DNA methylation contributes to the epigenetic regulation of many key developmental processes including genomic imprinting, X-inactivation, genome stability and gene regulation. Bisulfite conversion of genomic DNA combined with next-generation sequencing (BS-seq) is widely used to measure the methylation state of a whole genome, the methylome, at single-base resolution (Lister et al., 2009; Bock et al., 2010; Harris et al., 2010).
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Infers epiallelic haplotypes, annotated with CpG methylation marks and…
Infers epiallelic haplotypes, annotated with CpG methylation marks and polymorphisms, from whole genome bisulphite sequencing data, and nucleosome occupancy from NOMe-seq data. The performance of…
Allows to simultaneously account for both the over-dispersed, count-based…
Allows to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. MACAU is a binomial mixed model and an…
Identifies differentially methylated cytosines and regions. Hidden Markov model…
Identifies differentially methylated cytosines and regions. Hidden Markov model (HMM)-Fisher is efficient and robust in identifying heterogeneous differentially methylated (DM) regions. This method…
A method to map DNA methylation data from bisulfite sequencing approaches to…
A method to map DNA methylation data from bisulfite sequencing approaches to CpG sites measured with the widely used Illumina methylation bead-array platforms. Correlations and median absolute…
A software package to map and determine the methylation state of BS-Seq reads.…
A software package to map and determine the methylation state of BS-Seq reads. Bismark is easy to use, very flexible and is the first published BS-Seq aligner to seamlessly handle single- and…
An open-source software tool capable of analysing whole-genome bisulfite…
An open-source software tool capable of analysing whole-genome bisulfite sequencing data with either a gene-centric or gene-independent focus. GBSA’s output can be easily integrated with other…
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