Shareef Dabdoub's Projects
List of software packages for multi-omics analysis
List of software packages for repeated measures analysis in -omics data
Bioinformatics and Computational Biology Infrastructure for Julia
Collection of tools for interacting with biological databases.
The Biological Observation Matrix (BIOM) Format Project
Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html
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).
Facilitate creation and submission of HPC processing jobs to to distributed resource management systems (DRMS) like SLURM and PBS.
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.
Sphinx documentation for the FIND project
Kraken taxonomic sequence classification system
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Statistical analysis for sparse high-throughput sequencing
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
Web-based visualization tools for metagenomic/transcriptomic data
Week 3 of the OSU CoMS Webinar: Introduction to Amplicon Sequencing (QIIME, DADA2, mothur) and Ecological Statistics
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Project documentation for QIIME-tools
Sphinx documentation for the ProkaryMetrics project
Visualize and analyze 3D biofilm data from fluorescent micrographs
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.
A QIIME2 plugin for running SCNIC
Simple parsing tools in python for SAM-format files
Core objects, functions and statistics for working with biological data in Python.
Interactive stacked bar chart implemented in Processing
Text and code for the second edition of Think Bayes, by Allen Downey.