justinshaffer
Microbial ecologist interested in understanding functional ecology underlying host-microbe interactions in plants and humans.
California State University, FresnoFresno, CA, USA
Pinned Repositories
2024-07-09-Software-Carpentry
Official website for the Carpentries workshop at Fresno State July 9-10, 2024
absolute_abundances_metagenomic_synDNA
Codebase for synDNA from Zaramela et al. 2022
cmi-workshops
Context-dependent-and-variable-effects-of-endohyphal-bacteria-on-interactions-between-fungi-and-seed
Data and code for analyses performed in this study
DEICODE
Robust Aitchison RPCA on sparse omics datasets
EBI_SRA_Downloader
A tool that allows users to efficiently fetch studies from the European Nucleotide Archive (ENA) and the Sequence Read Archive (SRA).
emp
Code repository of the Earth Microbiome Project.
Endohyphal_bacterium_alters_substrate_use_by_Fusarium_keratoplasticum
Biolog plate data and R code for analysis
Extraction_test_MagMAX
justinshaffer's Repositories
justinshaffer/Extraction_test_MagMAX
justinshaffer/2024-07-09-Software-Carpentry
Official website for the Carpentries workshop at Fresno State July 9-10, 2024
justinshaffer/absolute_abundances_metagenomic_synDNA
Codebase for synDNA from Zaramela et al. 2022
justinshaffer/cmi-workshops
justinshaffer/Context-dependent-and-variable-effects-of-endohyphal-bacteria-on-interactions-between-fungi-and-seed
Data and code for analyses performed in this study
justinshaffer/DEICODE
Robust Aitchison RPCA on sparse omics datasets
justinshaffer/EBI_SRA_Downloader
A tool that allows users to efficiently fetch studies from the European Nucleotide Archive (ENA) and the Sequence Read Archive (SRA).
justinshaffer/emp
Code repository of the Earth Microbiome Project.
justinshaffer/Endohyphal_bacterium_alters_substrate_use_by_Fusarium_keratoplasticum
Biolog plate data and R code for analysis
justinshaffer/Extraction_kit_benchmarking
Repository for code used for data processing and analysis of microbial sequence data generated from various DNA extraction kits designed for high-throughput extraction of microbiome samples.
justinshaffer/gapminder_project
Repository for iPlant software carpentry git exercises
justinshaffer/metagenomics_pooling_notebook
Jupyter notebooks to assist with sample processing
justinshaffer/qiita
Qiita - A multi-omics databasing effort
justinshaffer/R-ecology-lesson
:notebook: Data Carpentry R lessons on ecology.
justinshaffer/sepp
Ensemble of HMM methods (SEPP, TIPP, UPP)
justinshaffer/shell-novice
Software Carpentry introduction to the shell for novices.
justinshaffer/validation-notebooks
A collection of validation notebooks for benchmarking molecular and computational methods for performing a microbiome study
justinshaffer/zebra_filter
Filtering out false taxonomic hits from shotgun sequencing based on genome coverage