PoeticPremium6

3D_Metalloproteome_Ecoli

Integration of 3D Metalloproteins with ALE Mutations

BacArena

agent based modelling

gapseq

Informed prediction and analysis of bacteria metabolic pathways and genome-scale networks

LactoPRECISE

LactoPRECISE: A comprehensive framework exploring Lactobacillus reuteri's genetic diversity, regulatory networks, and functional annotations for personalized medicine and microbial therapeutics.

QSPACE

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

samsa2

SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.

SWIS-META

UTI-Microbiome-Model

Leveraging patient-specific metatranscriptome to reconstruct and simulate microbiome community model

PoeticPremium6/gapseq

Informed prediction and analysis of bacteria metabolic pathways and genome-scale networks

PoeticPremium6/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

PoeticPremium6/3D_Metalloproteome_Ecoli

Integration of 3D Metalloproteins with ALE Mutations

PoeticPremium6/BacArena

agent based modelling

PoeticPremium6/LactoPRECISE

LactoPRECISE: A comprehensive framework exploring Lactobacillus reuteri's genetic diversity, regulatory networks, and functional annotations for personalized medicine and microbial therapeutics.

PoeticPremium6/QSPACE

PoeticPremium6/samsa2

SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.

PoeticPremium6/SWIS-META

PoeticPremium6/UTI-Microbiome-Model

Leveraging patient-specific metatranscriptome to reconstruct and simulate microbiome community model