CondSigDetector [link]

A computational framework to detect condensate-like chromatin-associated protein co-occupancy signatures.

Ref: Yu et al. Decoding the genomic landscape of chromatin-associated biomolecular condensates. Nat Commun 2024; 15:6952.

PSPire [link]

A machine learning predictor for phase-separating proteins without intrinsically disordered regions.

Ref: Hou et al.  Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions. Nat Commun 2024; 15:2147.

ImSpiRE [link]

An image feature-aided spatial resolution enhancement method for in situ capturing spatial transcriptome.

Ref: Yang et al. ImSpiRE: Image feature-aided spatial resolution enhancement method. Sci China Life Sci (accepted).

PCAR [link]

A computational pipeline for CHM calling and scoring the allele-specific regulatory roles.

Ref: Yang et al. Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. Nat Cell Biol 2022; 24:783-92.

CStreet [link]

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 2021; 37(21):3774-80.

MethylTransition [link]

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 uncover 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.

NUCOME [link]

A comprehensive database of nucleosome organization in mammalian genomes.

Ref: Chen et al. NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. BMC Bioinformatics 2021; 22:321.

Dr.seq2 [link]

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.

CAM [link]

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.

CSTEA [link]

A webserver for the expression atlas of cell state transitions 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 [link]

A knowledgebase for chromatin modifying enzymes and chromatin remodelers.

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.

MethylPurify [link]

A statistical algorithm to infer tumor purity and detect differential methylation from a 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 for 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.