Repositories list

• Global_Search

  Public
  Code repository for the Coral Global Search project.

  rnaseqcoral

  rnaseqcoral

  Python

  •2•1•0•0•Updated Mar 30, 2026Mar 30, 2026

• bwa_pipeline

  Public
  Genomics pipeline based on Burrows Wheeler Aligment

  Python

  •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

• miner3

  Public
  mirror of matt wall's miner3

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•1•0•0•Updated May 21, 2025May 21, 2025

• mmSYGNAL-risk-prediction-models

  Public
  ML risk prediction models generated from mmSYGNAL

  HTML

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• RNASeq_Diatom

  Public
  Code repository for the RNA Seq on GEO Diatom data sets.

  Python

  •2•0•0•0•Updated Nov 6, 2024Nov 6, 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•1•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 c…

  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

  •14•26•10•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

• 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

• 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

• 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