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TnT:Interactive Visualization for Genomic Features
A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.
Maintained by Jialin Ma. Last updated 5 months ago.
infrastructurevisualizationbioconductorgenome-browserhtmlwidgetsshiny
18.7 match 14 stars 7.15 score 17 scriptsbioc
qsea:IP-seq data analysis and vizualization
qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.
Maintained by Matthias Lienhard. Last updated 5 months ago.
sequencingdnamethylationcpgislandchipseqpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationchiponchipdifferentialmethylation
3.5 match 3.30 score 7 scriptsbioc
EpiMix:EpiMix: an integrative tool for the population-level analysis of DNA methylation
EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.
Maintained by Yuanning Zheng. Last updated 5 months ago.
softwareepigeneticspreprocessingdnamethylationgeneexpressiondifferentialmethylation
2.3 match 1 stars 4.48 score 7 scripts 1 dependents