CRML – Web interface for locating muscle-specific regulatory modules in C. elegans sequences. Reference: Identification of muscle-specific regulatory modules in Caenorhabditis elegans, Zhao et al., 2007
C elegans PhyloNet – Whole Genome Conserved Motifs and Predicted cis-Regulatory Modules in Caenorhabditis elegans. Reference: Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans, Zhao et al., 2012
VirusSeeker: a set of fully automated and modular software package designed for mining next generation sequencing data form Illumina platform to identify sequences of viral origin. Reference: VirusSeeker, a computational pipeline for virus discovery and virome composition analysis, Zhao et al., 2017
VirusHunter : a fully automated and modular software package designed for mining sequence data (454 or long contigs) to identify sequences of microbial origin. Reference: Identification of Novel Viruses Using VirusHunter — an Automated Data Analysis Pipeline, Zhao et al., 2013
MORA: Motif Over Representation Analysis (MORA) is a fully automated pipeline to detect enrichment of known TF binding motifs in any query sequences. This repository provides source code and documentation of the single machine version of the pipeline.
EnsembleTFpredictor: EnsembleTFPredictor is an ensemble approach to rank putative causal transcription factors that regulate a set of query genes by prediction confidence. This repository provides source code and documentation of the Shiny R version of the application as well as a link and instructions for using the web portal. Reference: MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks, Boyer et al, 2023