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kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

phylotoast

Tools for phylogenetic data analysis including visualization and cluster-computing support.

MicrobiomeInformaticsWebinarWeek3

Week 3 of the OSU CoMS Webinar: Introduction to Amplicon Sequencing (QIIME, DADA2, mothur) and Ecological Statistics

PyMGRAST

A python interface to the MG-RAST API including executable scripts providing higher level functionality. Designed to utilize the resources of the Ohio Supercomputer Center (www.osc.edu), but can be implemented in any *nix-based system.

find

Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.

awesome-rm-omics

List of software packages for repeated measures analysis in -omics data

clark-biom

Create BIOM-format tables (http://biom-format.org) from CLARK output (http://clark.cs.ucr.edu/) for use with downstream tools such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org), PhyloToAST (http://phylotoast.org).

ProkaryMetrics

Visualize and analyze 3D biofilm data from fluorescent micrographs

ThinkBayes2

Text and code for the second edition of Think Bayes, by Allen Downey.

kraken

Kraken taxonomic sequence classification system

awesome-multi-omics

List of software packages for multi-omics analysis

Bio.jl

Bioinformatics and Computational Biology Infrastructure for Julia

biodbtools

Collection of tools for interacting with biological databases.

biom-format

The Biological Observation Matrix (BIOM) Format Project

biomformat

Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html

ClusterDistribute

Facilitate creation and submission of HPC processing jobs to to distributed resource management systems (DRMS) like SLURM and PBS.

find-docs

Sphinx documentation for the FIND project

metagenomeSeq

Statistical analysis for sparse high-throughput sequencing

metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

mgviz

Web-based visualization tools for metagenomic/transcriptomic data

MLRepo

phylotoast-docs

Project documentation for QIIME-tools

pkm-docs

Sphinx documentation for the ProkaryMetrics project

q2-SCNIC

A QIIME2 plugin for running SCNIC

sam

Simple parsing tools in python for SAM-format files

scikit-bio

Core objects, functions and statistics for working with biological data in Python.

stackedbars

Interactive stacked bar chart implemented in Processing

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