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.
Last updated 2 months ago
softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation
9.76 score 25 stars 5 dependents 254 scripts 837 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.
Last updated 2 months ago
dnamethylationdifferentialmethylationepigeneticsregressionmethylseqdifferential-methylationdna-methylation
7.37 score 17 stars 23 scripts 201 downloads