annotatr - Annotation of Genomic Regions to Genomic Annotations
Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.
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softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation
10.66 score 27 stars 6 dependents 518 scripts 1.2k downloadsmethylSig - MethylSig: Differential Methylation Testing for WGBS and RRBS Data
MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.
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dnamethylationdifferentialmethylationepigeneticsregressionmethylseqsequencingcoveragedifferential-methylationdna-methylation
8.19 score 21 stars 46 scripts 484 downloads