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.
Serves for bisulfite sequencing analysis. QUMA suits for bisulfite sequence alignment, trimming raw bisulfite sequence, checking sequence quality, quantifying the methylation profiles by various diagrams and calculation of statistics values. This software consists of two main separate analyses: a methylation status analysis mode using one group of bisulfite sequences and a statistical analysis mode that utilizes two groups of bisulfite sequences.
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 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.
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.
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 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.