Chenlab:Softwares

Chen Laboratory
Boston Children's Hospital
Harvard Medical School

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• MEBOCOST (BioRxiv, 2022): A computational technology to enable detection of cell-cell communications mediated by metabolites and their sensor proteins (receptor, transporter, etc) based on single-cell RNA-Seq data.

• MACMIC (Genomics, Proteomics and Bioinformatics, 2021): A statistical method to define epigenomic features that have maximal co-localization but minimal correlation across the genome.

• TADsplimer (Genome Biology, 2020): A bioinformatic toolkit to identify TAD splits and mergers between Hi-C samples.

• CEFCIG at GitHub or GoogleSite(Nature Communications, 2020): A Computational Epigenetic Framework for Cell Identity Gene discovery.

1. GridGO: a grid-based genetic algorithm for automatic optimization of epigenetic signature analysis on the basis of biological significance.
2. CIGdiscover: a logistic regression model for cell identity genes discovery
3. CIGnet: a novel network method to uncover master transcription factors for cell identity genes in an unbiased, knowledge-guided, and quantitatively testable manner.
4. CIGDB: A Cell Identity Gene Database.

• CAGRE (Science, 2019): A bioinformatic tool for Commulative Analysis of Genomic Region Enrichment.

• FAID (Nature, 2018): A bioinformatic tool for Feature Analysis of Inserted DNA in a genome.

• DANPOS2 (Nature Genetics, 2015): a set of 8 bioinformatics tools, including:

1. Dpos: comparative analysis of MNase-Seq data between samples.
2. Dpeak: comparative analysis ChIP-Seq data between samples.
3. Dregion: analyzing broad epigenetic domains, e.g., super enhancers.
4. Stat: statistical analysis of positions, peaks, or regions defined by DANPOS.
5. Selector: mapping positions, peaks, or regions to any given genomic features such as genes.
6. Profile: analyzing epigenetic signal at any given genomic regions, e.g., genes, enhancers.
7. Wiq: a tool for genome wide quantile normalization of epigenetic data.
8. Wig2Wiq: a tool for converting wiggle format file to wiq format.

• DANPOS (Genome Research, 2013): A tool for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing

• SpikeSCN (Genes & Development, 2013). Genome structure and copy number variation analysis based on genome sequencing with spike-in control.

• BarVar (Cell reports, 2013). A bioinformatics pipeline to screen for drug-resistant genetic variations from barcode sequencing data.

• NucHMM (GPB, 2010). A Hidden Markov Model for nucleosome positioning prediction based on DNA sequence feature.

• GenomePSD (Nucleic acids research, 2008). A Power Spectrum Density analysis tool for genome sequence.

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