GenoREAD is a web-based, sequence verification software that can be used to compare Sanger sequencing trace files against a reference sequence. Users can either submit their sequencing results one clone at a time, or they can submit a series of clones (as a project) to run at once. Resu...
diffReps is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that informatio...
featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge...
The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools ...
标签：Epigenomics, DNA methylation,Bisulfite Sequencing
RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically. RUbioSeq's variant anal...
标签：Exome analysis, Copy number estimation, Bisulfite Sequencing
SeqSite is an efficient and easy-to-use software tool implementing a novel method for identifying and pinpointing transcription factor binding sites. It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding si...
MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.