An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite sequencing protocols, but also MeDIP-seq and MBD-seq.
A reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNA methylation and genetic variation in hundreds of samples de novo. epiGBS method uses genotyping by sequencing of bisulfite-converted DNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNPs) versus methylation variation. The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.
Permits rigorous statistical investigation of genomic data. Genomic HyperBrowser can serve for a range of genomic investigations that query characteristics of individual tracks or relations between pairs of tracks along the genome. It is able to differentiate 15 types of tracks at the generic level. This tool furnishes programs for customizing data into forms that eases subsequent analyses.
A complete, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing. MOABS seamlessly integrates alignment, methylation calling, identification of hypomethylation for one sample and differential methylation for multiple samples, and other downstream analysis.
Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq, bisulfite-seq and ChIP-seq experiments. The software incorporates a graphical user interface (GUI), designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together. The modular structure permits easy adaptation and extension.
Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.
Integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. SAAP-RRBS facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation.
A pipeline for automatic analysis of Bisulfite sequencing (BSseq) reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment and generates BED methylome. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements and is optimized to process the upcoming. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and next generation sequencing (NGS) knowledge. P3BSseq identifies the available cores and main memory, and takes maximum advantage of them in function of the dataset requirements. P3BSseq adapts automatically to kmers trimming and thus improves the alignment by mapping uniquely twice more read.
Analyzes whole genome bisulfite sequencing (WGBS) data. bicycle is a next-generation sequencing (NGS) bioinformatic pipeline that can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols and from single-end and paired-end sequencing. It also performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH). It provides statistical methylcytosine calling and offers several filters to screen reads.
Allows to extract multiple types of information (such as DMCs, DMRs, SNPs and ASM) from various types of RRBS and Bis-seq data. SMAP is designed to be an easy-to-use, one-stop and sophisticated package for methylation analyses. The pipeline consists of seven operational stages: (i) reference preparation, (ii) read preparation, (iii) alignment, (iv) calculation of methylation rate, (v) differentially methylated regions (DMR) detection, (vi) single nucleotide polymorphism (SNP) and allele-specific DNA methylation (ASM) calling and (vii) summarization.
A software tool designed for the analysis of data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS). MethGo provides both genomic and epigenomic analyses including: 1) coverage distribution of each cytosine; 2) global cytosine methylation level; 3) cytosine methylation level distribution; 4) cytosine methylation level of genomic elements; 5) chromosome-wide cytosine methylation level distribution; 6) Gene-centric cytosine methylation level; 7) cytosine methylation levels at transcription factor binding sites (TFBSs); 8) single nucleotide polymorphism (SNP) calling, and 9) copy number variation (CNV) calling. MethGo is a simple and effective tool for the analysis of BS-Seq data including both WGBS and RRBS. It contains 9 analyses in 5 major modules to profile (epi)genome. It profiles genome-wide DNA methylation in global and in gene level scale. It can also analyze the methylation pattern around the transcription factor binding sites, and assess genetic variations such as SNPs and CNVs.
A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe is a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.
A web application to aid with the analysis of high-throughput sequencing data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-seq, Methyl-seq, RRBS, or DNA-seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.
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.
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.
Provides a platform for storing, handling and processing next generation sequencing (NGS) data. OTP performs both data management and processing and allows users to automate an entire process to raw data import from storage. The application includes functionalities for check quality control and sequence alignment and identify single-nucleotide and structural genomic events.
A virtual machine for DNA methylation profiling, genotyping and differential methylation analysis. The virtual machine is based on an extended version of our MethylExtract algorithm, Bismark/Bowtie2 for read alignment and methylKit for differential methylation analysis. Frequently DNA methylation research is carried out in the biomedical field, where privacy issues play an important role. Therefore, we implemented the pipeline into a virtual machine termed MethFlowVM which shares with a web-server its user-friendliness however, the decisive advantage is that the sequencing data does not leave the user desktop or server and therefore no privacy issues do exist. The virtual machine can be easily used by users without bioinformatics background.
Consists in a bioinformatics pipeline specifically designed for the analysis of large whole genome bisulfite sequencing (WGBS) data sets in a HPC environment. GEMBS implements two core modules: (i) GEM3, a high performance read aligner and (ii) BScall, a variant caller specifically for bisulfite sequencing data. GEMBS can be used for the analysis of CpG and non-cpg methylation, SNP from WGBS and allele specific methylation.
Assists users in analyzing next-generation sequencing (NGS) data. snakePipes provides DNA-mapping, ChIP-seq, ATAC-seq, RNA-seq, whole-genome bisulfite-seq (WGBS), HiC and single-cell RNA-seq workflows. It employs extensive quality-checks and produces reports that inform users about processing and analysis results. It provides workflows that allow processing and downstream analysis of data in an allele-specific manner.
Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq, MeDIP-seq and ChIP-seq experiments. This tool includes standard differential expression analysis for different experimental conditions, as well as differential splicing analysis. It can notice variants in the transcriptome and gene fusion events.
Supports compilation, analysis and presentation of bisulfite DNA methylation data. BDPC is a web application that supports data presentation by preparing publication grade figures showing methylation pattern of each Polymerase Chain Reaction (PCR) product. It provides a data summary for each PCR product, different result compilation files and supports further in-depth analysis by preparing a condensed output file, which contains all primary data.
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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