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Nextflow pipeline to assess the impact of positive selection on Identity by Descent (IBD)-based inferences, utilizing population genetic simulations and true IBD inferences.
Nextflow pipeline to analyze PacBio HiFi full-length 16S data
GFF and GTF file manipulation and interconversion
Test data to be used for automated testing with the nf-core pipelines
This repo collects the list of podcasts related to microbiome science: science, microbiology and bioinformatics.
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA
Github pages based template for hackathons
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
A library of shared system prompts for creating customized educational GPT agents.
Code and models for the paper: "In-domain versus out-of-domain transfer learning in plankton image classification"
A set of exercises for deliberate Git Practice
Hone computational biology skills by re-enacting Figure 1 of modern biology papers
A repository for the second version of our LTEE gene expression paper
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
Code repository for classification of plankton images from the MVCO IFCB using transfer learning on convolultional neural networks
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
Short lessons from FAS Informatics coffee hour
🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.
microlei / tamipami
Forked from USDA-ARS-GBRU/tamipamiA tool for finding the TAM and PAM sites of new Cas and transposon endonucleases from NGS screens
A tool for finding the TAM and PAM sites of new Cas and transposon endonucleases from NGS screens
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.