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@RamanLab Raman Lab, IIT Madras

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    55 repositories

    • Hospital_Microbiome

      Public
      Analysis of microbial interactions in hospital and other built environments
      Jupyter Notebook
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • TNBC-single-cell-markers

      Public
      Reproducible code for identifying TIL-based markers from single-cell RNA-seq data of TNBC patients
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 2, 2025Dec 2, 2025

    • FastSL

      Public
      A MATLAB toolbox to rapidly evaluate synthetic lethal sets in organisms using the genome-scale metabolic models
      MATLAB
      •6•7•0•0•Updated Nov 5, 2025Nov 5, 2025

    • community_assembly_for_marine_microbiome

      Public
      Community assembly for marine microbiome
      R
      •1•0•0•0•Updated Oct 2, 2025Oct 2, 2025

    • BenchmCommDetection

      Public
      Contains the python module to implement community detection algos along with the final results obtained from benchmark analysis
      Jupyter Notebook
      •1•0•0•0•Updated Jun 29, 2025Jun 29, 2025

    • spore-to-VO

      Public
      0•0•0•0•Updated May 16, 2025May 16, 2025

    • UNFOLD-Framework

      Public
      Python
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • SKG_Drug_repurposing

      Public
      Python
      •1•0•0•0•Updated May 10, 2025May 10, 2025

    • Host-Candida-metabolic-modelling

      Public
      MATLAB
      •0•0•0•0•Updated May 9, 2025May 9, 2025

    • Panera

      Public
      MATLAB repository to construct pan-genus metabolic models (PGMM)
      MATLAB
      •1•1•0•0•Updated Apr 29, 2025Apr 29, 2025

    • COSMOS

      Public
      Compares monocultures and cocultres in an identical environment to identify the optimal microbial system
      MATLAB
      •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • minMicrobiome

      Public
      Code for generation of Minimal Microbiomes using a constraint-based approach
      MATLAB
      •
      MIT License
      •2•4•1•0•Updated Mar 23, 2025Mar 23, 2025

    • metquest

      Public
      Enumerating biosynthetic pathways in metabolic networks
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •11•13•0•0•Updated Feb 5, 2025Feb 5, 2025

    • Neobacillus

      Public
      Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus
      0•0•0•0•Updated Jan 25, 2025Jan 25, 2025

    • CAMP

      Public
      MATLAB
      •0•2•0•0•Updated Dec 3, 2024Dec 3, 2024

    • fbc_curation_matlab

      Public
      fbc_curation contains MATLAB/COBRA helpers for reproducibility of fbc models.
      MATLAB
      •
      GNU Lesser General Public License v3.0
      •2•2•1•0•Updated Aug 29, 2024Aug 29, 2024

    • phoenix-novel-species

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 21, 2024Aug 21, 2024

    • NonLinearAdaptation

      Public
      This repository contains the necessary MATLAB and SIMULINK files for the simulation studies done in the manuscript titled, 'Design Principles for Global, Perfect Adaptation]{Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics'
      MATLAB
      •0•1•0•0•Updated May 29, 2024May 29, 2024

    • ISS_Enterobacter

      Public
      Python
      •0•0•0•0•Updated May 16, 2024May 16, 2024

    • DNA-Computing-for-the-Subset-Sum-Problem

      Public
      This repository contains the code I wrote for my undergraduate research project on 'DNA-based computing for the Subset Product Problem', done at IIT Madras.
      Jupyter Notebook
      •1•0•0•0•Updated May 6, 2024May 6, 2024

    • minRerouting

      Public
      Package to understand the compensatory mechanisms performing similar metabolic functions through analysis of Synthetic Lethals
      Jupyter Notebook
      •1•3•7•0•Updated Mar 19, 2024Mar 19, 2024

    • metquest2

      Public
      Enumerating biosynthetic pathways in metabolic networks
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •11•8•0•1•Updated Sep 6, 2023Sep 6, 2023

    • SysBioBook

      Public
      HTML
      •0•0•4•0•Updated Jul 6, 2023Jul 6, 2023

    • structure-based-drug-design

      Public
      Structure based Drug Design using Distance prediction with Graph Neural Networks - Dual Degree Project
      Jupyter Notebook
      •1•0•0•0•Updated Jun 3, 2023Jun 3, 2023

    • CASTLE

      Public
      HTML
      •0•0•0•0•Updated Jun 2, 2023Jun 2, 2023

    • FastSL-py

      Public
      Python implementation of FastSL
      linear-programmingcomputational-biologyflux-balance-analysissynthetic-lethality-analysis
      Python
      •
      GNU General Public License v3.0
      •1•0•0•2•Updated May 22, 2023May 22, 2023

    • Robust-Adaptation

      Public
      MATLAB
      •0•0•0•0•Updated Feb 20, 2023Feb 20, 2023

    • co-FSEOF

      Public
      MATLAB
      •1•2•1•0•Updated Jan 23, 2023Jan 23, 2023

    • cobratoolbox

      Public
      The COnstraint-Based Reconstruction and Analysis Toolbox
      MATLAB
      •
      Other
      •333•0•0•0•Updated Jul 9, 2022Jul 9, 2022

    • COWAVE

      Public
      COVID-19 Wave dataset, based on WHO dataset and labelled as waves based on a new definition.
      machine-learningdatasetxgboostclassificationcovid-19
      Jupyter Notebook
      •0•0•0•0•Updated Jul 4, 2022Jul 4, 2022