Web Servers          Packages

IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis.

GitHub     Publication     Bioconductor

scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses.

GitHub     Publication     scGNN online website

SeqATU: Predicting ATUs (alternative transcription units) of bacterial organisms. (2020)


LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data. (2019)

GitHub     Publication

DESSO: Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. (2019)

GitHub     Publication

QUBIC2.0: A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. (2019)

GitHub     Publication

rSeqTU: A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units. (2019)

GitHub     Publication

MetaQUBIC a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. (2019)

GitHub     Publication

EL-SMURF: An Ensemble Learning of SMOTE for Unbalancing samples and RF algorithm in PPI sites prediction. (2019)

GitHub     Publication

GeneQC: A tool for gene expression level quality control. (2018)

GitHub     Publication

SPP: A sigma-54 promoter predictor in prokaryotic genomes based on a machine learning method. (2018)

GitHub     Publication

ViDGER: An R package for interpretation of differential gene expression results of RNA-seq data. (2018)

GitHub     OMICtools     Publication

QUBIC-R package (2017)

GitHub     Bioconductor     Video Demonstration     Publication

A phylogenetic model for understanding the effect of gene duplication on cancer progression. (2014)

GitHub     Publication

Cancer-evolution: A phylogenetic model for understanding the effect of gene duplication on cancer progression. (2013)

GitHub     Publication

supercoil: Bacterial chromosome folding structure under different conditions. (2013)

GitHub     Google Code     Publication

BoBro 2.0: An integrated toolkit for prediction and analysis of cis-regulatory motifs. (2011, 2013)

GitHub     Publication(1.0)     Publication(2.0)

GOST: An orthology mapping tool for prokaryotes. (2011)

GitHub      Google Code     Publication

QUBIC: A biclustering tool for microarray data. (2009)

GitHub     Datasets     Publication

UberOperon: Detecting uber-operons in prokaryotic genomes

GitHub     Publication