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biocode

Bioinformatics script collection

chiron

Tools and utilities for running Dockerized metagenomics tools in the Cloud

cvd-scripts

disease-ontology

Disease Ontology

docker_lgtview

This repository houses a Dockerfile that can be used to build an example and customizable instance of LGTview

emergence

A biological sequence annotation and analysis system.

ergatis

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.

fadu

Feature Aggregate Depth Utility

gales

Genomic Annotation Logic and Execution System

gear

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.

grove-pipeline

The IGS RNASeq SNP pipeline

hmp_database_builder

Scripts to build the HMP database

imp

IGS Metagenome Assembler

lgthgt

Contains LGTView (http://www.igs.umaryland.edu/labs/lgthgt/analysis/lgt-view/) and all of its necessary installation components.

lgtseek-pipeline

The IGS lateral gene transfer pipeline

osdf

Open Science Data Framework (OSDF)

osdf-deb-docker

A docker container to generate the deb package for OSDF

osdf-nodejs-client

A node.js client for the Open Science Data Framework (OSDF)

osdf-python

A Python OSDF (Open Science Data Framework) client

portal-api

API for the IGS data portal

portal-manifest-downloader

Client for retrieving a Portal data manifest file from the cloud

portal-ui

UI for IGS project portals such as the HMP data portal found at https://portal.hmpdacc.org.

portal_client

Python-based client for downloading data made available through portals powered by the GDC-based portal system..

report-generator

Repository for new python based report and bdbag generator.

rnaseq-docker

Dockerized version of the IGS transciptomics pipeline and associated utilities

rnaseq-pipeline

IGS Transcriptomics Pipeline

twinblast

View 2 blast reports at once

unified-schema-ecosystem

vmrc-osdf-schemas

OSDF JSON-Schema files for the Vaginal Microbiome Research Consortium (VMRC)