This package is designed to:
bedtools
and deeptools
hitslib
or the kent source utilities
from the UCSC genome browserbigWig
R packageDESeq2
to calculate
differential expression in a manner that is robust to global changes1
DESeq2
analysis, e.g. to
exclude of specific sites/peaks from the analysis (not usually supported
by DESeq2)GRanges
” object), which
is already supported by a rich, user-friendly suite of tools that
greatly simplify working with datasets and annotationsData processing:
Signal counting and analysis:
Avoid the default behavior of calculating genewise dispersion across all samples present, which is invalid if any experimental condition causes broad changes↩︎