Epigenomics

• MAT: Model-based Analysis of Tiling-array (PNAS 2006)

• CEAS: Cis-regulatory Element Annotation System (Nucleic Acids Res 2006)

• MACS: Model-based Analysis of ChIP-sequencing (Genome Biology 2008)

• BSMAP/RRBSmap (new URL): Whole genome (RRBS) Bisulfite Sequence MAPping program (BMC Bioinformatics 2009; Bioinformatics 2012)

• DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013)

• BSeQC: Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)

• MOABS: Model based Analysis of Bisulfite Sequencing data (Genome Biology 2014)

• MACE: Model Based Analysis of ChIP-exo (Nucleic Acids Res 2014)

• DNA methylation Canyon: (Nature Genetics 2014)

• DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features (Science Advances 2020)

• NG-Circos: next-generation Circos for data visualization and interpretation (NAR Genomics and Bioinformatics 2020)

• CHALM: Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression (Nature Communications 2021)

Transcriptomics

• RSeQC: Quality Control of RNA-seq experiments (Bioinformatics 2012)

• CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model (Nucleic Acids Res 2013)

• DaPars: Dynamic analysis of Alternative PolyAdenylation from RNA-seq (Nature 2014; Nature Communications 2015)

• TC3A: The Cancer 3′ UTR Atlas (Nucleic Acids Res 2018); please download all the TC3A data at this link

• MAT3UTR: Model-based analysis of the trans effect of 3ʹ-UTR shortening (Nature Genetics 2018)

• 3`aQTLs: human 3′UTR alternative polyadenylation (APA) quantitative trait loci (Nature Genetics 2021)