
R workflows used to analyze microbial community sequence data
OTUStalker is a small software tool designed to be compatible with QIIME (v1.8.0). Its purpose is to retrieve data pertinent to a single taxonomic group, from a larger (presumably mixed) data set, therefore allowing the user to concentrate their efforts on the specific taxa of interest. In effect, OTUStalker is taking the place of a targeted PCR…
Historical sequence-analysis workflow for Trichoderma sequence clustering, OTU generation and NCBI preparation
Shiny app for file format conversion and taxonomy correction in OTU counts tables. (16S or ITS).
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