DNA methylation software tools | DNA modification data analysis
Epigenetic mechanisms, including DNA methylation, are responsible for determining and maintaining cell fate, stably differentiating the various tissues in our bodies. Increasing evidence shows that DNA methylation plays a significant role in cancer, from the silencing of tumor suppressors to the activation of oncogenes and the promotion of metastasis. Recent studies also suggest a role for DNA methylation in drug resistance.
Identifies DNA modifications in the case where 5-mC can be distinguished from cytosine by careful analysis of the electrical current signals. Nanopolish computes the log-likelihood ratio between an unmethylated version of a reference genome substring and a version that contained at least one ‘CG’ dinucleotide. It employs a signal-level hidden Markov model (HMM) method to work. This tool can increase the consensus accuracy around homopolymers.
Implements an approach for mapping N6-methyladenine (m6dA) events using single-molecule real-time (SMRT) sequencing, specifically designed for the study of eukaryotic genomes. SMRTER is an R package that can assist the study design, m6dA detection and interpretation using SMRT sequencing, as well as its critical integration with independent and complementary sequencing methods. It was applied to the study m6dA in green algae and human genomes.
Detects both hyper and hypomethylated genes. MethylMix performs the computation of the differential methylation value that allows users to distinguish abnormal methylation state from normal ones. This program can be applied to cancer subtyping as well as for clustering. Additionally, the package includes features intending to ease investigation related to the understanding of methylation-driven genes in data derived from The Cancer Genome Atlas (TCGA).
Provides a compression scheme tailor tool for bedMethyl files. METHCOMP depends on an integrated processing structure which encompasses deinterleaving several columns of bedMethyl files to enhance the corresponding coding schemes. This software is able to compact the files up to 2% of their original size via of the use of different compression strategies including adaptive arithmetic, runlength and differential encoding.
Enables secondary analysis of next-generation sequencing (NGS) data. DRAGEN uses a reconfigurable field-programmable gate array (FPGA) to provide hardware-accelerated implementations of secondary analysis pipeline algorithms, such as BCL conversion, compression, mapping, alignment, sorting, duplicate marking, and haplotype variant calling. This software can be leveraged as a blended hybrid of the onsite and Cloud solutions.
Provides a kernel density estimation (KDE) based tool in order to estimate the level of DNA methylation. Notos is composed of two separate programs which allows to calculate the CpG o/e ratios of the sequences and also allows data preparation and analysis of distribution of the CpG 61 o/e ratios using KDE.
Furnishes a model to quantify the proportion of neurons to glia based on DNA methylation measures across multiple CETS markers. CETS includes a technique for transforming existing DNA methylation data sets, derived from bulk tissue preparations generated on Illumina microarrays, to remove cell-type heterogeneity bias from DNA methylation profiles. Moreover, this tool can be used for analyzing DNA methylation differences in major depressive disorder (MDD), with age, and across brain regions.