Jonathan Josephs-Spaulding's repositories
RNA-SEQ--Raw-reads-to-Counts
A variety of RNA-Seq pipelines are presented: Tuxedo for bacteria, Tuxedo for Humans, and HISAT2 for Humans. Additionally, you can find scripts for normalization of RNA-Seq Counts and scripts for visualization of DEGs
BacArena
agent based modelling
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LactoPRECISE
LactoPRECISE: A comprehensive framework exploring Lactobacillus reuteri's genetic diversity, regulatory networks, and functional annotations for personalized medicine and microbial therapeutics.
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samsa2
SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.
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UTI-Microbiome-Model
Leveraging patient-specific metatranscriptome to reconstruct and simulate microbiome community model