Bradley Lab
- 2 followers
- United States of America
- https://bradleylab.science/
- https://microbiology.osu.edu/
- https://coms.osu.edu/
- https://idi.osu.edu/
Popular repositories Loading
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phylogenize
phylogenize PublicA tool for phylogenetic comparison and analysis of microbe including gene's environmental association
R 2
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2023-anvio-comparison
2023-anvio-comparison PublicComparison of multiple annotation methods (Kofamscan, Microbeannotator, and anvi'o) using multiple prokaryotic families found across varying environments.
R 2
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rnaseq-quantification-pipeline
rnaseq-quantification-pipeline PublicDevelopmental RNASeq pipeline for bacterial quantification.
Python 1
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phylogenize-db-prep
phylogenize-db-prep PublicThis workflow is meant to be a compliment to the Phylogenize package by Bradley and Pollard, 2020. Databases are generated at the species level with protein clustering for the package to use. The w…
Python
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Sapiens_be_gone
Sapiens_be_gone PublicRemoves primate contamination with a focus on human contamination removal
Python
Repositories
- phylogenize Public
A tool for phylogenetic comparison and analysis of microbe including gene's environmental association
- phylogenize-db-prep Public
This workflow is meant to be a compliment to the Phylogenize package by Bradley and Pollard, 2020. Databases are generated at the species level with protein clustering for the package to use. The workflow starts from nucleotide level pangenomes and generates a taxonomy matrix of peptide clusters. It can then be run on the backend for databases
- genome_annotation_matrix Public
Annotate a set of genomes with protein families (e.g. UniRef50), select genomes using different methods, and simulate power under these approaches.
- phylogenize_v2_2025_paper Public
Holds all scripts used for generation of data and figures for phylogenzie v2.
- split_homology Public
Repository for pipeline in "Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome."
- 2023-anvio-comparison Public
Comparison of multiple annotation methods (Kofamscan, Microbeannotator, and anvi'o) using multiple prokaryotic families found across varying environments.
- culturomics_seqmatch Public
Rmd pipeline for processing Sanger data, aligning to database, and plotting results
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