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Download FASTQ files from SRA or ENA repositories.
R package for fetching and parsing data of the Human Microbiome Compendium
Transcript assembly and quantification for RNA-Seq
Full-Length Alternative Isoform analysis of RNA
Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
phylogenetics tools for linux (and other mostly posix compliant) computers
Efficient calculation of phylogenetic distance matrices.
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Set…
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
memote – the genome-scale metabolic model test suite
Asynchronous Arlo Component for Home Assistant
Discovery of conserved gene clusters in multiple genomes
creating reference databases for amplicon sequencing
Scripts used to analyze preterm infant fecal microbiome and metabolome. DOI: 10.1128/mSphere.00104-18
Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes
COBRApy is a package for constraint-based modeling of metabolic networks.
Public repository for cFMD - curatedFoodMetagenomicData
Metagenomic Estimation of Dietary Intake and Content.
Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the …
Structural variation caller using third generation sequencing
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
MethyLYZR: a Naïve Bayesian framework for rapid brain tumor classification from sparse epigenomic data
Genome modeling and design across all domains of life