Brent Lab http://mblab.wustl.edu/ 21 29 13 C Twinscan 2 0 Twinscan is a suite of software for gene-structure prediction. Twinscan is currently available for Mammals, Caenorhabditis (worm), Dicot plants, and Cryptococci. Nscan 1 0 N-SCAN is a suite of software for gene-structure prediction. N-SCAN is available for human and Drosophila (fruitfly). Jupyter Notebook TFPertRespExplainer 2 1 Predict genes' response to perturbations and explains which genomic factors determine the response predictions. Perl ppfinder 1 0 PPFINDER is a Perl-based procedure for finding processed pseudogenes in genome annotations (GTF format). PPFINDER identifies pseudogenes using two different methods, and creates a GTF file with pseudogene coordinates that can be used for masking the genome sequence. Python TFA-evaluation 2 1 yeastdnnexplorer 1 3 A development environment to explore implementations of deep neural networks for predicting the relationship between transcription factor and target genes using binding and perturbation data R NetProphet_2.0 12 5 A “data light” TF-network mapping algorithm using only gene expression and genome sequence data. NetProphet_3.0 2 1 GOeval 1 0 Gene Regulatory Network Evaluation Using Gene Ontology brentlabRnaSeqTools 0 1 Rust Dual_Threshold_Optimization 4 1 Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR Shell dockerize_rstudio_server 1 0
