MIRA - Methylation-Based Inference of Regulatory Activity
DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.
Last updated 21 days ago
immunooncologydnamethylationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencingepigeneticscoverage
7.52 score 11 stars 1 packages 7 scripts 208 downloadsCOCOA - Coordinate Covariation Analysis
COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.
Last updated 21 days ago
epigeneticsdnamethylationatacseqdnaseseqmethylseqmethylationarrayprincipalcomponentgenomicvariationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqsequencingimmunooncologydna-methylationpca
6.00 score 10 stars 20 scripts 220 downloads