A cell state trajectory inference method for time-series scRNA-seq data.
Ref: Zhao et al. CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data. Bioinformatics (accepted).
A DNA methylation state transition model for characterizing methylation changes during one or a few cell cycles at single-cell resolution.
Ref: Zhao et al. A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos. Genome Biol 2020; 21: 277.
ncHMR detector [software link][webserver link]
A computational framework to systematically reveal non-classical functions of histone modification regulators.
Ref: Hu et al. ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators. Genome Biol 2020; 21: 48.
A comprehensive database of nucleosome organizations in mammalian genomes
Ref: Chen et al. NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. BMC Bioinformatics 2021; 22:321.
A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data
Ref 1: Zhao et al. Dr.seq2: a quality control and analysis pipeline for parallel single cell transcriptome and epigenome data. PLoS ONE 2017; 12(7):e0180583.
Ref 2: Huo et al. Dr.seq: a quality control and analysis pipeline for droplet sequencing. Bioinformatics 2016; 32: 2221-3.
A quality control and analysis pipeline for MNase-seq data
Ref: Hu et al. CAM: a quality control pipeline for MNase-seq data. PLoS ONE 2017; 12(8):e0182771.
gRNA Designer for Zebrafish [link]
A webserver for zebrafish gRNA selection based on chromatin accessibility features
Ref: Chen et al. Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. PLoS ONE 2017; 12(8):e0182528.
A webserver for cell state transition expression atlas in human and mouse
Ref: Zhu et al. CSTEA: a webserver for the cell state transition expression atlas. Nucleic Acids Res 2017; 45: W103-8.
Cistrome Chromatin Regulator
A knowledgebase for chromatin modifying enzymes and chromatin remodelers (Temporarily unavailable)
Ref: Wang et al. CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Res 2014; 42:D450-8.
A statistical algorithm to infer tumor purity and detect differential methylation from single tumor BS-seq experiment
Ref: Zheng et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol 2014; 15:419.
Generalized fold change (GFOLD) [link]
Generalized fold change for ranking differentially expressed genes based on RNA-seq
Ref: Feng et al. GFOLD: a generalized fold change for ranking differentially ex-pressed genes from RNA-seq data. Bioinformatics 2012; 28(21):2782-8.
Differential Nucleosome positioning (DiNuP) [link]
An unbiased algorithm from detecting genomic regions with dynamic nucleosome positioning
Ref: Fu et al. DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 2012; 28(15):1965-71.
Genome Segmentation from Intra-Chromosomal Associations (GeSICA) [link]
A two-step algorithm for genome segmentation into functional blocks from Hi-C experiments
Ref: Liu et al. GeSICA: genome segmentation from intra-chromosomal associations. BMC Genomics 2012; 13:164.
Model-based Analysis of ChIP-Seq (MACS) [link]
A model-based algorithm for finding enriched regions in ChIP-Seq experiments
Ref: Zhang et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008; 9:R137.
Nucleosome Positioning from Sequencing (NPS) [link]
A signal processing-based algorithm for identifying positioned nucleosomes from sequencing experiments at the nucleosome level
Ref: Zhang et al. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 2008; 9:537.