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Epiviz
An interactive visualization tool for functional genomics data. Epiviz supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. Epiviz sets a precedent for genomic data analysis collaborative workflows by enabling reproducible and shareable steps, and allowing custom user code to be dynamically incorporated, while guaranteeing the security and integrity of user data.
chroGPS
Allows users to integrate and visualize the associations between epigenetic factors and their relation to functional genetic elements in low-dimensional maps. chroGPS is a dimensionality reduction technique that is able to analyze genomic data. This tool is a map-generating tool applicable to a wide range of situations. It works with two types of map: chroGPS'factors that describes similarities between epigenetic factors, and chroGPS'genes that integrates epigenetic marks and describes the epigenetic context of gene expression.
SeqMonk
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A program to enable the visualisation and analysis of mapped sequence data. SeqMonk was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are: (i) Import of mapped data from mapped data (BAM/SAM/bowtie etc), (ii) Creation of data groups for visualisation and analysis, (iii) Visualisation of mapped regions against an annotated genom, (iv) Flexible quantitation of the mapped data to allow comparisons between data sets, (v) Statistical analysis of data to find regions of interest and (vi) Creation of reports containing data and genome annotation.
DMEAS / DNA Methylation Entropy Analysis Software
Analyzes the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. DMEAS supports the analysis of both locus-specific and genome-wide bisulfite sequencing data. It progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It determines the DNA methylation level and calculates methylation entropy for genomic segments to enable the quantitative assessment of DNA methylation variations observed in cell populations.
BSviewer
Allows visualization of bisulfite sequencing data. BSviewer allows users to inspect the DNA methylation dynamics at nucleotide level. The software supports both paired-end and single-end sequencing data. A testing dataset, provided within the package, illustrates the usage of BSviewer. It contains bisulfite sequencing reads from the human placental tissue obtained from a previous work. The software helps users to visualize, interpret and mine more details from their bisulfite sequencing data.
Methy-Pipe
A software tool that not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data annotation and visualization. Specifically, Methy-Pipe uses Burrow-Wheeler Transform (BWT) algorithm to directly align bisulfite sequencing reads to a reference genome and implements a novel sliding window based approach with statistical methods for the identification of differentially methylated regions (DMRs). The capability of processing data parallelly allows it to outperform a number of other bisulfite alignment software packages.
WBSA / Web Service for Bisulfite Sequencing Data Analysis
A free web application for analysis of whole-genome bisulfite-sequencing (WGBS) and genome-wide reduced representation bisulfite sequencing (RRBS) data. WBSA not only focuses on CpG methylation, but also allows CHG and CHH analysis. BWA is incorporated as its mapping software. WBSA can be applied to DNA methylation researches for animals and plants and it provides advanced analysis for both WGBS and RRBS. It can also identify differently methylated regions (DMRs) in different strings. WBSA includes six modules: Home, WGBS, RRBS, DMR, Documents and Downloads, and provides the executable package for downloads and local installation. WGBS and RRBS modules include four main steps: pre-processing of reads and reference, alignment to the reference, identification of methylcytosines and annotation. DMR module includes DMRs identification and annotation of the correlative genes.
methVisual
Enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. MethVisual allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. It has been developed for methylation data but can be also used for other data types for which binary coding can be inferred.
RRBS-Analyser
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A comprehensive genome-scale DNA methylation analysis server based on RRBS data. RRBS-Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite-treated short reads to reference genome, identify and annotate the methylcytosines (5mCs) and associate them with different genomic features in CG, CHG, and CHH content. RRBS-Analyser supports detection, annotation, and visualization of differentially methylated regions (DMRs) for multiple samples from nine reference organisms. Moreover, RRBS-Analyser provides researchers with detailed annotation of DMR-containing genes, which will greatly aid subsequent studies. The input of RRBS-Analyser can be raw FASTQ reads, generic SAM format, or self-defined format containing individual 5mC sites. RRBS-Analyser can be widely used by researchers wanting to unravel the complexities of DNA methylome in the epigenetic community.
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