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@baliga-lab Baliga lab at the Institute for Systems Biology

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    95 repositories

    • miner3

      Public
      mirror of matt wall's miner3
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Sep 30, 2024Sep 30, 2024

    • 3H11_R12_SynCom

      Public
      This repository contains data and code for the manuscript "Emergence and disruption of cooperativity in a denitrifying microbial community"
      Jupyter Notebook
      •1•2•0•0•Updated Sep 4, 2024Sep 4, 2024

    • Metabolic-Model-of-Syntrophy-for-Dv-and-Mm

      Public
      Syntrophic community model generated by integrating genome-scale metabolic network models of DvH and Mmp.
      MATLAB
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • GBM_Atlas

      Public
      Repository for the manuscript titled An atlas of causal and mechanistic drivers of interpatient heterogeneity in gliomas predicts treatment response based on cell states
      HTML
      •0•0•0•0•Updated May 24, 2024May 24, 2024

    • NanoVar-Micro

      Public
      Nanopore Microbial Variant Calling Pipeline
      Python
      •0•0•0•0•Updated May 23, 2024May 23, 2024

    • cmonkey2

      Public
      Python port of cMonkey, a machine-learning based method for clustering
      Python
      •
      GNU Lesser General Public License v3.0
      •16•26•9•0•Updated Apr 15, 2024Apr 15, 2024

    • resr_pipeline

      Public
      SNP calling pipeline based on ResR
      Python
      •0•0•0•0•Updated Mar 26, 2024Mar 26, 2024

    • wp_tfbsdb2

      Public
      Wordpress plugin for integrating TFBSDB2 API
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 6, 2024Feb 6, 2024

    • Global_Search

      Public
      Code repository for the Coral Global Search project.
      rnaseqcoral
      Python
      •1•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • tfbsdb2-DataProcess

      Public
      Data process for constructing the transcription factor (TF) to target gene interactions database.
      Python
      •0•0•0•0•Updated Dec 18, 2023Dec 18, 2023

    • bwa_pipeline

      Public
      Genomics pipeline based on Burrows Wheeler Aligment
      Python
      •0•0•0•0•Updated Nov 14, 2023Nov 14, 2023

    • tfbsdb2

      Public
      New version of Transcription Factor Binding Site database
      Python
      •0•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • wp_minerapi

      Public
      Wordpress plugin to display data from a MINER web API
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 3, 2023Oct 3, 2023

    • glioma_web

      Public
      Website backing publication.
      HTML
      •1•0•0•0•Updated Jul 26, 2023Jul 26, 2023

    • tfbsdb

      Public
      Django web application to search for transcription factor binding sites
      JavaScript
      •
      GNU Lesser General Public License v3.0
      •2•0•0•0•Updated Jul 25, 2023Jul 25, 2023

    • halodata

      Public
      Unified Halobacterium application
      Vue
      •1•0•1•0•Updated Jul 18, 2023Jul 18, 2023

    • tnseq_processing

      Public
      TNSeq processing package for R
      R
      •0•1•0•0•Updated Jun 28, 2023Jun 28, 2023

    • firm2

      Public
      Integrated, more user-friendly version of the FIRM pipeline
      Python
      •0•0•0•0•Updated Apr 28, 2023Apr 28, 2023

    • miner_webapi

      Public
      Generic data interface for ananlysis data generated with MINER
      Python
      •
      GNU Lesser General Public License v3.0
      •0•0•0•0•Updated Apr 17, 2023Apr 17, 2023

    • mmSYGNAL-risk-prediction-models

      Public
      ML risk prediction models generated from mmSYGNAL
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • pf1010-web

      Public
      Aquaponics web application for Project Feed 1010
      JavaScript
      •
      GNU Lesser General Public License v3.0
      •0•0•13•1•Updated Dec 28, 2022Dec 28, 2022

    • duffy_scripts

      Public
      Automation scripts for running DuffyNGS based RNA seq analysis
      Python
      •0•0•0•0•Updated Dec 12, 2022Dec 12, 2022

    • SNAPPER

      Public
      SNP identification work flow
      Python
      •0•0•0•0•Updated Oct 26, 2022Oct 26, 2022

    • mirvestigator-rust

      Public
      Standalone implementation of miRvestigator in Rust
      Rust
      •
      GNU Lesser General Public License v3.0
      •0•0•0•0•Updated Oct 8, 2022Oct 8, 2022

    • rnaseq_starsalmon_slurm

      Public
      RNA-Seq pipeline based on STAR Salmon for SLURM clusters
      Python
      •1•0•0•0•Updated Aug 25, 2022Aug 25, 2022

    • miRvestigator_www

      Public
      A web server version of the miRvestigator framework.
      HTML
      •2•0•0•0•Updated Aug 17, 2022Aug 17, 2022

    • tcell_web

      Public
      Mtb infection T cell regulatory network web site.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 16, 2022Aug 16, 2022

    • Cancer-miRNA-Regulatory-Network

      Public
      A database containing the predictions for the Cancer miRNA-Regulatory Network.
      HTML
      •
      GNU Lesser General Public License v3.0
      •6•0•0•0•Updated Aug 16, 2022Aug 16, 2022

    • network_portal

      Public
      A web-app for archiving and exploring gene-regulatory networks.
      JavaScript
      •
      Other
      •3•6•26•0•Updated Aug 15, 2022Aug 15, 2022

    • egrin2_django

      Public
      Django web application for EGRIN 2.0
      JavaScript
      •
      GNU Lesser General Public License v3.0
      •1•1•1•0•Updated Aug 15, 2022Aug 15, 2022