[Bioc-devel] Announcing a new package: DMRcaller

Radu Zabet n.r.zabet at gen.cam.ac.uk
Wed Apr 8 11:38:46 CEST 2015

Hi everyone,

I am happy to announce that our package DMRcaller is now available on
devel.  DMRcaller computes differentially methylated regions (DMRs) between
two samples in CG and non-CG contexts (thus, it is suitable for both plants
and mammalian systems) from Whole Genome Bisulfite Sequencing (WGBS) or
Reduced Representation Bisulfite Sequencing (RRBS) data. Briefly, the
package implements four methods to compute the DMRs: (i) applies a noise
filter (there are several filters implemented) and then calls
differentially methylated positions on the genome, (ii) bins the data in
tilling bins and then computes the differentially methylated bins, (iii)
computes the differentially methylated cytosines and (iv) checks whether a
set of regions (e.g. genes, exons, transposons) are differentially
methylated. For the former three methods adjacent positions/bins/cytosines
are merged only if by merging them the larger region remains differentially
methylated. The input is the CX report files produced by Bismark and the
output is a list of DMRs stored as GRanges objects. Finally, the package
also implements several additional plotting methods.

We would highly appreciate feedback and suggestions to help improve the

Best regards,

Dr Nicolae Radu Zabet
Postdoctoral Research Associate,
The Sainsbury Laboratory,
University of Cambridge,
Bateman Street, Cambridge, CB2 1LR
United Kingdom

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list