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    29 repositories

    • gEAR

      Public
      The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
      rna-seqgene-expressionsingle-cellsingle-cell-analysisbulk-rna-seqdata-archive
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •4•13•256•0•Updated Oct 3, 2024Oct 3, 2024

    • FADU

      Public
      Feature Aggregate Depth Utility
      Julia
      •
      GNU Affero General Public License v3.0
      •1•10•1•0•Updated Aug 20, 2024Aug 20, 2024

    • rnaseq-docker

      Public
      Dockerized version of the IGS transciptomics pipeline and associated utilities
      Python
      •0•0•0•2•Updated Jul 6, 2024Jul 6, 2024

    • ergatis

      Public
      Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.
      Perl
      •
      Other
      •15•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • osdf-nodejs-client

      Public
      A node.js client for the Open Science Data Framework (OSDF)
      nodejsjavascriptsciencescientific-computingnode-module
      JavaScript
      •
      MIT License
      •0•1•0•1•Updated Jun 17, 2024Jun 17, 2024

    • portal_client

      Public
      Python-based client for downloading data made available through portals powered by the GDC-based portal system..
      pythoncliawscloudaws-s3data-transferresearch-toolasperagoogle-cloud-platformaspera-client
      Python
      •
      MIT License
      •17•17•13•0•Updated May 18, 2023May 18, 2023

    • disease-ontology

      Public
      Disease Ontology
      0•0•0•0•Updated Mar 6, 2023Mar 6, 2023

    • report-generator

      Public
      Repository for new python based report and bdbag generator.
      Python
      •0•0•0•0•Updated Jan 12, 2023Jan 12, 2023

    • portal-ui

      Public
      UI for IGS project portals such as the HMP data portal found at https://portal.hmpdacc.org.
      JavaScript
      •
      Apache License 2.0
      •19•4•0•2•Updated Dec 13, 2022Dec 13, 2022

    • rnaseq-pipeline

      Public
      IGS Transcriptomics Pipeline
      Perl
      •0•1•0•0•Updated Mar 16, 2022Mar 16, 2022

    • grove-pipeline

      Public
      The IGS RNASeq SNP pipeline
      Perl
      •0•0•0•0•Updated Feb 3, 2022Feb 3, 2022

    • lgtseek-pipeline

      Public
      The IGS lateral gene transfer pipeline
      Perl
      •0•0•0•0•Updated Feb 3, 2022Feb 3, 2022

    • portal-api

      Public
      API for the IGS data portal
      Python
      •3•9•1•1•Updated May 6, 2021May 6, 2021

    • biocode

      Public
      Bioinformatics script collection
      Python
      •
      MIT License
      •246•7•0•0•Updated Aug 24, 2020Aug 24, 2020

    • GALES

      Public
      Genomic Annotation Logic and Execution System
      Python
      •
      MIT License
      •6•0•0•0•Updated Aug 18, 2020Aug 18, 2020

    • unified-schema-ecosystem

      Public
      Python
      •0•1•0•0•Updated Mar 30, 2020Mar 30, 2020

    • OSDF

      Public
      Open Science Data Framework (OSDF)
      JavaScript
      •
      MIT License
      •3•8•0•1•Updated Nov 1, 2019Nov 1, 2019

    • vmrc-osdf-schemas

      Public
      OSDF JSON-Schema files for the Vaginal Microbiome Research Consortium (VMRC)
      0•0•0•0•Updated Aug 15, 2019Aug 15, 2019

    • Chiron

      Public
      Tools and utilities for running Dockerized metagenomics tools in the Cloud
      clouddocker-imagemetagenomics
      C++
      •
      MIT License
      •18•23•0•0•Updated Apr 8, 2019Apr 8, 2019

    • LGTHGT

      Public
      Contains LGTView (http://www.igs.umaryland.edu/labs/lgthgt/analysis/lgt-view/) and all of its necessary installation components.
      HTML
      •0•0•0•0•Updated Feb 22, 2019Feb 22, 2019

    • osdf-python

      Public
      A Python OSDF (Open Science Data Framework) client
      Python
      •
      MIT License
      •3•3•0•0•Updated Feb 18, 2019Feb 18, 2019

    • HMP_database_builder

      Public
      Scripts to build the HMP database
      Python
      •0•2•0•0•Updated Feb 14, 2019Feb 14, 2019

    • portal-manifest-downloader

      Public archive
      Client for retrieving a Portal data manifest file from the cloud
      Python
      •0•0•0•0•Updated Nov 1, 2018Nov 1, 2018

    • osdf-deb-docker

      Public
      A docker container to generate the deb package for OSDF
      Shell
      •
      MIT License
      •1•1•0•0•Updated Jan 8, 2018Jan 8, 2018

    • cvd-scripts

      Public archive
      Python
      •0•0•0•0•Updated Oct 11, 2017Oct 11, 2017

    • imp

      Public
      IGS Metagenome Assembler
      Perl
      •0•1•0•0•Updated Jun 5, 2017Jun 5, 2017

    • docker_lgtview

      Public
      This repository houses a Dockerfile that can be used to build an example and customizable instance of LGTview
      Shell
      •1•0•0•0•Updated Jul 14, 2016Jul 14, 2016

    • twinblast

      Public
      View 2 blast reports at once
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jun 22, 2016Jun 22, 2016

    • Emergence

      Public archive
      A biological sequence annotation and analysis system.
      Python
      •
      Other
      •0•0•0•0•Updated Sep 16, 2013Sep 16, 2013