Quantitative Microbiome Profiling

Preprocessing of single-cell RNA-Seq data for input to kallisto

MMseqs2: ultra fast and sensitive search and clustering suite

Versatile open-source tool for metagenomics

Sample search by metadata and features

Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript

Zero-inflated dimensionality reduction algorithm for single-cell data

Accurate sample inference from amplicon data with single nucleotide resolution

Clustering through Imputation and Dimensionality Reduction

Rarefaction scripts

Escape Excel: a tool for preventing gene symbol and accession conversion errors

Codes associated with the Poran et al. paper titled "Single-cell RNA-seq reveals a signature of sexual commitment in malaria parasites".

visJS2jupyter is a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells

Unix filters for manipulating and analysing (samples of) phylogenetic trees represented in the Newick format

DistMap

Curated and processed metagenomic data through ExperimentHub

Workflow Description Language - Specification and Implementations

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.

Material and note of the course of Applied ML in Python

An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and…

Short Read Sequence Typing for Bacterial Pathogens

Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

ISA tools API

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

NGS Language Bindings

microbiome R package

PyCogent: Official repository for software and unit tests

Source of biopython.org website, migrated from MediaWiki

Hierarchical probabilistic models for multiple gene/variant associations based on NGS data