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camp

castle

castle-v0

Computational Analysis of SynThetic LEthals

castle_new

co-fseof

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox

comm-synleth-virgo

Repository for running FastSL on the community models of Human gut microbes on the Virgo cluster at IIT Madras.

compass

A tool to predict sub-networks from metabolic networks

cowave

COVID-19 Wave dataset, based on WHO dataset and labelled as waves based on a new definition.

ctag

curated-bifidobacterial-gsm

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

curated-bifidobacterial-gsm-1

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

diseasemoduleidentification

fastsl

A MATLAB toolbox to rapidly evaluate synthetic lethal sets in organisms using the genome-scale metabolic models

fastsl-py

Python implementation of FastSL

fbc_curation_matlab

fbc_curation contains MATLAB/COBRA helpers for reproducibility of fbc models.

gutrecoverymetabolicnets

Companion repository for manuscript on "Unraveling microbial interactions in the gut microbiome associated with antibiotic recovery"

icomic

icomic_doc

iCOMIC is an open source genomic data analysis tool characterized by a user friendly GUI. It integrates many independent core workflows for Whole Genome/Exome Sequencing and RNA-Seq data analysis.

identifytsgog

iss_enterobacter

metabolic-modelling-of-the-iss-microbiome

Created on 2020-11-04 to maintain versions of the project from this time point onwards.

metquest

Enumerating biosynthetic pathways in metabolic networks

metquest-old

Enumeration of biosynthetic pathways from metabolic networks

metquest2

Enumerating biosynthetic pathways in metabolic networks

minmicrobiome

Code for generation of Minimal Microbiomes using a constraint-based approach

minreact

minrerouting

Package to understand the compensatory mechanisms performing similar metabolic functions through analysis of Synthetic Lethals

nbdriver

Codes required to reproduce the results from the NBDriver manuscript

nbfpeg